---
_id: '12668'
abstract:
- lang: eng
text: "Background: Plant and animal embryogenesis have conserved and distinct features.
Cell fate transitions occur during embryogenesis in both plants and animals. The
epigenomic processes regulating plant embryogenesis remain largely elusive.\r\n\r\nResults:
Here, we elucidate chromatin and transcriptomic dynamics during embryogenesis
of the most cultivated crop, hexaploid wheat. Time-series analysis reveals stage-specific
and proximal–distal distinct chromatin accessibility and dynamics concordant with
transcriptome changes. Following fertilization, the remodeling kinetics of H3K4me3,
H3K27ac, and H3K27me3 differ from that in mammals, highlighting considerable species-specific
epigenomic dynamics during zygotic genome activation. Polycomb repressive complex
2 (PRC2)-mediated H3K27me3 deposition is important for embryo establishment. Later
H3K27ac, H3K27me3, and chromatin accessibility undergo dramatic remodeling to
establish a permissive chromatin environment facilitating the access of transcription
factors to cis-elements for fate patterning. Embryonic maturation is characterized
by increasing H3K27me3 and decreasing chromatin accessibility, which likely participates
in restricting totipotency while preventing extensive organogenesis. Finally,
epigenomic signatures are correlated with biased expression among homeolog triads
and divergent expression after polyploidization, revealing an epigenomic contributor
to subgenome diversification in an allohexaploid genome.\r\n\r\nConclusions: Collectively,
we present an invaluable resource for comparative and mechanistic analysis of
the epigenomic regulation of crop embryogenesis."
article_number: '7'
article_processing_charge: No
article_type: original
author:
- first_name: Long
full_name: Zhao, Long
last_name: Zhao
- first_name: Yiman
full_name: Yang, Yiman
last_name: Yang
- first_name: Jinchao
full_name: Chen, Jinchao
last_name: Chen
- first_name: Xuelei
full_name: Lin, Xuelei
last_name: Lin
- first_name: Hao
full_name: Zhang, Hao
last_name: Zhang
- first_name: Hao
full_name: Wang, Hao
last_name: Wang
- first_name: Hongzhe
full_name: Wang, Hongzhe
last_name: Wang
- first_name: Xiaomin
full_name: Bie, Xiaomin
last_name: Bie
- first_name: Jiafu
full_name: Jiang, Jiafu
last_name: Jiang
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Xiangdong
full_name: Fu, Xiangdong
last_name: Fu
- first_name: Xiansheng
full_name: Zhang, Xiansheng
last_name: Zhang
- first_name: Zhuo
full_name: Du, Zhuo
last_name: Du
- first_name: Jun
full_name: Xiao, Jun
last_name: Xiao
citation:
ama: Zhao L, Yang Y, Chen J, et al. Dynamic chromatin regulatory programs during
embryogenesis of hexaploid wheat. Genome Biology. 2023;24. doi:10.1186/s13059-022-02844-2
apa: Zhao, L., Yang, Y., Chen, J., Lin, X., Zhang, H., Wang, H., … Xiao, J. (2023).
Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat.
Genome Biology. Springer Nature. https://doi.org/10.1186/s13059-022-02844-2
chicago: Zhao, Long, Yiman Yang, Jinchao Chen, Xuelei Lin, Hao Zhang, Hao Wang,
Hongzhe Wang, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis
of Hexaploid Wheat.” Genome Biology. Springer Nature, 2023. https://doi.org/10.1186/s13059-022-02844-2.
ieee: L. Zhao et al., “Dynamic chromatin regulatory programs during embryogenesis
of hexaploid wheat,” Genome Biology, vol. 24. Springer Nature, 2023.
ista: Zhao L, Yang Y, Chen J, Lin X, Zhang H, Wang H, Wang H, Bie X, Jiang J, Feng
X, Fu X, Zhang X, Du Z, Xiao J. 2023. Dynamic chromatin regulatory programs during
embryogenesis of hexaploid wheat. Genome Biology. 24, 7.
mla: Zhao, Long, et al. “Dynamic Chromatin Regulatory Programs during Embryogenesis
of Hexaploid Wheat.” Genome Biology, vol. 24, 7, Springer Nature, 2023,
doi:10.1186/s13059-022-02844-2.
short: L. Zhao, Y. Yang, J. Chen, X. Lin, H. Zhang, H. Wang, H. Wang, X. Bie, J.
Jiang, X. Feng, X. Fu, X. Zhang, Z. Du, J. Xiao, Genome Biology 24 (2023).
date_created: 2023-02-23T09:13:49Z
date_published: 2023-01-13T00:00:00Z
date_updated: 2023-05-08T10:52:49Z
day: '13'
department:
- _id: XiFe
doi: 10.1186/s13059-022-02844-2
extern: '1'
external_id:
pmid:
- '36639687'
intvolume: ' 24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/s13059-022-02844-2
month: '01'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
issn:
- 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamic chromatin regulatory programs during embryogenesis of hexaploid wheat
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2023'
...
---
_id: '12669'
abstract:
- lang: eng
text: The study of RNAs has become one of the most influential research fields in
contemporary biology and biomedicine. In the last few years, new sequencing technologies
have produced an explosion of new and exciting discoveries in the field but have
also given rise to many open questions. Defining these questions, together with
old, long-standing gaps in our knowledge, is the spirit of this article. The breadth
of topics within RNA biology research is vast, and every aspect of the biology
of these molecules contains countless exciting open questions. Here, we asked
12 groups to discuss their most compelling question among some plant RNA biology
topics. The following vignettes cover RNA alternative splicing; RNA dynamics;
RNA translation; RNA structures; R-loops; epitranscriptomics; long non-coding
RNAs; small RNA production and their functions in crops; small RNAs during gametogenesis
and in cross-kingdom RNA interference; and RNA-directed DNA methylation. In each
section, we will present the current state-of-the-art in plant RNA biology research
before asking the questions that will surely motivate future discoveries in the
field. We hope this article will spark a debate about the future perspective on
RNA biology and provoke novel reflections in the reader.
article_number: koac346
article_processing_charge: No
article_type: original
author:
- first_name: Pablo A
full_name: Manavella, Pablo A
last_name: Manavella
- first_name: Micaela A
full_name: Godoy Herz, Micaela A
last_name: Godoy Herz
- first_name: Alberto R
full_name: Kornblihtt, Alberto R
last_name: Kornblihtt
- first_name: Reed
full_name: Sorenson, Reed
last_name: Sorenson
- first_name: Leslie E
full_name: Sieburth, Leslie E
last_name: Sieburth
- first_name: Kentaro
full_name: Nakaminami, Kentaro
last_name: Nakaminami
- first_name: Motoaki
full_name: Seki, Motoaki
last_name: Seki
- first_name: Yiliang
full_name: Ding, Yiliang
last_name: Ding
- first_name: Qianwen
full_name: Sun, Qianwen
last_name: Sun
- first_name: Hunseung
full_name: Kang, Hunseung
last_name: Kang
- first_name: Federico D
full_name: Ariel, Federico D
last_name: Ariel
- first_name: Martin
full_name: Crespi, Martin
last_name: Crespi
- first_name: Axel J
full_name: Giudicatti, Axel J
last_name: Giudicatti
- first_name: Qiang
full_name: Cai, Qiang
last_name: Cai
- first_name: Hailing
full_name: Jin, Hailing
last_name: Jin
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Yijun
full_name: Qi, Yijun
last_name: Qi
- first_name: Craig S
full_name: Pikaard, Craig S
last_name: Pikaard
citation:
ama: 'Manavella PA, Godoy Herz MA, Kornblihtt AR, et al. Beyond transcription: compelling
open questions in plant RNA biology. The Plant Cell. 2023;35(6). doi:10.1093/plcell/koac346'
apa: 'Manavella, P. A., Godoy Herz, M. A., Kornblihtt, A. R., Sorenson, R., Sieburth,
L. E., Nakaminami, K., … Pikaard, C. S. (2023). Beyond transcription: compelling
open questions in plant RNA biology. The Plant Cell. Oxford University
Press. https://doi.org/10.1093/plcell/koac346'
chicago: 'Manavella, Pablo A, Micaela A Godoy Herz, Alberto R Kornblihtt, Reed Sorenson,
Leslie E Sieburth, Kentaro Nakaminami, Motoaki Seki, et al. “Beyond Transcription:
Compelling Open Questions in Plant RNA Biology.” The Plant Cell. Oxford
University Press, 2023. https://doi.org/10.1093/plcell/koac346.'
ieee: 'P. A. Manavella et al., “Beyond transcription: compelling open questions
in plant RNA biology,” The Plant Cell, vol. 35, no. 6. Oxford University
Press, 2023.'
ista: 'Manavella PA, Godoy Herz MA, Kornblihtt AR, Sorenson R, Sieburth LE, Nakaminami
K, Seki M, Ding Y, Sun Q, Kang H, Ariel FD, Crespi M, Giudicatti AJ, Cai Q, Jin
H, Feng X, Qi Y, Pikaard CS. 2023. Beyond transcription: compelling open questions
in plant RNA biology. The Plant Cell. 35(6), koac346.'
mla: 'Manavella, Pablo A., et al. “Beyond Transcription: Compelling Open Questions
in Plant RNA Biology.” The Plant Cell, vol. 35, no. 6, koac346, Oxford
University Press, 2023, doi:10.1093/plcell/koac346.'
short: P.A. Manavella, M.A. Godoy Herz, A.R. Kornblihtt, R. Sorenson, L.E. Sieburth,
K. Nakaminami, M. Seki, Y. Ding, Q. Sun, H. Kang, F.D. Ariel, M. Crespi, A.J.
Giudicatti, Q. Cai, H. Jin, X. Feng, Y. Qi, C.S. Pikaard, The Plant Cell 35 (2023).
date_created: 2023-02-23T09:14:59Z
date_published: 2023-06-01T00:00:00Z
date_updated: 2023-10-04T09:48:43Z
day: '01'
department:
- _id: XiFe
doi: 10.1093/plcell/koac346
extern: '1'
external_id:
pmid:
- '36477566'
intvolume: ' 35'
issue: '6'
keyword:
- Cell Biology
- Plant Science
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/plcell/koac346
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: The Plant Cell
publication_identifier:
eissn:
- 1532-298X
issn:
- 1040-4651
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Beyond transcription: compelling open questions in plant RNA biology'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 35
year: '2023'
...
---
_id: '12672'
abstract:
- lang: eng
text: Cytosine methylation within CG dinucleotides (mCG) can be epigenetically inherited
over many generations. Such inheritance is thought to be mediated by a semiconservative
mechanism that produces binary present/absent methylation patterns. However, we
show here that in Arabidopsis thaliana h1ddm1 mutants, intermediate heterochromatic
mCG is stably inherited across many generations and is quantitatively associated
with transposon expression. We develop a mathematical model that estimates the
rates of semiconservative maintenance failure and de novo methylation at each
transposon, demonstrating that mCG can be stably inherited at any level via a
dynamic balance of these activities. We find that DRM2 – the core methyltransferase
of the RNA-directed DNA methylation pathway – catalyzes most of the heterochromatic
de novo mCG, with de novo rates orders of magnitude higher than previously thought,
whereas chromomethylases make smaller contributions. Our results demonstrate that
stable epigenetic inheritance of mCG in plant heterochromatin is enabled by extensive
de novo methylation.
acknowledgement: The authors would like to thank Jasper Rine for advice and mentorship
to D.B.L., Lesley Philips, Timothy Wells, Sophie Able, and Christina Wistrom for
support with plant growth, and Bhagyshree Jamge and Frédéric Berger for help with
analysis of ddm1 × WT RNA-sequencing data. This work was supported by BBSRC Institute
Strategic Program GEN (BB/P013511/1) to X.F., M.H., and D.Z., a European Research
Council grant MaintainMeth (725746) to D.Z., and a postdoctoral fellowship from
the Helen Hay Whitney Foundation to D.B.L.
article_number: '112132'
article_processing_charge: Yes
article_type: original
author:
- first_name: David B.
full_name: Lyons, David B.
last_name: Lyons
- first_name: Amy
full_name: Briffa, Amy
last_name: Briffa
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Jaemyung
full_name: Choi, Jaemyung
last_name: Choi
- first_name: Elizabeth
full_name: Hollwey, Elizabeth
id: b8c4f54b-e484-11eb-8fdc-a54df64ef6dd
last_name: Hollwey
- first_name: Jack
full_name: Colicchio, Jack
last_name: Colicchio
- first_name: Ian
full_name: Anderson, Ian
last_name: Anderson
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Martin
full_name: Howard, Martin
last_name: Howard
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Lyons DB, Briffa A, He S, et al. Extensive de novo activity stabilizes epigenetic
inheritance of CG methylation in Arabidopsis transposons. Cell Reports.
