---
_id: '9487'
abstract:
- lang: eng
text: Cytosine DNA methylation is considered to be a stable epigenetic mark, but
active demethylation has been observed in both plants and animals. In Arabidopsis
thaliana, DNA glycosylases of the DEMETER (DME) family remove methylcytosines
from DNA. Demethylation by DME is necessary for genomic imprinting, and demethylation
by a related protein, REPRESSOR OF SILENCING1, prevents gene silencing in a transgenic
background. However, the extent and function of demethylation by DEMETER-LIKE
(DML) proteins in WT plants is not known. Using genome-tiling microarrays, we
mapped DNA methylation in mutant and WT plants and identified 179 loci actively
demethylated by DML enzymes. Mutations in DML genes lead to locus-specific DNA
hypermethylation. Reintroducing WT DML genes restores most loci to the normal
pattern of methylation, although at some loci, hypermethylated epialleles persist.
Of loci demethylated by DML enzymes, >80% are near or overlap genes. Genic demethylation
by DML enzymes primarily occurs at the 5′ and 3′ ends, a pattern opposite to the
overall distribution of WT DNA methylation. Our results show that demethylation
by DML DNA glycosylases edits the patterns of DNA methylation within the Arabidopsis
genome to protect genes from potentially deleterious methylation.
article_processing_charge: No
article_type: original
author:
- first_name: Jon
full_name: Penterman, Jon
last_name: Penterman
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Jin Hoe
full_name: Huh, Jin Hoe
last_name: Huh
- first_name: Tracy
full_name: Ballinger, Tracy
last_name: Ballinger
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
- first_name: Robert L.
full_name: Fischer, Robert L.
last_name: Fischer
citation:
ama: Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. DNA
demethylation in the Arabidopsis genome. Proceedings of the National Academy
of Sciences. 2007;104(16):6752-6757. doi:10.1073/pnas.0701861104
apa: Penterman, J., Zilberman, D., Huh, J. H., Ballinger, T., Henikoff, S., &
Fischer, R. L. (2007). DNA demethylation in the Arabidopsis genome. Proceedings
of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.0701861104
chicago: Penterman, Jon, Daniel Zilberman, Jin Hoe Huh, Tracy Ballinger, Steven
Henikoff, and Robert L. Fischer. “DNA Demethylation in the Arabidopsis Genome.”
Proceedings of the National Academy of Sciences. National Academy of Sciences,
2007. https://doi.org/10.1073/pnas.0701861104.
ieee: J. Penterman, D. Zilberman, J. H. Huh, T. Ballinger, S. Henikoff, and R. L.
Fischer, “DNA demethylation in the Arabidopsis genome,” Proceedings of the
National Academy of Sciences, vol. 104, no. 16. National Academy of Sciences,
pp. 6752–6757, 2007.
ista: Penterman J, Zilberman D, Huh JH, Ballinger T, Henikoff S, Fischer RL. 2007.
DNA demethylation in the Arabidopsis genome. Proceedings of the National Academy
of Sciences. 104(16), 6752–6757.
mla: Penterman, Jon, et al. “DNA Demethylation in the Arabidopsis Genome.” Proceedings
of the National Academy of Sciences, vol. 104, no. 16, National Academy of
Sciences, 2007, pp. 6752–57, doi:10.1073/pnas.0701861104.
short: J. Penterman, D. Zilberman, J.H. Huh, T. Ballinger, S. Henikoff, R.L. Fischer,
Proceedings of the National Academy of Sciences 104 (2007) 6752–6757.
date_created: 2021-06-07T09:38:21Z
date_published: 2007-04-17T00:00:00Z
date_updated: 2021-12-14T08:55:12Z
day: '17'
department:
- _id: DaZi
doi: 10.1073/pnas.0701861104
extern: '1'
external_id:
pmid:
- '17409185'
intvolume: ' 104'
issue: '16'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1073/pnas.0701861104
month: '04'
oa: 1
oa_version: Published Version
page: 6752-6757
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 in the Arabidopsis genome
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 104
year: '2007'
...
---
_id: '9504'
article_processing_charge: No
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
citation:
ama: Zilberman D. The Human Promoter Methylome. Vol 39. Nature Publishing
Group; 2007:442-443. doi:10.1038/ng0407-442
apa: Zilberman, D. (2007). The human promoter methylome. Nature Genetics
(Vol. 39, pp. 442–443). Nature Publishing Group. https://doi.org/10.1038/ng0407-442
chicago: Zilberman, Daniel. The Human Promoter Methylome. Nature Genetics.
Vol. 39. Nature Publishing Group, 2007. https://doi.org/10.1038/ng0407-442.
ieee: D. Zilberman, The human promoter methylome, vol. 39, no. 4. Nature
Publishing Group, 2007, pp. 442–443.
ista: Zilberman D. 2007. The human promoter methylome, Nature Publishing Group,p.
mla: Zilberman, Daniel. “The Human Promoter Methylome.” Nature Genetics,
vol. 39, no. 4, Nature Publishing Group, 2007, pp. 442–43, doi:10.1038/ng0407-442.
short: D. Zilberman, The Human Promoter Methylome, Nature Publishing Group, 2007.
date_created: 2021-06-07T12:08:24Z
date_published: 2007-04-01T00:00:00Z
date_updated: 2021-12-14T08:55:46Z
day: '01'
department:
- _id: DaZi
doi: 10.1038/ng0407-442
extern: '1'
external_id:
pmid:
- '17392803'
intvolume: ' 39'
issue: '4'
language:
- iso: eng
month: '04'
oa_version: None
page: 442-443
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
status: public
title: The human promoter methylome
type: other_academic_publication
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 39
year: '2007'
...
---
_id: '9524'
abstract:
- lang: eng
text: Cytosine methylation is the most common covalent modification of DNA in eukaryotes.
DNA methylation has an important role in many aspects of biology, including development
and disease. Methylation can be detected using bisulfite conversion, methylation-sensitive
restriction enzymes, methyl-binding proteins and anti-methylcytosine antibodies.
Combining these techniques with DNA microarrays and high-throughput sequencing
has made the mapping of DNA methylation feasible on a genome-wide scale. Here
we discuss recent developments and future directions for identifying and mapping
methylation, in an effort to help colleagues to identify the approaches that best
serve their research interests.
article_processing_charge: No
article_type: review
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: Zilberman D, Henikoff S. Genome-wide analysis of DNA methylation patterns.
Development. 2007;134(22):3959-3965. doi:10.1242/dev.001131
apa: Zilberman, D., & Henikoff, S. (2007). Genome-wide analysis of DNA methylation
patterns. Development. The Company of Biologists. https://doi.org/10.1242/dev.001131
chicago: Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation
Patterns.” Development. The Company of Biologists, 2007. https://doi.org/10.1242/dev.001131.
ieee: D. Zilberman and S. Henikoff, “Genome-wide analysis of DNA methylation patterns,”
Development, vol. 134, no. 22. The Company of Biologists, pp. 3959–3965,
2007.
ista: Zilberman D, Henikoff S. 2007. Genome-wide analysis of DNA methylation patterns.