2023;42(3). doi:10.1016/j.celrep.2023.112132
apa: Lyons, D. B., Briffa, A., He, S., Choi, J., Hollwey, E., Colicchio, J., … Zilberman,
D. (2023). Extensive de novo activity stabilizes epigenetic inheritance of CG
methylation in Arabidopsis transposons. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.112132
chicago: Lyons, David B., Amy Briffa, Shengbo He, Jaemyung Choi, Elizabeth Hollwey,
Jack Colicchio, Ian Anderson, Xiaoqi Feng, Martin Howard, and Daniel Zilberman.
“Extensive de Novo Activity Stabilizes Epigenetic Inheritance of CG Methylation
in Arabidopsis Transposons.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.112132.
ieee: D. B. Lyons et al., “Extensive de novo activity stabilizes epigenetic
inheritance of CG methylation in Arabidopsis transposons,” Cell Reports,
vol. 42, no. 3. Elsevier, 2023.
ista: Lyons DB, Briffa A, He S, Choi J, Hollwey E, Colicchio J, Anderson I, Feng
X, Howard M, Zilberman D. 2023. Extensive de novo activity stabilizes epigenetic
inheritance of CG methylation in Arabidopsis transposons. Cell Reports. 42(3),
112132.
mla: Lyons, David B., et al. “Extensive de Novo Activity Stabilizes Epigenetic Inheritance
of CG Methylation in Arabidopsis Transposons.” Cell Reports, vol. 42, no.
3, 112132, Elsevier, 2023, doi:10.1016/j.celrep.2023.112132.
short: D.B. Lyons, A. Briffa, S. He, J. Choi, E. Hollwey, J. Colicchio, I. Anderson,
X. Feng, M. Howard, D. Zilberman, Cell Reports 42 (2023).
date_created: 2023-02-23T09:17:44Z
date_published: 2023-03-28T00:00:00Z
date_updated: 2023-11-02T12:23:45Z
day: '28'
ddc:
- '580'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1016/j.celrep.2023.112132
ec_funded: 1
external_id:
isi:
- '000944921600001'
file:
- access_level: open_access
checksum: 6cbc44fdb18bf18834c9e2a5b9c67123
content_type: application/pdf
creator: kschuh
date_created: 2023-05-11T10:41:42Z
date_updated: 2023-05-11T10:41:42Z
file_id: '12941'
file_name: 2023_CellReports_Lyons.pdf
file_size: 8401261
relation: main_file
success: 1
file_date_updated: 2023-05-11T10:41:42Z
has_accepted_license: '1'
intvolume: ' 42'
isi: 1
issue: '3'
language:
- iso: eng
month: '03'
oa: 1
oa_version: Published Version
project:
- _id: 62935a00-2b32-11ec-9570-eff30fa39068
call_identifier: H2020
grant_number: '725746'
name: Quantitative analysis of DNA methylation maintenance with chromatin
publication: Cell Reports
publication_identifier:
eissn:
- 2211-1247
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extensive de novo activity stabilizes epigenetic inheritance of CG methylation
in Arabidopsis transposons
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87
volume: 42
year: '2023'
...
---
_id: '12670'
abstract:
- lang: eng
text: DNA methylation plays essential homeostatic functions in eukaryotic genomes.
In animals, DNA methylation is also developmentally regulated and, in turn, regulates
development. In the past two decades, huge research effort has endorsed the understanding
that DNA methylation plays a similar role in plant development, especially during
sexual reproduction. The power of whole-genome sequencing and cell isolation techniques,
as well as bioinformatics tools, have enabled recent studies to reveal dynamic
changes in DNA methylation during germline development. Furthermore, the combination
of these technological advances with genetics, developmental biology and cell
biology tools has revealed functional methylation reprogramming events that control
gene and transposon activities in flowering plant germlines. In this review, we
discuss the major advances in our knowledge of DNA methylation dynamics during
male and female germline development in flowering plants.
article_processing_charge: No
article_type: review
author:
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: He S, Feng X. DNA methylation dynamics during germline development. Journal
of Integrative Plant Biology. 2022;64(12):2240-2251. doi:10.1111/jipb.13422
apa: He, S., & Feng, X. (2022). DNA methylation dynamics during germline development.
Journal of Integrative Plant Biology. Wiley. https://doi.org/10.1111/jipb.13422
chicago: He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline
Development.” Journal of Integrative Plant Biology. Wiley, 2022. https://doi.org/10.1111/jipb.13422.
ieee: S. He and X. Feng, “DNA methylation dynamics during germline development,”
Journal of Integrative Plant Biology, vol. 64, no. 12. Wiley, pp. 2240–2251,
2022.
ista: He S, Feng X. 2022. DNA methylation dynamics during germline development.
Journal of Integrative Plant Biology. 64(12), 2240–2251.
mla: He, Shengbo, and Xiaoqi Feng. “DNA Methylation Dynamics during Germline Development.”
Journal of Integrative Plant Biology, vol. 64, no. 12, Wiley, 2022, pp.
2240–51, doi:10.1111/jipb.13422.
short: S. He, X. Feng, Journal of Integrative Plant Biology 64 (2022) 2240–2251.
date_created: 2023-02-23T09:15:57Z
date_published: 2022-12-07T00:00:00Z
date_updated: 2023-05-08T10:59:00Z
day: '07'
department:
- _id: XiFe
doi: 10.1111/jipb.13422
extern: '1'
external_id:
pmid:
- '36478632'
intvolume: ' 64'
issue: '12'
keyword:
- Plant Science
- General Biochemistry
- Genetics and Molecular Biology
- Biochemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1111/jipb.13422
month: '12'
oa: 1
oa_version: Published Version
page: 2240-2251
pmid: 1
publication: Journal of Integrative Plant Biology
publication_identifier:
eissn:
- 1744-7909
issn:
- 1672-9072
publication_status: published
publisher: Wiley
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation dynamics during germline development
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 64
year: '2022'
...
---
_id: '12671'
abstract:
- lang: eng
text: Sperm chromatin is typically transformed by protamines into a compact and
transcriptionally inactive state1,2. Sperm cells of flowering plants lack protamines,
yet they have small, transcriptionally active nuclei with chromatin condensed
through an unknown mechanism3,4. Here we show that a histone variant, H2B.8, mediates
sperm chromatin and nuclear condensation in Arabidopsis thaliana. Loss of H2B.8
causes enlarged sperm nuclei with dispersed chromatin, whereas ectopic expression
in somatic cells produces smaller nuclei with aggregated chromatin. This result
demonstrates that H2B.8 is sufficient for chromatin condensation. H2B.8 aggregates
transcriptionally inactive AT-rich chromatin into phase-separated condensates,
which facilitates nuclear compaction without reducing transcription. Reciprocal
crosses show that mutation of h2b.8 reduces male transmission, which suggests
that H2B.8-mediated sperm compaction is important for fertility. Altogether, our
results reveal a new mechanism of nuclear compaction through global aggregation
of unexpressed chromatin. We propose that H2B.8 is an evolutionary innovation
of flowering plants that achieves nuclear condensation compatible with active
transcription.
article_processing_charge: No
article_type: original
author:
- first_name: Toby
full_name: Buttress, Toby
last_name: Buttress
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Liang
full_name: Wang, Liang
last_name: Wang
- first_name: Shaoli
full_name: Zhou, Shaoli
last_name: Zhou
- first_name: Gerhard
full_name: Saalbach, Gerhard
last_name: Saalbach
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Guohong
full_name: Li, Guohong
last_name: Li
- first_name: Pilong
full_name: Li, Pilong
last_name: Li
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Buttress T, He S, Wang L, et al. Histone H2B.8 compacts flowering plant sperm
through chromatin phase separation. Nature. 2022;611(7936):614-622. doi:10.1038/s41586-022-05386-6
apa: Buttress, T., He, S., Wang, L., Zhou, S., Saalbach, G., Vickers, M., … Feng,
X. (2022). Histone H2B.8 compacts flowering plant sperm through chromatin phase
separation. Nature. Springer Nature. https://doi.org/10.1038/s41586-022-05386-6
chicago: Buttress, Toby, Shengbo He, Liang Wang, Shaoli Zhou, Gerhard Saalbach,
Martin Vickers, Guohong Li, Pilong Li, and Xiaoqi Feng. “Histone H2B.8 Compacts
Flowering Plant Sperm through Chromatin Phase Separation.” Nature. Springer
Nature, 2022. https://doi.org/10.1038/s41586-022-05386-6.
ieee: T. Buttress et al., “Histone H2B.8 compacts flowering plant sperm through
chromatin phase separation,” Nature, vol. 611, no. 7936. Springer Nature,
pp. 614–622, 2022.
ista: Buttress T, He S, Wang L, Zhou S, Saalbach G, Vickers M, Li G, Li P, Feng
X. 2022. Histone H2B.8 compacts flowering plant sperm through chromatin phase
separation. Nature. 611(7936), 614–622.
mla: Buttress, Toby, et al. “Histone H2B.8 Compacts Flowering Plant Sperm through
Chromatin Phase Separation.” Nature, vol. 611, no. 7936, Springer Nature,
2022, pp. 614–22, doi:10.1038/s41586-022-05386-6.
short: T. Buttress, S. He, L. Wang, S. Zhou, G. Saalbach, M. Vickers, G. Li, P.
Li, X. Feng, Nature 611 (2022) 614–622.
date_created: 2023-02-23T09:17:05Z
date_published: 2022-11-17T00:00:00Z
date_updated: 2023-05-08T10:59:22Z
day: '17'
department:
- _id: XiFe
doi: 10.1038/s41586-022-05386-6
extern: '1'
external_id:
pmid:
- '36323776'
intvolume: ' 611'
issue: '7936'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41586-022-05386-6
month: '11'
oa: 1
oa_version: Published Version
page: 614-622
pmid: 1
publication: Nature
publication_identifier:
eissn:
- 1476-4687
issn:
- 0028-0836
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Histone H2B.8 compacts flowering plant sperm through chromatin phase separation
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 611
year: '2022'
...
---
_id: '12186'
abstract:
- lang: eng
text: Activation of cell-surface and intracellular receptor-mediated immunity results
in rapid transcriptional reprogramming that underpins disease resistance. However,
the mechanisms by which co-activation of both immune systems lead to transcriptional
changes are not clear. Here, we combine RNA-seq and ATAC-seq to define changes
in gene expression and chromatin accessibility. Activation of cell-surface or
intracellular receptor-mediated immunity, or both, increases chromatin accessibility
at induced defence genes. Analysis of ATAC-seq and RNA-seq data combined with
publicly available information on transcription factor DNA-binding motifs enabled
comparison of individual gene regulatory networks activated by cell-surface or
intracellular receptor-mediated immunity, or by both. These results and analyses
reveal overlapping and conserved transcriptional regulatory mechanisms between
the two immune systems.
acknowledgement: "We thank the Gatsby Foundation (UK) for funding to the JDGJ laboratory.
PD acknowledges support from the European Union’s Horizon 2020 Research and Innovation
Program under Marie Skłodowska Curie Actions (grant agreement: 656243) and a Future
Leader Fellowship from the Biotechnology and Biological Sciences Research Council
(BBSRC) (grant agreement: BB/R012172/1). TS, RKS, DM, and JDGJ were supported by
the Gatsby Foundation funding to the\r\nSainsbury Laboratory. NMP and KV were supported
by a BOF grant from Ghent University (grant agreement: BOF24Y2019001901). WG and
RZ were supported by the Scottish Government Rural and Environment Science and Analytical
Services division (RESAS), and RZ also acknowledges the support from a BBSRC Bioinformatics
and Biological Resources Fund (grant agreement: BB/S020160/1).BPMN was supported
by the Norwich Research Park (NRP) Biosciences Doctoral Training Partnership (DTP)
funded by the BBSRC (grant agreement: BB/M011216/1). SH and XF were supported by
a BBSRC Responsive Mode grant (grant agreement: BB/S009620/1) and a European Research
Council Starting grant ‘SexMeth’ (grant agreement: 804981). CL was supported by
Deutsche Forschungsgemeinschaft (grant agreement: LI 2862/4). "
article_processing_charge: No
article_type: original
author:
- first_name: Pingtao
full_name: Ding, Pingtao
last_name: Ding
- first_name: Toshiyuki
full_name: Sakai, Toshiyuki
last_name: Sakai
- first_name: Ram
full_name: Krishna Shrestha, Ram
last_name: Krishna Shrestha
- first_name: Nicolas
full_name: Manosalva Perez, Nicolas
last_name: Manosalva Perez
- first_name: Wenbin
full_name: Guo, Wenbin
last_name: Guo
- first_name: Bruno Pok Man
full_name: Ngou, Bruno Pok Man
last_name: Ngou
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Chang
full_name: Liu, Chang
last_name: Liu
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Runxuan
full_name: Zhang, Runxuan
last_name: Zhang
- first_name: Klaas
full_name: Vandepoele, Klaas
last_name: Vandepoele
- first_name: Dan
full_name: MacLean, Dan
last_name: MacLean
- first_name: Jonathan D G
full_name: Jones, Jonathan D G
last_name: Jones
citation:
ama: Ding P, Sakai T, Krishna Shrestha R, et al. Chromatin accessibility landscapes
activated by cell-surface and intracellular immune receptors. Journal of Experimental
Botany. 2021;72(22):7927-7941. doi:10.1093/jxb/erab373
apa: Ding, P., Sakai, T., Krishna Shrestha, R., Manosalva Perez, N., Guo, W., Ngou,
B. P. M., … Jones, J. D. G. (2021). Chromatin accessibility landscapes activated
by cell-surface and intracellular immune receptors. Journal of Experimental
Botany. Oxford University Press. https://doi.org/10.1093/jxb/erab373
chicago: Ding, Pingtao, Toshiyuki Sakai, Ram Krishna Shrestha, Nicolas Manosalva
Perez, Wenbin Guo, Bruno Pok Man Ngou, Shengbo He, et al. “Chromatin Accessibility
Landscapes Activated by Cell-Surface and Intracellular Immune Receptors.” Journal
of Experimental Botany. Oxford University Press, 2021. https://doi.org/10.1093/jxb/erab373.
ieee: P. Ding et al., “Chromatin accessibility landscapes activated by cell-surface
and intracellular immune receptors,” Journal of Experimental Botany, vol.
72, no. 22. Oxford University Press, pp. 7927–7941, 2021.
ista: Ding P, Sakai T, Krishna Shrestha R, Manosalva Perez N, Guo W, Ngou BPM, He
S, Liu C, Feng X, Zhang R, Vandepoele K, MacLean D, Jones JDG. 2021. Chromatin
accessibility landscapes activated by cell-surface and intracellular immune receptors.
Journal of Experimental Botany. 72(22), 7927–7941.
mla: Ding, Pingtao, et al. “Chromatin Accessibility Landscapes Activated by Cell-Surface
and Intracellular Immune Receptors.” Journal of Experimental Botany, vol.
72, no. 22, Oxford University Press, 2021, pp. 7927–41, doi:10.1093/jxb/erab373.
short: P. Ding, T. Sakai, R. Krishna Shrestha, N. Manosalva Perez, W. Guo, B.P.M.
Ngou, S. He, C. Liu, X. Feng, R. Zhang, K. Vandepoele, D. MacLean, J.D.G. Jones,
Journal of Experimental Botany 72 (2021) 7927–7941.
date_created: 2023-01-16T09:14:35Z
date_published: 2021-08-13T00:00:00Z
date_updated: 2023-05-08T11:01:18Z
day: '13'
department:
- _id: XiFe
doi: 10.1093/jxb/erab373
extern: '1'
external_id:
pmid:
- '34387350'
intvolume: ' 72'
issue: '22'
keyword:
- Plant Science
- Physiology
language:
- iso: eng
month: '08'
oa_version: None
page: 7927-7941
pmid: 1
publication: Journal of Experimental Botany
publication_identifier:
issn:
- 0022-0957
- 1460-2431
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromatin accessibility landscapes activated by cell-surface and intracellular
immune receptors
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 72
year: '2021'
...
---
_id: '12187'
abstract:
- lang: eng
text: Genomes of germ cells present an existential vulnerability to organisms because
germ cell mutations will propagate to future generations. Transposable elements
are one source of such mutations. In the small flowering plant Arabidopsis, Long
et al. found that genome methylation in the male germline is directed by small
interfering RNAs (siRNAs) imperfectly transcribed from transposons (see the Perspective
by Mosher). These germline siRNAs silence germline transposons and establish inherited
methylation patterns in sperm, thus maintaining the integrity of the plant genome
across generations.
acknowledgement: 'We thank the John Innes Centre Bioimaging Facility (S. Lopez, E.
Wegel, and K. Findlay) for their assistance with microscopy and the Norwich BioScience
Institute Partnership Computing Infrastructure for Science Group for high-performance
computing resources. Funding: This work was funded by a European Research Council
Starting Grant (“SexMeth” 804981; J.L., J.W., and X.F.), a Sainsbury Charitable
Foundation studentship (J.W.), two Biotechnology and Biological Sciences Research
Council (BBSRC) grants (BBS0096201 and BBP0135111; W.S., M.V., and X.F.), two John
Innes Foundation studentships (B.A. and S.D.), and a BBSRC David Phillips Fellowship
(BBL0250431; H.G. and X.F.). Author contributions: J.L., J.W., and X.F. designed
the study and wrote the manuscript; J.L., W.S., B.A., H.G., and S.D. performed the
experiments; and J.L., J.W., B.A., H.G., S.D., M.V., and X.F. analyzed the data.
Competing interests: The authors declare no competing interests. Data and material
availability: All sequencing data have been deposited in the Gene Expression Omnibus
(GEO) under accession no. GSE161625. Accession nos. of published datasets used in
this study are listed in table S6. Published software used in this study include
Bowtie v1.2.2 (https://doi.org/10.1002/0471250953.bi1107s32), Bismark v0.22.2 (https://doi.org/10.1093/bioinformatics/btr167),
Kallisto v0.43.0 (https://doi.org/10.1038/nbt0816-888d), Shortstack v3.8.5 (https://doi.org/10.1534/g3.116.030452),
and Cutadapt v1.15 (https://doi.org/10.1089/cmb.2017.0096). TrimGalore v0.4.1 and
MarkDuplicates v1.141 are available from https://github.com/FelixKrueger/TrimGalore
and https://github.com/broadinstitute/picard, respectively. All remaining data are
in the main paper or the supplementary materials.'
article_processing_charge: No
article_type: original
author:
- first_name: Jincheng
full_name: Long, Jincheng
last_name: Long
- first_name: James
full_name: Walker, James
last_name: Walker
- first_name: Wenjing
full_name: She, Wenjing
last_name: She
- first_name: Billy
full_name: Aldridge, Billy
last_name: Aldridge
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Samuel
full_name: Deans, Samuel
last_name: Deans
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Long J, Walker J, She W, et al. Nurse cell--derived small RNAs define paternal
epigenetic inheritance in Arabidopsis. Science. 2021;373(6550). doi:10.1126/science.abh0556
apa: Long, J., Walker, J., She, W., Aldridge, B., Gao, H., Deans, S., … Feng, X.
(2021). Nurse cell--derived small RNAs define paternal epigenetic inheritance
in Arabidopsis. Science. American Association for the Advancement of Science
(AAAS). https://doi.org/10.1126/science.abh0556
chicago: Long, Jincheng, James Walker, Wenjing She, Billy Aldridge, Hongbo Gao,
Samuel Deans, Martin Vickers, and Xiaoqi Feng. “Nurse Cell--Derived Small RNAs
Define Paternal Epigenetic Inheritance in Arabidopsis.” Science. American
Association for the Advancement of Science (AAAS), 2021. https://doi.org/10.1126/science.abh0556.
ieee: J. Long et al., “Nurse cell--derived small RNAs define paternal epigenetic
inheritance in Arabidopsis,” Science, vol. 373, no. 6550. American Association
for the Advancement of Science (AAAS), 2021.
ista: Long J, Walker J, She W, Aldridge B, Gao H, Deans S, Vickers M, Feng X. 2021.
Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis.
Science. 373(6550).
mla: Long, Jincheng, et al. “Nurse Cell--Derived Small RNAs Define Paternal Epigenetic
Inheritance in Arabidopsis.” Science, vol. 373, no. 6550, American Association
for the Advancement of Science (AAAS), 2021, doi:10.1126/science.abh0556.
short: J. Long, J. Walker, W. She, B. Aldridge, H. Gao, S. Deans, M. Vickers, X.
Feng, Science 373 (2021).
date_created: 2023-01-16T09:15:14Z
date_published: 2021-07-02T00:00:00Z
date_updated: 2023-05-08T10:56:39Z
day: '02'
department:
- _id: XiFe
doi: 10.1126/science.abh0556
extern: '1'
external_id:
pmid:
- '34210850'
intvolume: ' 373'
issue: '6550'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '07'
oa_version: None
pmid: 1
publication: Science
publication_identifier:
issn:
- 0036-8075
- 1095-9203
publication_status: published
publisher: American Association for the Advancement of Science (AAAS)
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nurse cell--derived small RNAs define paternal epigenetic inheritance in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 373
year: '2021'
...
---
_id: '12188'
abstract:
- lang: eng
text: Molecular mechanisms enabling the switching and maintenance of epigenetic
states are not fully understood. Distinct histone modifications are often associated
with ON/OFF epigenetic states, but how these states are stably maintained through
DNA replication, yet in certain situations switch from one to another remains
unclear. Here, we address this problem through identification of Arabidopsis INCURVATA11
(ICU11) as a Polycomb Repressive Complex 2 accessory protein. ICU11 robustly immunoprecipitated
in vivo with PRC2 core components and the accessory proteins, EMBRYONIC FLOWER
1 (EMF1), LIKE HETEROCHROMATIN PROTEIN1 (LHP1), and TELOMERE_REPEAT_BINDING FACTORS
(TRBs). ICU11 encodes a 2-oxoglutarate-dependent dioxygenase, an activity associated
with histone demethylation in other organisms, and mutant plants show defects
in multiple aspects of the Arabidopsis epigenome. To investigate its primary molecular
function we identified the Arabidopsis FLOWERING LOCUS C (FLC) as a direct target
and found icu11 disrupted the cold-induced, Polycomb-mediated silencing underlying
vernalization. icu11 prevented reduction in H3K36me3 levels normally seen during
the early cold phase, supporting a role for ICU11 in H3K36me3 demethylation. This
was coincident with an attenuation of H3K27me3 at the internal nucleation site
in FLC, and reduction in H3K27me3 levels across the body of the gene after plants
were returned to the warm. Thus, ICU11 is required for the cold-induced epigenetic
switching between the mutually exclusive chromatin states at FLC, from the active
H3K36me3 state to the silenced H3K27me3 state. These data support the importance
of physical coupling of histone modification activities to promote epigenetic
switching between opposing chromatin states.
acknowledgement: We would like to thank Scott Berry for help with ICU-GFP nuclear
localization microscopy, Hao Yu and Lisha Shen for assistance with 6mA DNA methylation
analysis, Donna Gibson for graphic design assistance, and members of the C.D. and
Howard laboratories for helpful discussions. This work was funded by the European
Research Council grants to “MEXTIM” (to C.D.) and “SexMeth” (to X. Feng), by the
Biotechnological and Biological Sciences Research Council (BBSRC) Institute Strategic
Programmes GRO (BB/J004588/1), GEN (BB/P013511/1), BBSRC grant (to X. Feng) (BB/S009620/1),
and the Marie Sklodowska–Curie Postdoctoral Fellowships “UNRAVEL” (to R.H.B.) and
"WISDOM" (to X. Fang). Additional funding via the Wellcome Trust through a Senior
Research Fellowship (to J.R.) (103139) and a multiuser equipment grant (108504).