Development. 134(22), 3959–3965.
mla: Zilberman, Daniel, and Steven Henikoff. “Genome-Wide Analysis of DNA Methylation
Patterns.” Development, vol. 134, no. 22, The Company of Biologists, 2007,
pp. 3959–65, doi:10.1242/dev.001131.
short: D. Zilberman, S. Henikoff, Development 134 (2007) 3959–3965.
date_created: 2021-06-08T06:29:50Z
date_published: 2007-11-15T00:00:00Z
date_updated: 2021-12-14T08:57:58Z
day: '15'
department:
- _id: DaZi
doi: 10.1242/dev.001131
extern: '1'
external_id:
pmid:
- '17928417'
intvolume: ' 134'
issue: '22'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1242/dev.001131
month: '11'
oa: 1
oa_version: Published Version
page: 3959-3965
pmid: 1
publication: Development
publication_identifier:
eissn:
- 1477-9129
issn:
- 0950-1991
publication_status: published
publisher: The Company of Biologists
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide analysis of DNA methylation patterns
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 134
year: '2007'
...
---
_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'
...
---
_id: '9505'
abstract:
- lang: eng
text: 'Cytosine methylation, a common form of DNA modification that antagonizes
transcription, is found at transposons and repeats in vertebrates, plants and
fungi. Here we have mapped DNA methylation in the entire Arabidopsis thaliana
genome at high resolution. DNA methylation covers transposons and is present within
a large fraction of A. thaliana genes. Methylation within genes is conspicuously
biased away from gene ends, suggesting a dependence on RNA polymerase transit.
Genic methylation is strongly influenced by transcription: moderately transcribed
genes are most likely to be methylated, whereas genes at either extreme are least
likely. In turn, transcription is influenced by methylation: short methylated
genes are poorly expressed, and loss of methylation in the body of a gene leads
to enhanced transcription. Our results indicate that genic transcription and DNA
methylation are closely interwoven processes.'
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Mary
full_name: Gehring, Mary
last_name: Gehring
- first_name: Robert K.
full_name: Tran, Robert K.
last_name: Tran
- first_name: Tracy
full_name: Ballinger, Tracy
last_name: Ballinger
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. Genome-wide analysis
of Arabidopsis thaliana DNA methylation uncovers an interdependence between methylation
and transcription. Nature Genetics. 2006;39(1):61-69. doi:10.1038/ng1929
apa: Zilberman, D., Gehring, M., Tran, R. K., Ballinger, T., & Henikoff, S.
(2006). Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers
an interdependence between methylation and transcription. Nature Genetics.
Nature Publishing Group. https://doi.org/10.1038/ng1929
chicago: Zilberman, Daniel, Mary Gehring, Robert K. Tran, Tracy Ballinger, and Steven
Henikoff. “Genome-Wide Analysis of Arabidopsis Thaliana DNA Methylation Uncovers
an Interdependence between Methylation and Transcription.” Nature Genetics.
Nature Publishing Group, 2006. https://doi.org/10.1038/ng1929.
ieee: D. Zilberman, M. Gehring, R. K. Tran, T. Ballinger, and S. Henikoff, “Genome-wide
analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between
methylation and transcription,” Nature Genetics, vol. 39, no. 1. Nature
Publishing Group, pp. 61–69, 2006.
ista: Zilberman D, Gehring M, Tran RK, Ballinger T, Henikoff S. 2006. Genome-wide
analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence between
methylation and transcription. Nature Genetics. 39(1), 61–69.
mla: Zilberman, Daniel, et al. “Genome-Wide Analysis of Arabidopsis Thaliana DNA
Methylation Uncovers an Interdependence between Methylation and Transcription.”
Nature Genetics, vol. 39, no. 1, Nature Publishing Group, 2006, pp. 61–69,
doi:10.1038/ng1929.
short: D. Zilberman, M. Gehring, R.K. Tran, T. Ballinger, S. Henikoff, Nature Genetics
39 (2006) 61–69.
date_created: 2021-06-07T12:19:31Z
date_published: 2006-11-26T00:00:00Z
date_updated: 2021-12-14T09:02:51Z
day: '26'
department:
- _id: DaZi
doi: 10.1038/ng1929
extern: '1'
external_id:
pmid:
- '17128275'
intvolume: ' 39'
issue: '1'
language:
- iso: eng
month: '11'
oa_version: None
page: 61-69
pmid: 1
publication: Nature Genetics
publication_identifier:
eissn:
- 1546-1718
issn:
- 1061-4036
publication_status: published
publisher: Nature Publishing Group
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genome-wide analysis of Arabidopsis thaliana DNA methylation uncovers an interdependence
between methylation and transcription
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 39
year: '2006'
...
---
_id: '9491'
abstract:
- lang: eng
text: Cytosine DNA methylation in vertebrates is widespread, but methylation in
plants is found almost exclusively at transposable elements and repetitive DNA
[1]. Within regions of methylation, methylcytosines are typically found in CG,
CNG, and asymmetric contexts. CG sites are maintained by a plant homolog of mammalian
Dnmt1 acting on hemi-methylated DNA after replication. Methylation of CNG and
asymmetric sites appears to be maintained at each cell cycle by other mechanisms.
We report a new type of DNA methylation in Arabidopsis, dense CG methylation clusters
found at scattered sites throughout the genome. These clusters lack non-CG methylation
and are preferentially found in genes, although they are relatively deficient
toward the 5′ end. CG methylation clusters are present in lines derived from different
accessions and in mutants that eliminate de novo methylation, indicating that
CG methylation clusters are stably maintained at specific sites. Because 5-methylcytosine
is mutagenic, the appearance of CG methylation clusters over evolutionary time
predicts a genome-wide deficiency of CG dinucleotides and an excess of C(A/T)G
trinucleotides within transcribed regions. This is exactly what we find, implying
that CG methylation clusters have contributed profoundly to plant gene evolution.