The Wellcome Centre for Cell Biology is supported by core funding from the Wellcome
Trust (203149).
article_processing_charge: No
article_type: original
author:
- first_name: Rebecca H.
full_name: Bloomer, Rebecca H.
last_name: Bloomer
- first_name: Claire E.
full_name: Hutchison, Claire E.
last_name: Hutchison
- first_name: Isabel
full_name: Bäurle, Isabel
last_name: Bäurle
- first_name: James
full_name: Walker, James
last_name: Walker
- first_name: Xiaofeng
full_name: Fang, Xiaofeng
last_name: Fang
- first_name: Pumi
full_name: Perera, Pumi
last_name: Perera
- first_name: Christos N.
full_name: Velanis, Christos N.
last_name: Velanis
- first_name: Serin
full_name: Gümüs, Serin
last_name: Gümüs
- first_name: Christos
full_name: Spanos, Christos
last_name: Spanos
- first_name: Juri
full_name: Rappsilber, Juri
last_name: Rappsilber
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Justin
full_name: Goodrich, Justin
last_name: Goodrich
- first_name: Caroline
full_name: Dean, Caroline
last_name: Dean
citation:
ama: Bloomer RH, Hutchison CE, Bäurle I, et al. The Arabidopsis epigenetic regulator
ICU11 as an accessory protein of polycomb repressive complex 2. Proceedings
of the National Academy of Sciences. 2020;117(28):16660-16666. doi:10.1073/pnas.1920621117
apa: Bloomer, R. H., Hutchison, C. E., Bäurle, I., Walker, J., Fang, X., Perera,
P., … Dean, C. (2020). The Arabidopsis epigenetic regulator ICU11 as an accessory
protein of polycomb repressive complex 2. Proceedings of the National Academy
of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1920621117
chicago: Bloomer, Rebecca H., Claire E. Hutchison, Isabel Bäurle, James Walker,
Xiaofeng Fang, Pumi Perera, Christos N. Velanis, et al. “The Arabidopsis Epigenetic
Regulator ICU11 as an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings
of the National Academy of Sciences. Proceedings of the National Academy of
Sciences, 2020. https://doi.org/10.1073/pnas.1920621117.
ieee: R. H. Bloomer et al., “The Arabidopsis epigenetic regulator ICU11
as an accessory protein of polycomb repressive complex 2,” Proceedings of the
National Academy of Sciences, vol. 117, no. 28. Proceedings of the National
Academy of Sciences, pp. 16660–16666, 2020.
ista: Bloomer RH, Hutchison CE, Bäurle I, Walker J, Fang X, Perera P, Velanis CN,
Gümüs S, Spanos C, Rappsilber J, Feng X, Goodrich J, Dean C. 2020. The Arabidopsis
epigenetic regulator ICU11 as an accessory protein of polycomb repressive complex
2. Proceedings of the National Academy of Sciences. 117(28), 16660–16666.
mla: Bloomer, Rebecca H., et al. “The Arabidopsis Epigenetic Regulator ICU11 as
an Accessory Protein of Polycomb Repressive Complex 2.” Proceedings of the
National Academy of Sciences, vol. 117, no. 28, Proceedings of the National
Academy of Sciences, 2020, pp. 16660–66, doi:10.1073/pnas.1920621117.
short: R.H. Bloomer, C.E. Hutchison, I. Bäurle, J. Walker, X. Fang, P. Perera, C.N.
Velanis, S. Gümüs, C. Spanos, J. Rappsilber, X. Feng, J. Goodrich, C. Dean, Proceedings
of the National Academy of Sciences 117 (2020) 16660–16666.
date_created: 2023-01-16T09:15:44Z
date_published: 2020-05-22T00:00:00Z
date_updated: 2023-05-08T10:53:55Z
day: '22'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.1073/pnas.1920621117
extern: '1'
external_id:
pmid:
- '32601198'
file:
- access_level: open_access
checksum: cedee184cb12f454f2fba4158ff47db9
content_type: application/pdf
creator: alisjak
date_created: 2023-02-07T11:29:55Z
date_updated: 2023-02-07T11:29:55Z
file_id: '12526'
file_name: 2020_PNAS_Bloomer.pdf
file_size: 1105414
relation: main_file
success: 1
file_date_updated: 2023-02-07T11:29:55Z
has_accepted_license: '1'
intvolume: ' 117'
issue: '28'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7368280/
month: '05'
oa: 1
oa_version: Published Version
page: 16660-16666
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
issn:
- 0027-8424
- 1091-6490
publication_status: published
publisher: Proceedings of the National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Arabidopsis epigenetic regulator ICU11 as an accessory protein of polycomb
repressive complex 2
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 117
year: '2020'
...
---
_id: '12189'
abstract:
- lang: eng
text: Meiotic crossovers (COs) are important for reshuffling genetic information
between homologous chromosomes and they are essential for their correct segregation.
COs are unevenly distributed along chromosomes and the underlying mechanisms controlling
CO localization are not well understood. We previously showed that meiotic COs
are mis-localized in the absence of AXR1, an enzyme involved in the neddylation/rubylation
protein modification pathway in Arabidopsis thaliana. Here, we report that in
axr1-/-, male meiocytes show a strong defect in chromosome pairing whereas the
formation of the telomere bouquet is not affected. COs are also redistributed
towards subtelomeric chromosomal ends where they frequently form clusters, in
contrast to large central regions depleted in recombination. The CO suppressed
regions correlate with DNA hypermethylation of transposable elements (TEs) in
the CHH context in axr1-/- meiocytes. Through examining somatic methylomes, we
found axr1-/- affects DNA methylation in a plant, causing hypermethylation in
all sequence contexts (CG, CHG and CHH) in TEs. Impairment of the main pathways
involved in DNA methylation is epistatic over axr1-/- for DNA methylation in somatic
cells but does not restore regular chromosome segregation during meiosis. Collectively,
our findings reveal that the neddylation pathway not only regulates hormonal perception
and CO distribution but is also, directly or indirectly, a major limiting pathway
of TE DNA methylation in somatic cells.
acknowledgement: The authors wish to thank Cécile Raynaud, Eric Jenczewski, Rajeev
Kumar, Raphaël Mercier and Jean Molinier for critical reading of the manuscript.
article_number: e1008894
article_processing_charge: No
article_type: original
author:
- first_name: Nicolas
full_name: Christophorou, Nicolas
last_name: Christophorou
- first_name: Wenjing
full_name: She, Wenjing
last_name: She
- first_name: Jincheng
full_name: Long, Jincheng
last_name: Long
- first_name: Aurélie
full_name: Hurel, Aurélie
last_name: Hurel
- first_name: Sébastien
full_name: Beaubiat, Sébastien
last_name: Beaubiat
- first_name: Yassir
full_name: Idir, Yassir
last_name: Idir
- first_name: Marina
full_name: Tagliaro-Jahns, Marina
last_name: Tagliaro-Jahns
- first_name: Aurélie
full_name: Chambon, Aurélie
last_name: Chambon
- first_name: Victor
full_name: Solier, Victor
last_name: Solier
- first_name: Daniel
full_name: Vezon, Daniel
last_name: Vezon
- first_name: Mathilde
full_name: Grelon, Mathilde
last_name: Grelon
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Nicolas
full_name: Bouché, Nicolas
last_name: Bouché
- first_name: Christine
full_name: Mézard, Christine
last_name: Mézard
citation:
ama: Christophorou N, She W, Long J, et al. AXR1 affects DNA methylation independently
of its role in regulating meiotic crossover localization. PLOS Genetics.
2020;16(6). doi:10.1371/journal.pgen.1008894
apa: Christophorou, N., She, W., Long, J., Hurel, A., Beaubiat, S., Idir, Y., …
Mézard, C. (2020). AXR1 affects DNA methylation independently of its role in regulating
meiotic crossover localization. PLOS Genetics. Public Library of Science
(PLoS). https://doi.org/10.1371/journal.pgen.1008894
chicago: Christophorou, Nicolas, Wenjing She, Jincheng Long, Aurélie Hurel, Sébastien
Beaubiat, Yassir Idir, Marina Tagliaro-Jahns, et al. “AXR1 Affects DNA Methylation
Independently of Its Role in Regulating Meiotic Crossover Localization.” PLOS
Genetics. Public Library of Science (PLoS), 2020. https://doi.org/10.1371/journal.pgen.1008894.
ieee: N. Christophorou et al., “AXR1 affects DNA methylation independently
of its role in regulating meiotic crossover localization,” PLOS Genetics,
vol. 16, no. 6. Public Library of Science (PLoS), 2020.
ista: Christophorou N, She W, Long J, Hurel A, Beaubiat S, Idir Y, Tagliaro-Jahns
M, Chambon A, Solier V, Vezon D, Grelon M, Feng X, Bouché N, Mézard C. 2020. AXR1
affects DNA methylation independently of its role in regulating meiotic crossover
localization. PLOS Genetics. 16(6), e1008894.
mla: Christophorou, Nicolas, et al. “AXR1 Affects DNA Methylation Independently
of Its Role in Regulating Meiotic Crossover Localization.” PLOS Genetics,
vol. 16, no. 6, e1008894, Public Library of Science (PLoS), 2020, doi:10.1371/journal.pgen.1008894.
short: N. Christophorou, W. She, J. Long, A. Hurel, S. Beaubiat, Y. Idir, M. Tagliaro-Jahns,
A. Chambon, V. Solier, D. Vezon, M. Grelon, X. Feng, N. Bouché, C. Mézard, PLOS
Genetics 16 (2020).
date_created: 2023-01-16T09:16:10Z
date_published: 2020-06-29T00:00:00Z
date_updated: 2023-05-08T10:54:39Z
day: '29'
department:
- _id: XiFe
doi: 10.1371/journal.pgen.1008894
extern: '1'
external_id:
pmid:
- '32598340'
intvolume: ' 16'
issue: '6'
keyword:
- Cancer Research
- Genetics (clinical)
- Genetics
- Molecular Biology
- Ecology
- Evolution
- Behavior and Systematics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7351236/
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: PLOS Genetics
publication_identifier:
issn:
- 1553-7404
publication_status: published
publisher: Public Library of Science (PLoS)
quality_controlled: '1'
scopus_import: '1'
status: public
title: AXR1 affects DNA methylation independently of its role in regulating meiotic
crossover localization
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 16
year: '2020'
...