We suggest that CG methylation clusters silence cryptic promoters that arise sporadically
within transcription units.
article_processing_charge: No
article_type: original
author:
- first_name: Robert K.
full_name: Tran, Robert K.
last_name: Tran
- first_name: Jorja G.
full_name: Henikoff, Jorja G.
last_name: Henikoff
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Renata F.
full_name: Ditt, Renata F.
last_name: Ditt
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. DNA methylation
profiling identifies CG methylation clusters in Arabidopsis genes. Current
Biology. 2005;15(2):154-159. doi:10.1016/j.cub.2005.01.008
apa: Tran, R. K., Henikoff, J. G., Zilberman, D., Ditt, R. F., Jacobsen, S. E.,
& Henikoff, S. (2005). DNA methylation profiling identifies CG methylation
clusters in Arabidopsis genes. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2005.01.008
chicago: Tran, Robert K., Jorja G. Henikoff, Daniel Zilberman, Renata F. Ditt, Steven
E. Jacobsen, and Steven Henikoff. “DNA Methylation Profiling Identifies CG Methylation
Clusters in Arabidopsis Genes.” Current Biology. Elsevier, 2005. https://doi.org/10.1016/j.cub.2005.01.008.
ieee: R. K. Tran, J. G. Henikoff, D. Zilberman, R. F. Ditt, S. E. Jacobsen, and
S. Henikoff, “DNA methylation profiling identifies CG methylation clusters in
Arabidopsis genes,” Current Biology, vol. 15, no. 2. Elsevier, pp. 154–159,
2005.
ista: Tran RK, Henikoff JG, Zilberman D, Ditt RF, Jacobsen SE, Henikoff S. 2005.
DNA methylation profiling identifies CG methylation clusters in Arabidopsis genes.
Current Biology. 15(2), 154–159.
mla: Tran, Robert K., et al. “DNA Methylation Profiling Identifies CG Methylation
Clusters in Arabidopsis Genes.” Current Biology, vol. 15, no. 2, Elsevier,
2005, pp. 154–59, doi:10.1016/j.cub.2005.01.008.
short: R.K. Tran, J.G. Henikoff, D. Zilberman, R.F. Ditt, S.E. Jacobsen, S. Henikoff,
Current Biology 15 (2005) 154–159.
date_created: 2021-06-07T10:24:30Z
date_published: 2005-01-26T00:00:00Z
date_updated: 2021-12-14T09:12:26Z
day: '26'
department:
- _id: DaZi
doi: 10.1016/j.cub.2005.01.008
extern: '1'
external_id:
pmid:
- '15668172 '
intvolume: ' 15'
issue: '2'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2005.01.008
month: '01'
oa: 1
oa_version: Published Version
page: 154-159
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: DNA methylation profiling identifies CG methylation clusters in Arabidopsis
genes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 15
year: '2005'
...
---
_id: '9514'
abstract:
- lang: eng
text: "Background:\r\nDNA methylation occurs at preferred sites in eukaryotes. In
Arabidopsis, DNA cytosine methylation is maintained by three subfamilies of methyltransferases
with distinct substrate specificities and different modes of action. Targeting
of cytosine methylation at selected loci has been found to sometimes involve histone
H3 methylation and small interfering (si)RNAs. However, the relationship between
different cytosine methylation pathways and their preferred targets is not known.\r\nResults:\r\nWe
used a microarray-based profiling method to explore the involvement of Arabidopsis
CMT3 and DRM DNA methyltransferases, a histone H3 lysine-9 methyltransferase (KYP)
and an Argonaute-related siRNA silencing component (AGO4) in methylating target
loci. We found that KYP targets are also CMT3 targets, suggesting that histone
methylation maintains CNG methylation genome-wide. CMT3 and KYP targets show similar
proximal distributions that correspond to the overall distribution of transposable
elements of all types, whereas DRM targets are distributed more distally along
the chromosome. We find an inverse relationship between element size and loss
of methylation in ago4 and drm mutants.\r\nConclusion:\r\nWe conclude that the
targets of both DNA methylation and histone H3K9 methylation pathways are transposable
elements genome-wide, irrespective of element type and position. Our findings
also suggest that RNA-directed DNA methylation is required to silence isolated
elements that may be too small to be maintained in a silent state by a chromatin-based
mechanism alone. Thus, parallel pathways would be needed to maintain silencing
of transposable elements."
article_number: R90
article_processing_charge: No
article_type: original
author:
- first_name: Robert K.
full_name: Tran, Robert K.
last_name: Tran
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Cecilia
full_name: de Bustos, Cecilia
last_name: de Bustos
- first_name: Renata F.
full_name: Ditt, Renata F.
last_name: Ditt
- first_name: Jorja G.
full_name: Henikoff, Jorja G.
last_name: Henikoff
- first_name: Anders M.
full_name: Lindroth, Anders M.
last_name: Lindroth
- first_name: Jeffrey
full_name: Delrow, Jeffrey
last_name: Delrow
- first_name: Tom
full_name: Boyle, Tom
last_name: Boyle
- first_name: Samson
full_name: Kwong, Samson
last_name: Kwong
- first_name: Terri D.
full_name: Bryson, Terri D.
last_name: Bryson
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: Tran RK, Zilberman D, de Bustos C, et al. Chromatin and siRNA pathways cooperate
to maintain DNA methylation of small transposable elements in Arabidopsis. Genome
Biology. 2005;6(11). doi:10.1186/gb-2005-6-11-r90
apa: Tran, R. K., Zilberman, D., de Bustos, C., Ditt, R. F., Henikoff, J. G., Lindroth,
A. M., … Henikoff, S. (2005). Chromatin and siRNA pathways cooperate to maintain
DNA methylation of small transposable elements in Arabidopsis. Genome Biology.
Springer Nature. https://doi.org/10.1186/gb-2005-6-11-r90
chicago: Tran, Robert K., Daniel Zilberman, Cecilia de Bustos, Renata F. Ditt, Jorja
G. Henikoff, Anders M. Lindroth, Jeffrey Delrow, et al. “Chromatin and SiRNA Pathways
Cooperate to Maintain DNA Methylation of Small Transposable Elements in Arabidopsis.”
Genome Biology. Springer Nature, 2005. https://doi.org/10.1186/gb-2005-6-11-r90.
ieee: R. K. Tran et al., “Chromatin and siRNA pathways cooperate to maintain
DNA methylation of small transposable elements in Arabidopsis,” Genome Biology,
vol. 6, no. 11. Springer Nature, 2005.
ista: Tran RK, Zilberman D, de Bustos C, Ditt RF, Henikoff JG, Lindroth AM, Delrow
J, Boyle T, Kwong S, Bryson TD, Jacobsen SE, Henikoff S. 2005. Chromatin and siRNA
pathways cooperate to maintain DNA methylation of small transposable elements
in Arabidopsis. Genome Biology. 6(11), R90.
mla: Tran, Robert K., et al. “Chromatin and SiRNA Pathways Cooperate to Maintain
DNA Methylation of Small Transposable Elements in Arabidopsis.” Genome Biology,
vol. 6, no. 11, R90, Springer Nature, 2005, doi:10.1186/gb-2005-6-11-r90.
short: R.K. Tran, D. Zilberman, C. de Bustos, R.F. Ditt, J.G. Henikoff, A.M. Lindroth,
J. Delrow, T. Boyle, S. Kwong, T.D. Bryson, S.E. Jacobsen, S. Henikoff, Genome
Biology 6 (2005).
date_created: 2021-06-07T13:12:41Z
date_published: 2005-10-19T00:00:00Z
date_updated: 2021-12-14T09:09:41Z
day: '19'
department:
- _id: DaZi
doi: 10.1186/gb-2005-6-11-r90
extern: '1'
external_id:
pmid:
- '16277745'
intvolume: ' 6'
issue: '11'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/gb-2005-6-11-r90
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
eissn:
- 1465-6906
issn:
- 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Chromatin and siRNA pathways cooperate to maintain DNA methylation of small
transposable elements in Arabidopsis
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2005'
...