---
_id: '12190'
abstract:
- lang: eng
text: Meiotic crossover frequency varies within genomes, which influences genetic
diversity and adaptation. In turn, genetic variation within populations can act
to modify crossover frequency in cis and trans. To identify genetic variation
that controls meiotic crossover frequency, we screened Arabidopsis accessions
using fluorescent recombination reporters. We mapped a genetic modifier of crossover
frequency in Col × Bur populations of Arabidopsis to a premature stop codon within
TBP-ASSOCIATED FACTOR 4b (TAF4b), which encodes a subunit of the RNA polymerase
II general transcription factor TFIID. The Arabidopsis taf4b mutation is a rare
variant found in the British Isles, originating in South-West Ireland. Using genetics,
genomics, and immunocytology, we demonstrate a genome-wide decrease in taf4b crossovers,
with strongest reduction in the sub-telomeric regions. Using RNA sequencing (RNA-seq)
from purified meiocytes, we show that TAF4b expression is meiocyte enriched, whereas
its paralog TAF4 is broadly expressed. Consistent with the role of TFIID in promoting
gene expression, RNA-seq of wild-type and taf4b meiocytes identified widespread
transcriptional changes, including in genes that regulate the meiotic cell cycle
and recombination. Therefore, TAF4b duplication is associated with acquisition
of meiocyte-specific expression and promotion of germline transcription, which
act directly or indirectly to elevate crossovers. This identifies a novel mode
of meiotic recombination control via a general transcription factor.
acknowledgement: "We thank Gregory Copenhaver (University of North Carolina), Avraham
Levy (The Weizmann Institute), and Scott Poethig (University of Pennsylvania) for
FTLs; Piotr Ziolkowski for Col-420/Bur seed; Sureshkumar Balasubramanian\r\n(Monash
University) for providing British and Irish Arabidopsis accessions; Mathilde Grelon
(INRA, Versailles) for providing the MLH1 antibody; and the Gurdon Institute for
access to microscopes. This work was supported by a BBSRC DTP studentship (E.J.L.),
European Research Area Network for Coordinating Action in Plant Sciences/BBSRC ‘‘DeCOP’’
(BB/M004937/1; C.L.), a BBSRC David Phillips Fellowship (BB/L025043/1; H.G. and
X.F.), the European Research Council (CoG ‘‘SynthHotspot,’’ A.J.T., C.L., and I.R.H.;
StG ‘‘SexMeth,’’ X.F.), and a Sainsbury Charitable Foundation Studentship (A.R.B.)."
article_processing_charge: No
article_type: original
author:
- first_name: Emma J.
full_name: Lawrence, Emma J.
last_name: Lawrence
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Andrew J.
full_name: Tock, Andrew J.
last_name: Tock
- first_name: Christophe
full_name: Lambing, Christophe
last_name: Lambing
- first_name: Alexander R.
full_name: Blackwell, Alexander R.
last_name: Blackwell
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Ian R.
full_name: Henderson, Ian R.
last_name: Henderson
citation:
ama: Lawrence EJ, Gao H, Tock AJ, et al. Natural variation in TBP-ASSOCIATED FACTOR
4b controls meiotic crossover and germline transcription in Arabidopsis. Current
Biology. 2019;29(16):2676-2686.e3. doi:10.1016/j.cub.2019.06.084
apa: Lawrence, E. J., Gao, H., Tock, A. J., Lambing, C., Blackwell, A. R., Feng,
X., & Henderson, I. R. (2019). Natural variation in TBP-ASSOCIATED FACTOR
4b controls meiotic crossover and germline transcription in Arabidopsis. Current
Biology. Elsevier BV. https://doi.org/10.1016/j.cub.2019.06.084
chicago: Lawrence, Emma J., Hongbo Gao, Andrew J. Tock, Christophe Lambing, Alexander
R. Blackwell, Xiaoqi Feng, and Ian R. Henderson. “Natural Variation in TBP-ASSOCIATED
FACTOR 4b Controls Meiotic Crossover and Germline Transcription in Arabidopsis.”
Current Biology. Elsevier BV, 2019. https://doi.org/10.1016/j.cub.2019.06.084.
ieee: E. J. Lawrence et al., “Natural variation in TBP-ASSOCIATED FACTOR
4b controls meiotic crossover and germline transcription in Arabidopsis,” Current
Biology, vol. 29, no. 16. Elsevier BV, p. 2676–2686.e3, 2019.
ista: Lawrence EJ, Gao H, Tock AJ, Lambing C, Blackwell AR, Feng X, Henderson IR.
2019. Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover
and germline transcription in Arabidopsis. Current Biology. 29(16), 2676–2686.e3.
mla: Lawrence, Emma J., et al. “Natural Variation in TBP-ASSOCIATED FACTOR 4b Controls
Meiotic Crossover and Germline Transcription in Arabidopsis.” Current Biology,
vol. 29, no. 16, Elsevier BV, 2019, p. 2676–2686.e3, doi:10.1016/j.cub.2019.06.084.
short: E.J. Lawrence, H. Gao, A.J. Tock, C. Lambing, A.R. Blackwell, X. Feng, I.R.
Henderson, Current Biology 29 (2019) 2676–2686.e3.
date_created: 2023-01-16T09:16:33Z
date_published: 2019-08-19T00:00:00Z
date_updated: 2023-05-08T10:54:54Z
day: '19'
department:
- _id: XiFe
doi: 10.1016/j.cub.2019.06.084
extern: '1'
external_id:
pmid:
- '31378616'
intvolume: ' 29'
issue: '16'
keyword:
- General Agricultural and Biological Sciences
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '08'
oa_version: None
page: 2676-2686.e3
pmid: 1
publication: Current Biology
publication_identifier:
issn:
- 0960-9822
publication_status: published
publisher: Elsevier BV
quality_controlled: '1'
scopus_import: '1'
status: public
title: Natural variation in TBP-ASSOCIATED FACTOR 4b controls meiotic crossover and
germline transcription in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 29
year: '2019'
...
---
_id: '12192'
abstract:
- lang: eng
text: Transposable elements (TEs), the movement of which can damage the genome,
are epigenetically silenced in eukaryotes. Intriguingly, TEs are activated in
the sperm companion cell – vegetative cell (VC) – of the flowering plant Arabidopsis
thaliana. However, the extent and mechanism of this activation are unknown. Here
we show that about 100 heterochromatic TEs are activated in VCs, mostly by DEMETER-catalyzed
DNA demethylation. We further demonstrate that DEMETER access to some of these
TEs is permitted by the natural depletion of linker histone H1 in VCs. Ectopically
expressed H1 suppresses TEs in VCs by reducing DNA demethylation and via a methylation-independent
mechanism. We demonstrate that H1 is required for heterochromatin condensation
in plant cells and show that H1 overexpression creates heterochromatic foci in
the VC progenitor cell. Taken together, our results demonstrate that the natural
depletion of H1 during male gametogenesis facilitates DEMETER-directed DNA demethylation,
heterochromatin relaxation, and TE activation.
acknowledgement: We thank David Twell for the pDONR-P4-P1R-pLAT52 and pDONR-P2R-P3-mRFP
vectors, the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant Calder)
for their assistance with microscopy, and the Norwich BioScience Institute Partnership
Computing infrastructure for Science Group for High Performance Computing resources.
This work was funded by a Biotechnology and Biological Sciences Research Council
(BBSRC) David Phillips Fellowship (BB/L025043/1; SH, JZ and XF), a European Research
Council Starting Grant ('SexMeth' 804981; XF) and a Grant to Exceptional Researchers
by the Gatsby Charitable Foundation (SH and XF).
article_number: '42530'
article_processing_charge: No
article_type: original
author:
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Jingyi
full_name: Zhang, Jingyi
last_name: Zhang
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: He S, Vickers M, Zhang J, Feng X. Natural depletion of histone H1 in sex cells
causes DNA demethylation, heterochromatin decondensation and transposon activation.
eLife. 2019;8. doi:10.7554/elife.42530
apa: He, S., Vickers, M., Zhang, J., & Feng, X. (2019). Natural depletion of
histone H1 in sex cells causes DNA demethylation, heterochromatin decondensation
and transposon activation. ELife. eLife Sciences Publications, Ltd. https://doi.org/10.7554/elife.42530
chicago: He, Shengbo, Martin Vickers, Jingyi Zhang, and Xiaoqi Feng. “Natural Depletion
of Histone H1 in Sex Cells Causes DNA Demethylation, Heterochromatin Decondensation
and Transposon Activation.” ELife. eLife Sciences Publications, Ltd, 2019.
https://doi.org/10.7554/elife.42530.
ieee: S. He, M. Vickers, J. Zhang, and X. Feng, “Natural depletion of histone H1
in sex cells causes DNA demethylation, heterochromatin decondensation and transposon
activation,” eLife, vol. 8. eLife Sciences Publications, Ltd, 2019.
ista: He S, Vickers M, Zhang J, Feng X. 2019. Natural depletion of histone H1 in
sex cells causes DNA demethylation, heterochromatin decondensation and transposon
activation. eLife. 8, 42530.
mla: He, Shengbo, et al. “Natural Depletion of Histone H1 in Sex Cells Causes DNA
Demethylation, Heterochromatin Decondensation and Transposon Activation.” ELife,
vol. 8, 42530, eLife Sciences Publications, Ltd, 2019, doi:10.7554/elife.42530.
short: S. He, M. Vickers, J. Zhang, X. Feng, ELife 8 (2019).
date_created: 2023-01-16T09:17:21Z
date_published: 2019-05-28T00:00:00Z
date_updated: 2023-05-08T10:54:12Z
day: '28'
ddc:
- '580'
department:
- _id: XiFe
doi: 10.7554/elife.42530
extern: '1'
external_id:
unknown:
- '31135340'
file:
- access_level: open_access
checksum: ea6b89c20d59e5eb3646916fe5d568ad
content_type: application/pdf
creator: alisjak
date_created: 2023-02-07T09:42:46Z
date_updated: 2023-02-07T09:42:46Z
file_id: '12525'
file_name: 2019_elife_He.pdf
file_size: 2493837
relation: main_file
success: 1
file_date_updated: 2023-02-07T09:42:46Z
has_accepted_license: '1'
intvolume: ' 8'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6594752/
month: '05'
oa: 1
oa_version: Published Version
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications, Ltd
quality_controlled: '1'
scopus_import: '1'
status: public
title: Natural depletion of histone H1 in sex cells causes DNA demethylation, heterochromatin
decondensation and transposon activation
tmp:
image: /images/cc_by.png
legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode
name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)
short: CC BY (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2019'
...
---
_id: '12193'
abstract:
- lang: eng
text: DNA methylation regulates eukaryotic gene expression and is extensively reprogrammed
during animal development. However, whether developmental methylation reprogramming
during the sporophytic life cycle of flowering plants regulates genes is presently
unknown. Here we report a distinctive gene-targeted RNA-directed DNA methylation
(RdDM) activity in the Arabidopsis thaliana male sexual lineage that regulates
gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing
of the MPS1 gene (also known as PRD2), thereby disrupting meiosis. Our results
establish a regulatory paradigm in which de novo methylation creates a cell-lineage-specific
epigenetic signature that controls gene expression and contributes to cellular
function in flowering plants.
acknowledgement: We thank Daniel Zilberman for intellectual contributions to this
work and assistance with manuscript preparation. We also thank Caroline Dean, Kirsten
Bomblies, Vinod Kumar, Siobhan Brady and Sophien Kamoun for comments on the manuscript,
Hugh Dickinson and Josephine Hellberg for developing the meiocyte isolation method,
Giles Oldroyd for the pGWB13-Bar vector, Elisa Fiume for the pMDC107-NTF vector,
Matthew Hartley, Matthew Couchman and Tjelvar Sten Gunnar Olsson for bioinformatics
support, and the John Innes Centre Bioimaging Facility (Elaine Barclay and Grant
Calder) for their assistance with microscopy. This work was funded by a Biotechnology
and Biological Sciences Research Council (BBSRC) David Phillips Fellowship (BBL0250431)
to X.F., a BBSRC grant (BBM01973X1) to J.H., and a Sainsbury PhD Studentship to
J.W.
article_processing_charge: No
article_type: original
author:
- first_name: James
full_name: Walker, James
last_name: Walker
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Jingyi
full_name: Zhang, Jingyi
last_name: Zhang
- first_name: Billy
full_name: Aldridge, Billy
last_name: Aldridge
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: James D.
full_name: Higgins, James D.
last_name: Higgins
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Walker J, Gao H, Zhang J, et al. Sexual-lineage-specific DNA methylation regulates
meiosis in Arabidopsis. Nature Genetics. 2017;50(1):130-137. doi:10.1038/s41588-017-0008-5
apa: Walker, J., Gao, H., Zhang, J., Aldridge, B., Vickers, M., Higgins, J. D.,
& Feng, X. (2017). Sexual-lineage-specific DNA methylation regulates meiosis
in Arabidopsis. Nature Genetics. Nature Research. https://doi.org/10.1038/s41588-017-0008-5
chicago: Walker, James, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers,
James D. Higgins, and Xiaoqi Feng. “Sexual-Lineage-Specific DNA Methylation Regulates
Meiosis in Arabidopsis.” Nature Genetics. Nature Research, 2017. https://doi.org/10.1038/s41588-017-0008-5.
ieee: J. Walker et al., “Sexual-lineage-specific DNA methylation regulates
meiosis in Arabidopsis,” Nature Genetics, vol. 50, no. 1. Nature Research,
pp. 130–137, 2017.
ista: Walker J, Gao H, Zhang J, Aldridge B, Vickers M, Higgins JD, Feng X. 2017.
Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis. Nature
Genetics. 50(1), 130–137.
mla: Walker, James, et al. “Sexual-Lineage-Specific DNA Methylation Regulates Meiosis
in Arabidopsis.” Nature Genetics, vol. 50, no. 1, Nature Research, 2017,
pp. 130–37, doi:10.1038/s41588-017-0008-5.
short: J. Walker, H. Gao, J. Zhang, B. Aldridge, M. Vickers, J.D. Higgins, X. Feng,
Nature Genetics 50 (2017) 130–137.
date_created: 2023-01-16T09:18:05Z
date_published: 2017-12-18T00:00:00Z
date_updated: 2023-10-18T07:21:53Z
day: '18'
department:
- _id: XiFe
doi: 10.1038/s41588-017-0008-5
external_id:
pmid:
- '29255257'
intvolume: ' 50'
issue: '1'
keyword:
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7611288/
month: '12'
oa: 1
oa_version: None
page: 130-137
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Nature Research
quality_controlled: '1'
scopus_import: '1'
status: public
title: Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 50
year: '2017'
...
---
_id: '9473'
abstract:
- lang: eng
text: Cytosine DNA methylation regulates the expression of eukaryotic genes and
transposons. Methylation is copied by methyltransferases after DNA replication,
which results in faithful transmission of methylation patterns during cell division
and, at least in flowering plants, across generations. Transgenerational inheritance
is mediated by a small group of cells that includes gametes and their progenitors.
However, methylation is usually analyzed in somatic tissues that do not contribute
to the next generation, and the mechanisms of transgenerational inheritance are
inferred from such studies. To gain a better understanding of how DNA methylation
is inherited, we analyzed purified Arabidopsis thaliana sperm and vegetative cells-the
cell types that comprise pollen-with mutations in the DRM, CMT2, and CMT3 methyltransferases.
We find that DNA methylation dependency on these enzymes is similar in sperm,
vegetative cells, and somatic tissues, although DRM activity extends into heterochromatin
in vegetative cells, likely reflecting transcription of heterochromatic transposons
in this cell type. We also show that lack of histone H1, which elevates heterochromatic
DNA methylation in somatic tissues, does not have this effect in pollen. Instead,
levels of CG methylation in wild-type sperm and vegetative cells, as well as in
wild-type microspores from which both pollen cell types originate, are substantially
higher than in wild-type somatic tissues and similar to those of H1-depleted roots.
Our results demonstrate that the mechanisms of methylation maintenance are similar
between pollen and somatic cells, but the efficiency of CG methylation is higher
in pollen, allowing methylation patterns to be accurately inherited across generations.
article_processing_charge: No
article_type: original
author:
- first_name: Ping-Hung
full_name: Hsieh, Ping-Hung
last_name: Hsieh
- first_name: Shengbo
full_name: He, Shengbo
last_name: He
- first_name: Toby
full_name: Buttress, Toby
last_name: Buttress
- first_name: Hongbo
full_name: Gao, Hongbo
last_name: Gao
- first_name: Matthew
full_name: Couchman, Matthew
last_name: Couchman
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
citation:
ama: Hsieh P-H, He S, Buttress T, et al. Arabidopsis male sexual lineage exhibits
more robust maintenance of CG methylation than somatic tissues. Proceedings
of the National Academy of Sciences. 2016;113(52):15132-15137. doi:10.1073/pnas.1619074114
apa: Hsieh, P.-H., He, S., Buttress, T., Gao, H., Couchman, M., Fischer, R. L.,
… Feng, X. (2016). Arabidopsis male sexual lineage exhibits more robust maintenance
of CG methylation than somatic tissues. Proceedings of the National Academy
of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1619074114
chicago: Hsieh, Ping-Hung, Shengbo He, Toby Buttress, Hongbo Gao, Matthew Couchman,
Robert L. Fischer, Daniel Zilberman, and Xiaoqi Feng. “Arabidopsis Male Sexual
Lineage Exhibits More Robust Maintenance of CG Methylation than Somatic Tissues.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2016. https://doi.org/10.1073/pnas.1619074114.
ieee: P.-H. Hsieh et al., “Arabidopsis male sexual lineage exhibits more
robust maintenance of CG methylation than somatic tissues,” Proceedings of
the National Academy of Sciences, vol. 113, no. 52. National Academy of Sciences,
pp. 15132–15137, 2016.
ista: Hsieh P-H, He S, Buttress T, Gao H, Couchman M, Fischer RL, Zilberman D, Feng
X. 2016. Arabidopsis male sexual lineage exhibits more robust maintenance of CG
methylation than somatic tissues. Proceedings of the National Academy of Sciences.
113(52), 15132–15137.
mla: Hsieh, Ping-Hung, et al. “Arabidopsis Male Sexual Lineage Exhibits More Robust
Maintenance of CG Methylation than Somatic Tissues.” Proceedings of the National
Academy of Sciences, vol. 113, no. 52, National Academy of Sciences, 2016,
pp. 15132–37, doi:10.1073/pnas.1619074114.
short: P.-H. Hsieh, S. He, T. Buttress, H. Gao, M. Couchman, R.L. Fischer, D. Zilberman,
X. Feng, Proceedings of the National Academy of Sciences 113 (2016) 15132–15137.
date_created: 2021-06-07T06:21:39Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:40Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619074114
extern: '1'
external_id:
pmid:
- '27956643'
intvolume: ' 113'
issue: '52'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619074114
month: '12'
oa: 1
oa_version: Published Version
page: 15132-15137
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: Arabidopsis male sexual lineage exhibits more robust maintenance of CG methylation
than somatic tissues
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '9477'
abstract:
- lang: eng
text: Cytosine methylation is a DNA modification with important regulatory functions
in eukaryotes. In flowering plants, sexual reproduction is accompanied by extensive
DNA demethylation, which is required for proper gene expression in the endosperm,
a nutritive extraembryonic seed tissue. Endosperm arises from a fusion of a sperm
cell carried in the pollen and a female central cell. Endosperm DNA demethylation
is observed specifically on the chromosomes inherited from the central cell in
Arabidopsis thaliana, rice, and maize, and requires the DEMETER DNA demethylase
in Arabidopsis. DEMETER is expressed in the central cell before fertilization,
suggesting that endosperm demethylation patterns are inherited from the central
cell. Down-regulation of the MET1 DNA methyltransferase has also been proposed
to contribute to central cell demethylation. However, with the exception of three
maize genes, central cell DNA methylation has not been directly measured, leaving
the origin and mechanism of endosperm demethylation uncertain. Here, we report
genome-wide analysis of DNA methylation in the central cells of Arabidopsis and
rice—species that diverged 150 million years ago—as well as in rice egg cells.
We find that DNA demethylation in both species is initiated in central cells,
which requires DEMETER in Arabidopsis. However, we do not observe a global reduction
of CG methylation that would be indicative of lowered MET1 activity; on the contrary,
CG methylation efficiency is elevated in female gametes compared with nonsexual
tissues. Our results demonstrate that locus-specific, active DNA demethylation
in the central cell is the origin of maternal chromosome hypomethylation in the
endosperm.
article_processing_charge: No
article_type: original
author:
- first_name: Kyunghyuk
full_name: Park, Kyunghyuk
last_name: Park
- first_name: M. Yvonne
full_name: Kim, M. Yvonne
last_name: Kim
- first_name: Martin
full_name: Vickers, Martin
last_name: Vickers
- first_name: Jin-Sup
full_name: Park, Jin-Sup
last_name: Park
- first_name: Youbong
full_name: Hyun, Youbong
last_name: Hyun
- first_name: Takashi
full_name: Okamoto, Takashi
last_name: Okamoto
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Yeonhee
full_name: Choi, Yeonhee
last_name: Choi
- first_name: Stefan
full_name: Scholten, Stefan
last_name: Scholten
citation:
ama: Park K, Kim MY, Vickers M, et al. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
2016;113(52):15138-15143. doi:10.1073/pnas.1619047114
apa: Park, K., Kim, M. Y., Vickers, M., Park, J.-S., Hyun, Y., Okamoto, T., … Scholten,
S. (2016). DNA demethylation is initiated in the central cells of Arabidopsis
and rice. Proceedings of the National Academy of Sciences. National Academy
of Sciences. https://doi.org/10.1073/pnas.1619047114
chicago: Park, Kyunghyuk, M. Yvonne Kim, Martin Vickers, Jin-Sup Park, Youbong Hyun,
Takashi Okamoto, Daniel Zilberman, et al. “DNA Demethylation Is Initiated in the
Central Cells of Arabidopsis and Rice.” Proceedings of the National Academy
of Sciences. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1619047114.
ieee: K. Park et al., “DNA demethylation is initiated in the central cells
of Arabidopsis and rice,” Proceedings of the National Academy of Sciences,
vol. 113, no. 52. National Academy of Sciences, pp. 15138–15143, 2016.
ista: Park K, Kim MY, Vickers M, Park J-S, Hyun Y, Okamoto T, Zilberman D, Fischer
RL, Feng X, Choi Y, Scholten S. 2016. DNA demethylation is initiated in the central
cells of Arabidopsis and rice. Proceedings of the National Academy of Sciences.
113(52), 15138–15143.
mla: Park, Kyunghyuk, et al. “DNA Demethylation Is Initiated in the Central Cells
of Arabidopsis and Rice.” Proceedings of the National Academy of Sciences,
vol. 113, no. 52, National Academy of Sciences, 2016, pp. 15138–43, doi:10.1073/pnas.1619047114.
short: K. Park, M.Y. Kim, M. Vickers, J.-S. Park, Y. Hyun, T. Okamoto, D. Zilberman,
R.L. Fischer, X. Feng, Y. Choi, S. Scholten, Proceedings of the National Academy
of Sciences 113 (2016) 15138–15143.
date_created: 2021-06-07T07:10:59Z
date_published: 2016-12-27T00:00:00Z
date_updated: 2023-05-08T11:00:07Z
day: '27'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1073/pnas.1619047114
extern: '1'
external_id:
pmid:
- '27956642'
intvolume: ' 113'
issue: '52'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.1619047114
month: '12'
oa: 1
oa_version: Published Version
page: 15138-15143
pmid: 1
publication: Proceedings of the National Academy of Sciences
publication_identifier:
eissn:
- 1091-6490
issn:
- 0027-8424
publication_status: published
publisher: National Academy of Sciences
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA demethylation is initiated in the central cells of Arabidopsis and rice
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 113
year: '2016'
...
---
_id: '12196'
abstract:
- lang: eng
text: SNC1 (SUPPRESSOR OF NPR1, CONSTITUTIVE 1) is one of a suite of intracellular
Arabidopsis NOD-like receptor (NLR) proteins which, upon activation, result in
the induction of defense responses. However, the molecular mechanisms underlying
NLR activation and the subsequent provocation of immune responses are only partially
characterized. To identify negative regulators of NLR-mediated immunity, a forward
genetic screen was undertaken to search for enhancers of the dwarf, autoimmune
gain-of-function snc1 mutant. To avoid lethality resulting from severe dwarfism,
the screen was conducted using mos4 (modifier of snc1, 4) snc1 plants, which display
wild-type-like morphology and resistance. M2 progeny were screened for mutant,
snc1-enhancing (muse) mutants displaying a reversion to snc1-like phenotypes.