---
_id: '9529'
abstract:
- lang: eng
text: Eukaryotic organisms have the remarkable ability to inherit states of gene
activity without altering the underlying DNA sequence. This epigenetic inheritance
can persist over thousands of years, providing an alternative to genetic mutations
as a substrate for natural selection. Epigenetic inheritance might be propagated
by differences in DNA methylation, post-translational histone modifications, and
deposition of histone variants. Mounting evidence also indicates that small interfering
RNA (siRNA)-mediated mechanisms play central roles in setting up and maintaining
states of gene activity. Much of the epigenetic machinery of many organisms, including
Arabidopsis, appears to be directed at silencing viruses and transposable elements,
with epigenetic regulation of endogenous genes being mostly derived from such
processes.
article_processing_charge: No
article_type: review
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: 'Zilberman D, Henikoff S. Epigenetic inheritance in Arabidopsis: Selective
silence. Current Opinion in Genetics and Development. 2005;15(5):557-562.
doi:10.1016/j.gde.2005.07.002'
apa: 'Zilberman, D., & Henikoff, S. (2005). Epigenetic inheritance in Arabidopsis:
Selective silence. Current Opinion in Genetics and Development. Elsevier.
https://doi.org/10.1016/j.gde.2005.07.002'
chicago: 'Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis:
Selective Silence.” Current Opinion in Genetics and Development. Elsevier,
2005. https://doi.org/10.1016/j.gde.2005.07.002.'
ieee: 'D. Zilberman and S. Henikoff, “Epigenetic inheritance in Arabidopsis: Selective
silence,” Current Opinion in Genetics and Development, vol. 15, no. 5.
Elsevier, pp. 557–562, 2005.'
ista: 'Zilberman D, Henikoff S. 2005. Epigenetic inheritance in Arabidopsis: Selective
silence. Current Opinion in Genetics and Development. 15(5), 557–562.'
mla: 'Zilberman, Daniel, and Steven Henikoff. “Epigenetic Inheritance in Arabidopsis:
Selective Silence.” Current Opinion in Genetics and Development, vol. 15,
no. 5, Elsevier, 2005, pp. 557–62, doi:10.1016/j.gde.2005.07.002.'
short: D. Zilberman, S. Henikoff, Current Opinion in Genetics and Development 15
(2005) 557–562.
date_created: 2021-06-08T09:05:56Z
date_published: 2005-10-01T00:00:00Z
date_updated: 2021-12-14T09:13:13Z
department:
- _id: DaZi
doi: 10.1016/j.gde.2005.07.002
extern: '1'
external_id:
pmid:
- '16085410'
intvolume: ' 15'
issue: '5'
language:
- iso: eng
month: '10'
oa_version: None
page: 557-562
pmid: 1
publication: Current Opinion in Genetics and Development
publication_identifier:
issn:
- 0959-437X
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Epigenetic inheritance in Arabidopsis: Selective silence'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 15
year: '2005'
...
---
_id: '9454'
article_processing_charge: No
article_type: original
author:
- first_name: Simon W.-L.
full_name: Chan, Simon W.-L.
last_name: Chan
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: ' Zhixin'
full_name: Xie, Zhixin
last_name: Xie
- first_name: ' Lisa K.'
full_name: Johansen, Lisa K.
last_name: Johansen
- first_name: James C.
full_name: Carrington, James C.
last_name: Carrington
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Chan SW-L, Zilberman D, Xie Zhixin, Johansen Lisa K., Carrington JC, Jacobsen
SE. RNA silencing genes control de novo DNA methylation. Science. 2004;303(5662):1336.
doi:10.1126/science.1095989
apa: Chan, S. W.-L., Zilberman, D., Xie, Zhixin, Johansen, Lisa K., Carrington,
J. C., & Jacobsen, S. E. (2004). RNA silencing genes control de novo DNA methylation.
Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1095989
chicago: Chan, Simon W.-L., Daniel Zilberman, Zhixin Xie, Lisa K. Johansen, James
C. Carrington, and Steven E. Jacobsen. “RNA Silencing Genes Control de Novo DNA
Methylation.” Science. American Association for the Advancement of Science,
2004. https://doi.org/10.1126/science.1095989.
ieee: S. W.-L. Chan, D. Zilberman, Zhixin Xie, Lisa K. Johansen, J. C. Carrington,
and S. E. Jacobsen, “RNA silencing genes control de novo DNA methylation,” Science,
vol. 303, no. 5662. American Association for the Advancement of Science, p. 1336,
2004.
ista: Chan SW-L, Zilberman D, Xie Zhixin, Johansen Lisa K., Carrington JC, Jacobsen
SE. 2004. RNA silencing genes control de novo DNA methylation. Science. 303(5662),
1336.
mla: Chan, Simon W. L., et al. “RNA Silencing Genes Control de Novo DNA Methylation.”
Science, vol. 303, no. 5662, American Association for the Advancement of
Science, 2004, p. 1336, doi:10.1126/science.1095989.
short: S.W.-L. Chan, D. Zilberman, Zhixin Xie, Lisa K. Johansen, J.C. Carrington,
S.E. Jacobsen, Science 303 (2004) 1336.
date_created: 2021-06-04T11:12:35Z
date_published: 2004-02-27T00:00:00Z
date_updated: 2021-12-14T09:13:53Z
day: '27'
department:
- _id: DaZi
doi: 10.1126/science.1095989
extern: '1'
external_id:
pmid:
- '14988555'
intvolume: ' 303'
issue: '5662'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '02'
oa_version: None
page: '1336'
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: RNA silencing genes control de novo DNA methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 303
year: '2004'
...