The muse9 mos4 snc1 triple mutant was found to exhibit dwarf morphology, elevated
expression of the pPR2-GUS defense marker reporter gene and enhanced resistance
to the oomycete pathogen Hyaloperonospora arabidopsidis Noco2. Via map-based cloning
and Illumina sequencing, it was determined that the muse9 mutation is in the gene
encoding the SWI/SNF chromatin remodeler SYD (SPLAYED), and was thus renamed syd-10.
The syd-10 single mutant has no observable alteration from wild-type-like resistance,
although the syd-4 T-DNA insertion allele displays enhanced resistance to the
bacterial pathogen Pseudomonas syringae pv. maculicola ES4326. Transcription of
SNC1 is increased in both syd-4 and syd-10. These data suggest that SYD plays
a subtle, specific role in the regulation of SNC1 expression and SNC1-mediated
immunity. SYD may work with other proteins at the chromatin level to repress SNC1
transcription; such regulation is important for fine-tuning the expression of
NLR-encoding genes to prevent unpropitious autoimmunity.
acknowledgement: "This work was supported by the National Sciences and Engineering
Research Council of Canada [Canada Graduate\r\nScholarship–Doctoral to K.J.; Discovery
Grant to X.L.]; the department of Botany at the University of f British Columbia\r\n[the
Dewar Cooper Memorial Fund to X.L.].The authors would like to thank Dr. Yuelin Zhang
and Ms. Yan Li for their assistance with next-generation sequencing, and Mr. Charles
Copeland for critical reading of the manuscript."
article_processing_charge: No
article_type: original
author:
- first_name: Kaeli C.M.
full_name: Johnson, Kaeli C.M.
last_name: Johnson
- first_name: Shitou
full_name: Xia, Shitou
last_name: Xia
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Xin
full_name: Li, Xin
last_name: Li
citation:
ama: Johnson KCM, Xia S, Feng X, Li X. The chromatin remodeler SPLAYED negatively
regulates SNC1-mediated immunity. Plant and Cell Physiology. 2015;56(8):1616-1623.
doi:10.1093/pcp/pcv087
apa: Johnson, K. C. M., Xia, S., Feng, X., & Li, X. (2015). The chromatin remodeler
SPLAYED negatively regulates SNC1-mediated immunity. Plant and Cell Physiology.
Oxford University Press. https://doi.org/10.1093/pcp/pcv087
chicago: Johnson, Kaeli C.M., Shitou Xia, Xiaoqi Feng, and Xin Li. “The Chromatin
Remodeler SPLAYED Negatively Regulates SNC1-Mediated Immunity.” Plant and Cell
Physiology. Oxford University Press, 2015. https://doi.org/10.1093/pcp/pcv087.
ieee: K. C. M. Johnson, S. Xia, X. Feng, and X. Li, “The chromatin remodeler SPLAYED
negatively regulates SNC1-mediated immunity,” Plant and Cell Physiology,
vol. 56, no. 8. Oxford University Press, pp. 1616–1623, 2015.
ista: Johnson KCM, Xia S, Feng X, Li X. 2015. The chromatin remodeler SPLAYED negatively
regulates SNC1-mediated immunity. Plant and Cell Physiology. 56(8), 1616–1623.
mla: Johnson, Kaeli C. M., et al. “The Chromatin Remodeler SPLAYED Negatively Regulates
SNC1-Mediated Immunity.” Plant and Cell Physiology, vol. 56, no. 8, Oxford
University Press, 2015, pp. 1616–23, doi:10.1093/pcp/pcv087.
short: K.C.M. Johnson, S. Xia, X. Feng, X. Li, Plant and Cell Physiology 56 (2015)
1616–1623.
date_created: 2023-01-16T09:20:22Z
date_published: 2015-08-01T00:00:00Z
date_updated: 2023-05-08T11:03:23Z
department:
- _id: XiFe
doi: 10.1093/pcp/pcv087
extern: '1'
external_id:
pmid:
- '26063389'
intvolume: ' 56'
issue: '8'
keyword:
- Cell Biology
- Plant Science
- Physiology
- General Medicine
language:
- iso: eng
month: '08'
oa_version: None
page: 1616-1623
pmid: 1
publication: Plant and Cell Physiology
publication_identifier:
issn:
- 0032-0781
- 1471-9053
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: The chromatin remodeler SPLAYED negatively regulates SNC1-mediated immunity
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 56
year: '2015'
...
---
_id: '9520'
abstract:
- lang: eng
text: Plants undergo alternation of generation in which reproductive cells develop
in the plant body ("sporophytic generation") and then differentiate into a multicellular
gamete-forming "gametophytic generation." Different populations of helper cells
assist in this transgenerational journey, with somatic tissues supporting early
development and single nurse cells supporting gametogenesis. New data reveal a
two-way relationship between early reproductive cells and their helpers involving
complex epigenetic and signaling networks determining cell number and fate. Later,
the egg cell plays a central role in specifying accessory cells, whereas in both
gametophytes, companion cells contribute non-cell-autonomously to the epigenetic
landscape of the gamete genomes.
article_processing_charge: No
article_type: review
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Hugh
full_name: Dickinson, Hugh
last_name: Dickinson
citation:
ama: 'Feng X, Zilberman D, Dickinson H. A conversation across generations: Soma-germ
cell crosstalk in plants. Developmental Cell. 2013;24(3):215-225. doi:10.1016/j.devcel.2013.01.014'
apa: 'Feng, X., Zilberman, D., & Dickinson, H. (2013). A conversation across
generations: Soma-germ cell crosstalk in plants. Developmental Cell. Elsevier.
https://doi.org/10.1016/j.devcel.2013.01.014'
chicago: 'Feng, Xiaoqi, Daniel Zilberman, and Hugh Dickinson. “A Conversation across
Generations: Soma-Germ Cell Crosstalk in Plants.” Developmental Cell. Elsevier,
2013. https://doi.org/10.1016/j.devcel.2013.01.014.'
ieee: 'X. Feng, D. Zilberman, and H. Dickinson, “A conversation across generations:
Soma-germ cell crosstalk in plants,” Developmental Cell, vol. 24, no. 3.
Elsevier, pp. 215–225, 2013.'
ista: 'Feng X, Zilberman D, Dickinson H. 2013. A conversation across generations:
Soma-germ cell crosstalk in plants. Developmental Cell. 24(3), 215–225.'
mla: 'Feng, Xiaoqi, et al. “A Conversation across Generations: Soma-Germ Cell Crosstalk
in Plants.” Developmental Cell, vol. 24, no. 3, Elsevier, 2013, pp. 215–25,
doi:10.1016/j.devcel.2013.01.014.'
short: X. Feng, D. Zilberman, H. Dickinson, Developmental Cell 24 (2013) 215–225.
date_created: 2021-06-08T06:14:50Z
date_published: 2013-02-11T00:00:00Z
date_updated: 2023-05-08T11:00:59Z
day: '11'
department:
- _id: DaZi
- _id: XiFe
doi: 10.1016/j.devcel.2013.01.014
extern: '1'
external_id:
pmid:
- '23410937'
intvolume: ' 24'
issue: '3'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.devcel.2013.01.014
month: '02'
oa: 1
oa_version: Published Version
page: 215-225
pmid: 1
publication: Developmental Cell
publication_identifier:
eissn:
- 1878-1551
issn:
- 1534-5807
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'A conversation across generations: Soma-germ cell crosstalk in plants'
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 24
year: '2013'
...
---
_id: '12198'
abstract:
- lang: eng
text: The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes
DNA demethylation before fertilization, but the targeting preferences, mechanism,
and biological significance of this process remain unclear. Here, we show that
active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for
all of the demethylation in the central cell and preferentially targets small,
AT-rich, and nucleosome-depleted euchromatic transposable elements. The vegetative
cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation
of similar sequences, and lack of DEMETER in vegetative cells causes reduced small
RNA–directed DNA methylation of transposons in sperm. Our results demonstrate
that demethylation in companion cells reinforces transposon methylation in plant
gametes and likely contributes to stable silencing of transposable elements across
generations.
acknowledgement: We thank S. Harmer for assistance with the analysis of histone modifications,
the BioOptics team at the Vienna Biocenter Campus for sorting sperm and vegetative
cell nuclei, K. Slotkin for the LAT52p-amiRNA=GFP plasmid, and G. Drews for the
DD45p-GFP transgenic line. This work was partially funded by an NIH grant (GM69415)
to R.L.F., NSF grants (MCB-0918821 and IOS-1025890) to R.L.F. and D.Z., a Young
Investigator Grant from the Arnold and Mabel Beckman Foundation to D.Z., an Austrian
Science Fund (FWF) grant P21389-B03 to H.T., a Ruth L. Kirschstein NIH Predoctoral
Fellowship (GM093633) to C.A.I., a Fulbright Scholarship to J.A.R., a fellowship
from the Jane Coffin Childs Memorial Fund to A.Z., and a Robert and Colleen Haas
Scholarship to D.R. Sequencing data are deposited in GEO (GSE38935).
article_processing_charge: No
article_type: original
author:
- first_name: Christian A.
full_name: Ibarra, Christian A.
last_name: Ibarra
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Vera K.
full_name: Schoft, Vera K.
last_name: Schoft
- first_name: Tzung-Fu
full_name: Hsieh, Tzung-Fu
last_name: Hsieh
- first_name: Rie
full_name: Uzawa, Rie
last_name: Uzawa
- first_name: Jessica A.
full_name: Rodrigues, Jessica A.
last_name: Rodrigues
- first_name: Assaf
full_name: Zemach, Assaf
last_name: Zemach
- first_name: Nina
full_name: Chumak, Nina
last_name: Chumak
- first_name: Adriana
full_name: Machlicova, Adriana
last_name: Machlicova
- first_name: Toshiro
full_name: Nishimura, Toshiro
last_name: Nishimura
- first_name: Denisse
full_name: Rojas, Denisse
last_name: Rojas
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
- first_name: Hisashi
full_name: Tamaru, Hisashi
last_name: Tamaru
- first_name: Daniel
full_name: Zilberman, Daniel
last_name: Zilberman
citation:
ama: Ibarra CA, Feng X, Schoft VK, et al. Active DNA demethylation in plant companion
cells reinforces transposon methylation in gametes. Science. 2012;337(6100):1360-1364.
doi:10.1126/science.1224839
apa: Ibarra, C. A., Feng, X., Schoft, V. K., Hsieh, T.-F., Uzawa, R., Rodrigues,
J. A., … Zilberman, D. (2012). Active DNA demethylation in plant companion cells
reinforces transposon methylation in gametes. Science. American Association
for the Advancement of Science. https://doi.org/10.1126/science.1224839
chicago: Ibarra, Christian A., Xiaoqi Feng, Vera K. Schoft, Tzung-Fu Hsieh, Rie
Uzawa, Jessica A. Rodrigues, Assaf Zemach, et al. “Active DNA Demethylation in
Plant Companion Cells Reinforces Transposon Methylation in Gametes.” Science.
American Association for the Advancement of Science, 2012. https://doi.org/10.1126/science.1224839.
ieee: C. A. Ibarra et al., “Active DNA demethylation in plant companion cells
reinforces transposon methylation in gametes,” Science, vol. 337, no. 6100.