---
_id: '9493'
abstract:
- lang: eng
text: In a number of organisms, transgenes containing transcribed inverted repeats
(IRs) that produce hairpin RNA can trigger RNA-mediated silencing, which is associated
with 21-24 nucleotide small interfering RNAs (siRNAs). In plants, IR-driven RNA
silencing also causes extensive cytosine methylation of homologous DNA in both
the transgene "trigger" and any other homologous DNA sequences--"targets". Endogenous
genomic sequences, including transposable elements and repeated elements, are
also subject to RNA-mediated silencing. The RNA silencing gene ARGONAUTE4 (AGO4)
is required for maintenance of DNA methylation at several endogenous loci and
for the establishment of methylation at the FWA gene. Here, we show that mutation
of AGO4 substantially reduces the maintenance of DNA methylation triggered by
IR transgenes, but AGO4 loss-of-function does not block the initiation of DNA
methylation by IRs. AGO4 primarily affects non-CG methylation of the target sequences,
while the IR trigger sequences lose methylation in all sequence contexts. Finally,
we find that AGO4 and the DRM methyltransferase genes are required for maintenance
of siRNAs at a subset of endogenous sequences, but AGO4 is not required for the
accumulation of IR-induced siRNAs or a number of endogenous siRNAs, suggesting
that AGO4 may function downstream of siRNA production.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Xiaofeng
full_name: Cao, Xiaofeng
last_name: Cao
- first_name: Lisa K.
full_name: Johansen, Lisa K.
last_name: Johansen
- first_name: Zhixin
full_name: Xie, Zhixin
last_name: Xie
- first_name: James C.
full_name: Carrington, James C.
last_name: Carrington
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. Role of
Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted repeats.
Current Biology. 2004;14(13):1214-1220. doi:10.1016/j.cub.2004.06.055
apa: Zilberman, D., Cao, X., Johansen, L. K., Xie, Z., Carrington, J. C., &
Jacobsen, S. E. (2004). Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation
triggered by inverted repeats. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2004.06.055
chicago: Zilberman, Daniel, Xiaofeng Cao, Lisa K. Johansen, Zhixin Xie, James C.
Carrington, and Steven E. Jacobsen. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed
DNA Methylation Triggered by Inverted Repeats.” Current Biology. Elsevier,
2004. https://doi.org/10.1016/j.cub.2004.06.055.
ieee: D. Zilberman, X. Cao, L. K. Johansen, Z. Xie, J. C. Carrington, and S. E.
Jacobsen, “Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered
by inverted repeats,” Current Biology, vol. 14, no. 13. Elsevier, pp. 1214–1220,
2004.
ista: Zilberman D, Cao X, Johansen LK, Xie Z, Carrington JC, Jacobsen SE. 2004.
Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by inverted
repeats. Current Biology. 14(13), 1214–1220.
mla: Zilberman, Daniel, et al. “Role of Arabidopsis ARGONAUTE4 in RNA-Directed DNA
Methylation Triggered by Inverted Repeats.” Current Biology, vol. 14, no.
13, Elsevier, 2004, pp. 1214–20, doi:10.1016/j.cub.2004.06.055.
short: D. Zilberman, X. Cao, L.K. Johansen, Z. Xie, J.C. Carrington, S.E. Jacobsen,
Current Biology 14 (2004) 1214–1220.
date_created: 2021-06-07T10:33:00Z
date_published: 2004-07-13T00:00:00Z
date_updated: 2021-12-14T08:52:00Z
day: '13'
department:
- _id: DaZi
doi: 10.1016/j.cub.2004.06.055
extern: '1'
external_id:
pmid:
- '15242620 '
intvolume: ' 14'
issue: '13'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2004.06.055
month: '07'
oa: 1
oa_version: Published Version
page: 1214-1220
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Role of Arabidopsis ARGONAUTE4 in RNA-directed DNA methylation triggered by
inverted repeats
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 14
year: '2004'
...
---
_id: '9511'
abstract:
- lang: eng
text: Recent progress in understanding the silencing of transposable elements in
the model plant Arabidopsis has revealed an interplay between DNA methylation,
histone methylation and small interfering RNAs. DNA and histone methylation are
not always sufficient to maintain silencing, and RNA-based reinforcement can be
needed to maintain as well as initiate it.
article_number: '249'
article_processing_charge: No
article_type: review
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
citation:
ama: 'Zilberman D, Henikoff S. Silencing of transposons in plant genomes: kick them
when they’re down. Genome Biology. 2004;5(12). doi:10.1186/gb-2004-5-12-249'
apa: 'Zilberman, D., & Henikoff, S. (2004). Silencing of transposons in plant
genomes: kick them when they’re down. Genome Biology. Springer Nature.
https://doi.org/10.1186/gb-2004-5-12-249'
chicago: 'Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant
Genomes: Kick Them When They’re Down.” Genome Biology. Springer Nature,
2004. https://doi.org/10.1186/gb-2004-5-12-249.'
ieee: 'D. Zilberman and S. Henikoff, “Silencing of transposons in plant genomes:
kick them when they’re down,” Genome Biology, vol. 5, no. 12. Springer
Nature, 2004.'
ista: 'Zilberman D, Henikoff S. 2004. Silencing of transposons in plant genomes:
kick them when they’re down. Genome Biology. 5(12), 249.'
mla: 'Zilberman, Daniel, and Steven Henikoff. “Silencing of Transposons in Plant
Genomes: Kick Them When They’re Down.” Genome Biology, vol. 5, no. 12,
249, Springer Nature, 2004, doi:10.1186/gb-2004-5-12-249.'
short: D. Zilberman, S. Henikoff, Genome Biology 5 (2004).
date_created: 2021-06-07T12:58:06Z
date_published: 2004-11-16T00:00:00Z
date_updated: 2021-12-14T08:44:24Z
day: '16'
department:
- _id: DaZi
doi: 10.1186/gb-2004-5-12-249
extern: '1'
external_id:
pmid:
- '15575975'
intvolume: ' 5'
issue: '12'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1186/gb-2004-5-12-249
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: Genome Biology
publication_identifier:
eissn:
- 1465-6906
issn:
- 1474-760X
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Silencing of transposons in plant genomes: kick them when they''re down'
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 5
year: '2004'
...
---
_id: '9517'
abstract:
- lang: eng
text: Multicellular eukaryotes produce small RNA molecules (approximately 21–24
nucleotides) of two general types, microRNA (miRNA) and short interfering RNA
(siRNA). They collectively function as sequence-specific guides to silence or
regulate genes, transposons, and viruses and to modify chromatin and genome structure.
Formation or activity of small RNAs requires factors belonging to gene families
that encode DICER (or DICER-LIKE [DCL]) and ARGONAUTE proteins and, in the case
of some siRNAs, RNA-dependent RNA polymerase (RDR) proteins. Unlike many animals,
plants encode multiple DCL and RDR proteins. Using a series of insertion mutants
of Arabidopsis thaliana, unique functions for three DCL proteins in miRNA (DCL1),
endogenous siRNA (DCL3), and viral siRNA (DCL2) biogenesis were identified. One
RDR protein (RDR2) was required for all endogenous siRNAs analyzed. The loss of
endogenous siRNA in dcl3 and rdr2 mutants was associated with loss of heterochromatic
marks and increased transcript accumulation at some loci. Defects in siRNA-generation
activity in response to turnip crinkle virus in dcl2 mutant plants correlated
with increased virus susceptibility. We conclude that proliferation and diversification
of DCL and RDR genes during evolution of plants contributed to specialization
of small RNA-directed pathways for development, chromatin structure, and defense.
article_processing_charge: No
article_type: original
author:
- first_name: Zhixin
full_name: Xie, Zhixin
last_name: Xie
- first_name: Lisa K.
full_name: Johansen, Lisa K.
last_name: Johansen
- first_name: Adam M.
full_name: Gustafson, Adam M.
last_name: Gustafson
- first_name: Kristin D.
full_name: Kasschau, Kristin D.
last_name: Kasschau
- first_name: 'Andrew D. '
full_name: 'Lellis, Andrew D. '
last_name: Lellis
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
- first_name: James C.
full_name: Carrington, James C.
last_name: Carrington
citation:
ama: Xie Z, Johansen LK, Gustafson AM, et al. Genetic and functional diversification
of small RNA pathways in plants. PLoS Biology. 2004;2(5):0642-0652. doi:10.1371/journal.pbio.0020104
apa: Xie, Z., Johansen, L. K., Gustafson, A. M., Kasschau, K. D., Lellis, A. D.,
Zilberman, D., … Carrington, J. C. (2004). Genetic and functional diversification
of small RNA pathways in plants. PLoS Biology. Public Library of Science.
https://doi.org/10.1371/journal.pbio.0020104
chicago: Xie, Zhixin, Lisa K. Johansen, Adam M. Gustafson, Kristin D. Kasschau,
Andrew D. Lellis, Daniel Zilberman, Steven E. Jacobsen, and James C. Carrington.
“Genetic and Functional Diversification of Small RNA Pathways in Plants.” PLoS
Biology. Public Library of Science, 2004. https://doi.org/10.1371/journal.pbio.0020104.
ieee: Z. Xie et al., “Genetic and functional diversification of small RNA
pathways in plants,” PLoS Biology, vol. 2, no. 5. Public Library of Science,
pp. 0642–0652, 2004.
ista: Xie Z, Johansen LK, Gustafson AM, Kasschau KD, Lellis AD, Zilberman D, Jacobsen
SE, Carrington JC. 2004. Genetic and functional diversification of small RNA pathways
in plants. PLoS Biology. 2(5), 0642–0652.
mla: Xie, Zhixin, et al. “Genetic and Functional Diversification of Small RNA Pathways
in Plants.” PLoS Biology, vol. 2, no. 5, Public Library of Science, 2004,
pp. 0642–52, doi:10.1371/journal.pbio.0020104.
short: Z. Xie, L.K. Johansen, A.M. Gustafson, K.D. Kasschau, A.D. Lellis, D. Zilberman,
S.E. Jacobsen, J.C. Carrington, PLoS Biology 2 (2004) 0642–0652.
date_created: 2021-06-07T14:12:08Z
date_published: 2004-02-24T00:00:00Z
date_updated: 2021-12-14T08:43:57Z
day: '24'
department:
- _id: DaZi
doi: 10.1371/journal.pbio.0020104
extern: '1'
external_id:
pmid:
- '15024409'
intvolume: ' 2'
issue: '5'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1371/journal.pbio.0020104
month: '02'
oa: 1
oa_version: Published Version
page: 0642-0652
pmid: 1
publication: PLoS Biology
publication_identifier:
eissn:
- 1545-7885
issn:
- 1544-9173
publication_status: published
publisher: Public Library of Science
quality_controlled: '1'
scopus_import: '1'
status: public
title: Genetic and functional diversification of small RNA pathways in plants
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 2
year: '2004'
...
---
_id: '12203'
abstract:
- lang: eng
text: 'Geranylgeranyl diphosphate synthase (GGPPS, EC: 2.5.1.29) catalyzes the biosynthesis
of geranylgeranyl diphosphate (GGPP), which is a key precursor for ginkgolide
biosynthesis. Here we reported for the first time the cloning of a new full-length
cDNA encoding GGPPS from the living fossil plant Ginkgo biloba. The full-length
cDNA encoding G. biloba GGPPS (designated as GbGGPPS) was 1657bp long and contained
a 1176bp open reading frame encoding a 391 amino acid protein. Comparative analysis
showed that GbGGPPS possessed a 79 amino acid transit peptide at its N-terminal,
which directed GbGGPPS to target to the plastids. Bioinformatic analysis revealed
that GbGGPPS was a member of polyprenyltransferases with two highly conserved
aspartate-rich motifs like other plant GGPPSs. Phylogenetic tree analysis indicated
that plant GGPPSs could be classified into two groups, angiosperm and gymnosperm
GGPPSs, while GbGGPPS had closer relationship with gymnosperm plant GGPPSs.'
acknowledgement: This study was financially supported by China National High-Tech
“863” Program. The authors are very thankful to Dr Li Wang (School of Life Sciences,
Fudan University, Shanghai, China) for her kind help with constructing the phylogenetic
tree.
article_processing_charge: No
article_type: original
author:
- first_name: Zhihua
full_name: Liao, Zhihua
last_name: Liao
- first_name: Min
full_name: Chen, Min
last_name: Chen
- first_name: Yifu
full_name: Gong, Yifu
last_name: Gong
- first_name: Liang
full_name: Guo, Liang
last_name: Guo
- first_name: Qiumin
full_name: Tan, Qiumin
last_name: Tan
- first_name: Xiaoqi
full_name: Feng, Xiaoqi
id: e0164712-22ee-11ed-b12a-d80fcdf35958
last_name: Feng
orcid: 0000-0002-4008-1234
- first_name: Xiaofen
full_name: Sun, Xiaofen
last_name: Sun
- first_name: Feng
full_name: Tan, Feng
last_name: Tan
- first_name: Kexuan
full_name: Tang, Kexuan
last_name: Tang
citation:
ama: Liao Z, Chen M, Gong Y, et al. A new geranylgeranyl Diphosphate synthase gene
from Ginkgo biloba, which intermediates the biosynthesis of the key precursor
for ginkgolides. DNA Sequence. 2004;15(2):153-158. doi:10.1080/10425170410001667348
apa: Liao, Z., Chen, M., Gong, Y., Guo, L., Tan, Q., Feng, X., … Tang, K. (2004).