American Association for the Advancement of Science, pp. 1360–1364, 2012.
ista: Ibarra CA, Feng X, Schoft VK, Hsieh T-F, Uzawa R, Rodrigues JA, Zemach A,
Chumak N, Machlicova A, Nishimura T, Rojas D, Fischer RL, Tamaru H, Zilberman
D. 2012. Active DNA demethylation in plant companion cells reinforces transposon
methylation in gametes. Science. 337(6100), 1360–1364.
mla: Ibarra, Christian A., et al. “Active DNA Demethylation in Plant Companion Cells
Reinforces Transposon Methylation in Gametes.” Science, vol. 337, no. 6100,
American Association for the Advancement of Science, 2012, pp. 1360–64, doi:10.1126/science.1224839.
short: C.A. Ibarra, X. Feng, V.K. Schoft, T.-F. Hsieh, R. Uzawa, J.A. Rodrigues,
A. Zemach, N. Chumak, A. Machlicova, T. Nishimura, D. Rojas, R.L. Fischer, H.
Tamaru, D. Zilberman, Science 337 (2012) 1360–1364.
date_created: 2023-01-16T09:21:24Z
date_published: 2012-09-14T00:00:00Z
date_updated: 2023-10-16T09:27:26Z
day: '14'
department:
- _id: XiFe
doi: 10.1126/science.1224839
external_id:
pmid:
- '22984074'
intvolume: ' 337'
issue: '6100'
keyword:
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4034762/
month: '09'
oa: 1
oa_version: Published Version
page: 1360-1364
pmid: 1
publication: Science
publication_identifier:
eissn:
- 1095-9203
issn:
- 0036-8075
publication_status: published
publisher: American Association for the Advancement of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Active DNA demethylation in plant companion cells reinforces transposon methylation
in gametes
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 337
year: '2012'
...
---
_id: '12199'
abstract:
- lang: eng
text: The four microsporangia of the flowering plant anther develop from archesporial
cells in the L2 of the primordium. Within each microsporangium, developing microsporocytes
are surrounded by concentric monolayers of tapetal, middle layer and endothecial
cells. How this intricate array of tissues, each containing relatively few cells,
is established in an organ possessing no formal meristems is poorly understood.
We describe here the pivotal role of the LRR receptor kinase EXCESS MICROSPOROCYTES
1 (EMS1) in forming the monolayer of tapetal nurse cells in Arabidopsis. Unusually
for plants, tapetal cells are specified very early in development, and are subsequently
stimulated to proliferate by a receptor-like kinase (RLK) complex that includes
EMS1. Mutations in members of this EMS1 signalling complex and its putative ligand
result in male-sterile plants in which tapetal initials fail to proliferate. Surprisingly,
these cells continue to develop, isolated at the locular periphery. Mutant and
wild-type microsporangia expand at similar rates and the ‘tapetal’ space at the
periphery of mutant locules becomes occupied by microsporocytes. However, induction
of late expression of EMS1 in the few tapetal initials in ems1 plants results
in their proliferation to generate a functional tapetum, and this proliferation
suppresses microsporocyte number. Our experiments also show that integrity of
the tapetal monolayer is crucial for the maintenance of the polarity of divisions
within it. This unexpected autonomy of the tapetal ‘lineage’ is discussed in the
context of tissue development in complex plant organs, where constancy in size,
shape and cell number is crucial.
acknowledgement: 'We thank the following for providing mutant lines and reagents:
Hong Ma, De Ye, Sacco De Vries, and Rod Scott for providing the pA9::Barnase lines
and information on A9 expression patterns. Carla Galinha and Paolo Piazza gave valuable
help with in situ hybridisation and qRT-PCR, respectively, and we acknowledge Qing
Zhang, Helen Prescott and Matthew Dicks for providing excellent technical assistance.
We are indebted to Miltos Tsiantis and Angela Hay for helpful discussion, and the
research was funded by Oxford University through a Clarendon Scholarship to X.F.,
with additional financial support from Magdalen College (Oxford).'
article_processing_charge: No
article_type: original
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Hugh G.
full_name: Dickinson, Hugh G.
last_name: Dickinson
citation:
ama: Feng X, Dickinson HG. Tapetal cell fate, lineage and proliferation in the Arabidopsis
anther. Development. 2010;137(14):2409-2416. doi:10.1242/dev.049320
apa: Feng, X., & Dickinson, H. G. (2010). Tapetal cell fate, lineage and proliferation
in the Arabidopsis anther. Development. The Company of Biologists. https://doi.org/10.1242/dev.049320
chicago: Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation
in the Arabidopsis Anther.” Development. The Company of Biologists, 2010.
https://doi.org/10.1242/dev.049320.
ieee: X. Feng and H. G. Dickinson, “Tapetal cell fate, lineage and proliferation
in the Arabidopsis anther,” Development, vol. 137, no. 14. The Company
of Biologists, pp. 2409–2416, 2010.
ista: Feng X, Dickinson HG. 2010. Tapetal cell fate, lineage and proliferation in
the Arabidopsis anther. Development. 137(14), 2409–2416.
mla: Feng, Xiaoqi, and Hugh G. Dickinson. “Tapetal Cell Fate, Lineage and Proliferation
in the Arabidopsis Anther.” Development, vol. 137, no. 14, The Company
of Biologists, 2010, pp. 2409–16, doi:10.1242/dev.049320.
short: X. Feng, H.G. Dickinson, Development 137 (2010) 2409–2416.
date_created: 2023-01-16T09:21:54Z
date_published: 2010-07-15T00:00:00Z
date_updated: 2023-05-08T10:57:11Z
day: '15'
department:
- _id: XiFe
doi: 10.1242/dev.049320
extern: '1'
external_id:
pmid:
- '20570940'
intvolume: ' 137'
issue: '14'
keyword:
- Developmental Biology
- Molecular Biology
- Anther Tapetum
- Arabidopsis
- Cell Fate Establishment
- EMS1
- Reproductive Cell Lineage
language:
- iso: eng
month: '07'
oa_version: None
page: 2409-2416
pmid: 1
publication: Development
publication_identifier:
issn:
- 1477-9129
- 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tapetal cell fate, lineage and proliferation in the Arabidopsis anther
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 137
year: '2010'
...
---
_id: '12200'
abstract:
- lang: eng
text: Key steps in the evolution of the angiosperm anther include the patterning
of the concentrically organized microsporangium and the incorporation of four
such microsporangia into a leaf-like structure. Mutant studies in the model plant
Arabidopsis thaliana are leading to an increasingly accurate picture of (i) the
cell lineages culminating in the different cell types present in the microsporangium
(the microsporocytes, the tapetum, and the middle and endothecial layers), and
(ii) some of the genes responsible for specifying their fates. However, the processes
that confer polarity on the developing anther and position the microsporangia
within it remain unclear. Certainly, data from a range of experimental strategies
suggest that hormones play a central role in establishing polarity and the patterning
of the anther initial, and may be responsible for locating the microsporangia.
But the fact that microsporangia were originally positioned externally suggests
that their development is likely to be autonomous, perhaps with the reproductive
cells generating signals controlling the growth and division of the investing
anther epidermis. These possibilities are discussed in the context of the expression
of genes which initiate and maintain male and female reproductive development,
and in the perspective of our current views of anther evolution.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Hugh G.
full_name: Dickinson, Hugh G.
last_name: Dickinson
citation:
ama: Feng X, Dickinson HG. Cell–cell interactions during patterning of the Arabidopsis
anther. Biochemical Society Transactions. 2010;38(2):571-576. doi:10.1042/bst0380571
apa: Feng, X., & Dickinson, H. G. (2010). Cell–cell interactions during patterning
of the Arabidopsis anther. Biochemical Society Transactions. Portland
Press Ltd. https://doi.org/10.1042/bst0380571
chicago: Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning
of the Arabidopsis Anther.” Biochemical Society Transactions. Portland
Press Ltd., 2010. https://doi.org/10.1042/bst0380571.
ieee: X. Feng and H. G. Dickinson, “Cell–cell interactions during patterning of
the Arabidopsis anther,” Biochemical Society Transactions, vol.
38, no. 2. Portland Press Ltd., pp. 571–576, 2010.
ista: Feng X, Dickinson HG. 2010. Cell–cell interactions during patterning of the
Arabidopsis anther. Biochemical Society Transactions. 38(2), 571–576.
mla: Feng, Xiaoqi, and Hugh G. Dickinson. “Cell–Cell Interactions during Patterning
of the Arabidopsis Anther.” Biochemical Society Transactions, vol.
38, no. 2, Portland Press Ltd., 2010, pp. 571–76, doi:10.1042/bst0380571.
short: X. Feng, H.G. Dickinson, Biochemical Society Transactions 38 (2010) 571–576.
date_created: 2023-01-16T09:22:18Z
date_published: 2010-03-22T00:00:00Z
date_updated: 2023-05-08T10:57:59Z
day: '22'
department:
- _id: XiFe
doi: 10.1042/bst0380571
extern: '1'
external_id:
pmid:
- '20298223'
intvolume: ' 38'
issue: '2'
keyword:
- Biochemistry
- Anther Development
- Arabidopsis
- Cell Fate
- Microsporangium
- Polarity
- Receptor Kinase
language:
- iso: eng
month: '03'
oa_version: None
page: 571-576
pmid: 1
publication: Biochemical Society Transactions
publication_identifier:
issn:
- 0300-5127
- 1470-8752
publication_status: published
publisher: Portland Press Ltd.
quality_controlled: '1'
scopus_import: '1'
status: public
title: Cell–cell interactions during patterning of the Arabidopsis anther
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 38
year: '2010'
...
---
_id: '12201'
abstract:
- lang: eng
text: The development of plant lateral organs is interesting because, although many
of the same genes seem to be involved in the early growth of primordia, completely
different gene combinations are required for the complete development of organs
such as leaves and stamens. Thus, the genes common to the development of most
organs, which generally form and polarize the primordial ‘envelope’, must at some
stage interact with those that ‘install’ the functional content of the organ –
in the case of the stamen, the four microsporangia. Although distinct genetic
pathways of organ initiation, polarity establishment and setting up the reproductive
cell line can readily be recognized, they do not occur sequentially. Rather, they
are activated early and run in parallel. There is evidence for continuing crosstalk
between these pathways.
acknowledgement: X.F. holds a Clarendon Scholarship from the University of Oxford.
We thank Angela Hay and Jill Harrison for helpful advice and discussion.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Hugh G.
full_name: Dickinson, Hugh G.
last_name: Dickinson
citation:
ama: Feng X, Dickinson HG. Packaging the male germline in plants. Trends in Genetics.
2007;23(10):503-510. doi:10.1016/j.tig.2007.08.005
apa: Feng, X., & Dickinson, H. G. (2007). Packaging the male germline in plants.
Trends in Genetics. Elsevier BV. https://doi.org/10.1016/j.tig.2007.08.005
chicago: Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.”
Trends in Genetics. Elsevier BV, 2007. https://doi.org/10.1016/j.tig.2007.08.005.
ieee: X. Feng and H. G. Dickinson, “Packaging the male germline in plants,” Trends
in Genetics, vol. 23, no. 10. Elsevier BV, pp. 503–510, 2007.
ista: Feng X, Dickinson HG. 2007. Packaging the male germline in plants. Trends
in Genetics. 23(10), 503–510.
mla: Feng, Xiaoqi, and Hugh G. Dickinson. “Packaging the Male Germline in Plants.”
Trends in Genetics, vol. 23, no. 10, Elsevier BV, 2007, pp. 503–10, doi:10.1016/j.tig.2007.08.005.
short: X. Feng, H.G. Dickinson, Trends in Genetics 23 (2007) 503–510.
date_created: 2023-01-16T09:22:44Z
date_published: 2007-10-01T00:00:00Z
date_updated: 2023-05-08T10:58:47Z
department:
- _id: XiFe
doi: 10.1016/j.tig.2007.08.005
extern: '1'
external_id:
pmid:
- '17825943'
intvolume: ' 23'
issue: '10'
keyword:
- Genetics
language:
- iso: eng
month: '10'
oa_version: None
page: 503-510
pmid: 1
publication: Trends in Genetics
publication_identifier:
issn:
- 0168-9525
publication_status: published
publisher: Elsevier BV
quality_controlled: '1'
scopus_import: '1'
status: public
title: Packaging the male germline in plants
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 23
year: '2007'
...