A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates
the biosynthesis of the key precursor for ginkgolides. DNA Sequence. Informa
UK Limited. https://doi.org/10.1080/10425170410001667348
chicago: Liao, Zhihua, Min Chen, Yifu Gong, Liang Guo, Qiumin Tan, Xiaoqi Feng,
Xiaofen Sun, Feng Tan, and Kexuan Tang. “A New Geranylgeranyl Diphosphate Synthase
Gene from Ginkgo Biloba, Which Intermediates the Biosynthesis of the Key Precursor
for Ginkgolides.” DNA Sequence. Informa UK Limited, 2004. https://doi.org/10.1080/10425170410001667348.
ieee: Z. Liao et al., “A new geranylgeranyl Diphosphate synthase gene from
Ginkgo biloba, which intermediates the biosynthesis of the key precursor for ginkgolides,”
DNA Sequence, vol. 15, no. 2. Informa UK Limited, pp. 153–158, 2004.
ista: Liao Z, Chen M, Gong Y, Guo L, Tan Q, Feng X, Sun X, Tan F, Tang K. 2004.
A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates
the biosynthesis of the key precursor for ginkgolides. DNA Sequence. 15(2), 153–158.
mla: Liao, Zhihua, et al. “A New Geranylgeranyl Diphosphate Synthase Gene from Ginkgo
Biloba, Which Intermediates the Biosynthesis of the Key Precursor for Ginkgolides.”
DNA Sequence, vol. 15, no. 2, Informa UK Limited, 2004, pp. 153–58, doi:10.1080/10425170410001667348.
short: Z. Liao, M. Chen, Y. Gong, L. Guo, Q. Tan, X. Feng, X. Sun, F. Tan, K. Tang,
DNA Sequence 15 (2004) 153–158.
date_created: 2023-01-16T09:24:50Z
date_published: 2004-01-01T00:00:00Z
date_updated: 2023-05-08T10:58:29Z
department:
- _id: XiFe
doi: 10.1080/10425170410001667348
extern: '1'
external_id:
pmid:
- '15352294'
intvolume: ' 15'
issue: '2'
keyword:
- Endocrinology
- Genetics
- Molecular Biology
- Biochemistry
language:
- iso: eng
oa_version: None
page: 153-158
pmid: 1
publication: DNA Sequence
publication_identifier:
issn:
- 1042-5179
publication_status: published
publisher: Informa UK Limited
quality_controlled: '1'
scopus_import: '1'
status: public
title: A new geranylgeranyl Diphosphate synthase gene from Ginkgo biloba, which intermediates
the biosynthesis of the key precursor for ginkgolides
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 15
year: '2004'
...
---
_id: '9455'
abstract:
- lang: eng
text: Proteins of the ARGONAUTE family are important in diverse posttranscriptional
RNA-mediated gene-silencing systems as well as in transcriptional gene silencing
in Drosophila and fission yeast and in programmed DNA elimination in Tetrahymena.
We cloned ARGONAUTE4 (AGO4) from a screen for mutants that suppress silencing
of the Arabidopsis SUPERMAN(SUP) gene. The ago4-1 mutant reactivated silentSUP
alleles and decreased CpNpG and asymmetric DNA methylation as well as histone
H3 lysine-9 methylation. In addition,ago4-1 blocked histone and DNA methylation
and the accumulation of 25-nucleotide small interfering RNAs (siRNAs) that correspond
to the retroelement AtSN1. These results suggest that AGO4 and long siRNAs direct
chromatin modifications, including histone methylation and non-CpG DNA methylation.
article_processing_charge: No
article_type: original
author:
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: ' Xiaofeng'
full_name: Cao, Xiaofeng
last_name: Cao
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Zilberman D, Cao Xiaofeng, Jacobsen SE. ARGONAUTE4 control of locus-specific
siRNA accumulation and DNA and histone methylation. Science. 2003;299(5607):716-719.
doi:10.1126/science.1079695
apa: Zilberman, D., Cao, Xiaofeng, & Jacobsen, S. E. (2003). ARGONAUTE4 control
of locus-specific siRNA accumulation and DNA and histone methylation. Science.
American Association for the Advancement of Science. https://doi.org/10.1126/science.1079695
chicago: Zilberman, Daniel, Xiaofeng Cao, and Steven E. Jacobsen. “ARGONAUTE4 Control
of Locus-Specific SiRNA Accumulation and DNA and Histone Methylation.” Science.
American Association for the Advancement of Science, 2003. https://doi.org/10.1126/science.1079695.
ieee: D. Zilberman, Xiaofeng Cao, and S. E. Jacobsen, “ARGONAUTE4 control of locus-specific
siRNA accumulation and DNA and histone methylation,” Science, vol. 299,
no. 5607. American Association for the Advancement of Science, pp. 716–719, 2003.
ista: Zilberman D, Cao Xiaofeng, Jacobsen SE. 2003. ARGONAUTE4 control of locus-specific
siRNA accumulation and DNA and histone methylation. Science. 299(5607), 716–719.
mla: Zilberman, Daniel, et al. “ARGONAUTE4 Control of Locus-Specific SiRNA Accumulation
and DNA and Histone Methylation.” Science, vol. 299, no. 5607, American
Association for the Advancement of Science, 2003, pp. 716–19, doi:10.1126/science.1079695.
short: D. Zilberman, Xiaofeng Cao, S.E. Jacobsen, Science 299 (2003) 716–719.
date_created: 2021-06-04T11:26:26Z
date_published: 2003-01-31T00:00:00Z
date_updated: 2021-12-14T08:43:30Z
day: '31'
department:
- _id: DaZi
doi: 10.1126/science.1079695
extern: '1'
external_id:
pmid:
- '12522258'
intvolume: ' 299'
issue: '5607'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '01'
oa_version: None
page: 716-719
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: ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone
methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 299
year: '2003'
...
---
_id: '9495'
abstract:
- lang: eng
text: RNA interference is a conserved process in which double-stranded RNA is processed
into 21–25 nucleotide siRNAs that trigger posttranscriptional gene silencing.
In addition, plants display a phenomenon termed RNA-directed DNA methylation (RdDM)
in which DNA with sequence identity to silenced RNA is de novo methylated at its
cytosine residues. This methylation is not only at canonical CpG sites but also
at cytosines in CpNpG and asymmetric sequence contexts. In this report, we study
the role of the DRM and CMT3 DNA methyltransferase genes in the initiation and
maintenance of RdDM. Neither drm nor cmt3 mutants affected the maintenance of
preestablished RNA-directed CpG methylation. However, drm mutants showed a nearly
complete loss of asymmetric methylation and a partial loss of CpNpG methylation.
The remaining asymmetric and CpNpG methylation was dependent on the activity of
CMT3, showing that DRM and CMT3 act redundantly to maintain non-CpG methylation.
These DNA methyltransferases appear to act downstream of siRNAs, since drm1 drm2
cmt3 triple mutants show a lack of non-CpG methylation but elevated levels of
siRNAs. Finally, we demonstrate that DRM activity is required for the initial
establishment of RdDM in all sequence contexts including CpG, CpNpG, and asymmetric
sites.
article_processing_charge: No
article_type: original
author:
- first_name: Xiaofeng
full_name: Cao, Xiaofeng
last_name: Cao
- first_name: Werner
full_name: Aufsatz, Werner
last_name: Aufsatz
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: M.Florian
full_name: Mette, M.Florian
last_name: Mette
- first_name: Michael S.
full_name: Huang, Michael S.
last_name: Huang
- first_name: Marjori
full_name: Matzke, Marjori
last_name: Matzke
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Cao X, Aufsatz W, Zilberman D, et al. Role of the DRM and CMT3 methyltransferases
in RNA-directed DNA methylation. Current Biology. 2003;13(24):2212-2217.
doi:10.1016/j.cub.2003.11.052
apa: Cao, X., Aufsatz, W., Zilberman, D., Mette, M. F., Huang, M. S., Matzke, M.,
& Jacobsen, S. E. (2003). Role of the DRM and CMT3 methyltransferases in RNA-directed
DNA methylation. Current Biology. Elsevier. https://doi.org/10.1016/j.cub.2003.11.052
chicago: Cao, Xiaofeng, Werner Aufsatz, Daniel Zilberman, M.Florian Mette, Michael
S. Huang, Marjori Matzke, and Steven E. Jacobsen. “Role of the DRM and CMT3 Methyltransferases
in RNA-Directed DNA Methylation.” Current Biology. Elsevier, 2003. https://doi.org/10.1016/j.cub.2003.11.052.
ieee: X. Cao et al., “Role of the DRM and CMT3 methyltransferases in RNA-directed
DNA methylation,” Current Biology, vol. 13, no. 24. Elsevier, pp. 2212–2217,
2003.
ista: Cao X, Aufsatz W, Zilberman D, Mette MF, Huang MS, Matzke M, Jacobsen SE.
2003. Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation.
Current Biology. 13(24), 2212–2217.
mla: Cao, Xiaofeng, et al. “Role of the DRM and CMT3 Methyltransferases in RNA-Directed
DNA Methylation.” Current Biology, vol. 13, no. 24, Elsevier, 2003, pp.
2212–17, doi:10.1016/j.cub.2003.11.052.
short: X. Cao, W. Aufsatz, D. Zilberman, M.F. Mette, M.S. Huang, M. Matzke, S.E.
Jacobsen, Current Biology 13 (2003) 2212–2217.
date_created: 2021-06-07T10:43:02Z
date_published: 2003-12-16T00:00:00Z
date_updated: 2021-12-14T08:41:38Z
day: '16'
department:
- _id: DaZi
doi: 10.1016/j.cub.2003.11.052
extern: '1'
external_id:
pmid:
- '14680640'
intvolume: ' 13'
issue: '24'
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.cub.2003.11.052
month: '12'
oa: 1
oa_version: Published Version
page: 2212-2217
pmid: 1
publication: Current Biology
publication_identifier:
eissn:
- 1879-0445
issn:
- 0960-9822
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Role of the DRM and CMT3 methyltransferases in RNA-directed DNA methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 13
year: '2003'
...
---
_id: '9444'
abstract:
- lang: eng
text: Epigenetic silenced alleles of the Arabidopsis SUPERMANlocus (the clark kent
alleles) are associated with dense hypermethylation at noncanonical cytosines
(CpXpG and asymmetric sites, where X = A, T, C, or G). A genetic screen for suppressors
of a hypermethylated clark kent mutant identified nine loss-of-function alleles
of CHROMOMETHYLASE3(CMT3), a novel cytosine methyltransferase homolog. These cmt3
mutants display a wild-type morphology but exhibit decreased CpXpG methylation
of the SUP gene and of other sequences throughout the genome. They also show reactivated
expression of endogenous retrotransposon sequences. These results show that a
non-CpG DNA methyltransferase is responsible for maintaining epigenetic gene silencing.
article_processing_charge: No
article_type: original
author:
- first_name: A. M.
full_name: Lindroth, A. M.
last_name: Lindroth
- first_name: Xiaofeng
full_name: Cao, Xiaofeng
last_name: Cao
- first_name: James P.
full_name: Jackson, James P.
last_name: Jackson
- first_name: Daniel
full_name: Zilberman, Daniel
id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
last_name: Zilberman
orcid: 0000-0002-0123-8649
- first_name: Claire M.
full_name: McCallum, Claire M.
last_name: McCallum
- first_name: Steven
full_name: Henikoff, Steven
last_name: Henikoff
- first_name: Steven E.
full_name: Jacobsen, Steven E.
last_name: Jacobsen
citation:
ama: Lindroth AM, Cao X, Jackson JP, et al. Requirement of CHROMOMETHYLASE3 for
maintenance of CpXpG methylation. Science. 2001;292(5524):2077-2080. doi:10.1126/science.1059745
apa: Lindroth, A. M., Cao, X., Jackson, J. P., Zilberman, D., McCallum, C. M., Henikoff,
S., & Jacobsen, S. E. (2001). Requirement of CHROMOMETHYLASE3 for maintenance
of CpXpG methylation. Science. American Association for the Advancement
of Science. https://doi.org/10.1126/science.1059745
chicago: Lindroth, A. M., Xiaofeng Cao, James P. Jackson, Daniel Zilberman, Claire
M. McCallum, Steven Henikoff, and Steven E. Jacobsen. “Requirement of CHROMOMETHYLASE3
for Maintenance of CpXpG Methylation.” Science. American Association for
the Advancement of Science, 2001. https://doi.org/10.1126/science.1059745.
ieee: A. M. Lindroth et al., “Requirement of CHROMOMETHYLASE3 for maintenance
of CpXpG methylation,” Science, vol. 292, no. 5524. American Association
for the Advancement of Science, pp. 2077–2080, 2001.
ista: Lindroth AM, Cao X, Jackson JP, Zilberman D, McCallum CM, Henikoff S, Jacobsen
SE. 2001. Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation.
Science. 292(5524), 2077–2080.
mla: Lindroth, A. M., et al. “Requirement of CHROMOMETHYLASE3 for Maintenance of
CpXpG Methylation.” Science, vol. 292, no. 5524, American Association for
the Advancement of Science, 2001, pp. 2077–80, doi:10.1126/science.1059745.
short: A.M. Lindroth, X. Cao, J.P. Jackson, D. Zilberman, C.M. McCallum, S. Henikoff,
S.E. Jacobsen, Science 292 (2001) 2077–2080.
date_created: 2021-06-02T13:35:16Z
date_published: 2001-06-15T00:00:00Z
date_updated: 2021-12-14T08:40:32Z
day: '15'
department:
- _id: DaZi
doi: 10.1126/science.1059745
extern: '1'
external_id:
pmid:
- '11349138'
intvolume: ' 292'
issue: '5524'
keyword:
- Multidisciplinary
language:
- iso: eng
month: '06'
oa_version: None
page: 2077-2080
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: Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 292
year: '2001'
...