---
_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: '11059'
abstract:
- lang: eng
text: The genome is packaged and organized nonrandomly within the 3D space of the
nucleus to promote efficient gene expression and to faithfully maintain silencing
of heterochromatin. The genome is enclosed within the nucleus by the nuclear envelope
membrane, which contains a set of proteins that actively participate in chromatin
organization and gene regulation. Technological advances are providing views of
genome organization at unprecedented resolution and are beginning to reveal the
ways that cells co-opt the structures of the nuclear periphery for nuclear organization
and gene regulation. These genome regulatory roles of proteins of the nuclear
periphery have important influences on development, disease and ageing.
article_processing_charge: No
article_type: review
author:
- first_name: Abigail
full_name: Buchwalter, Abigail
last_name: Buchwalter
- first_name: Jeanae M.
full_name: Kaneshiro, Jeanae M.
last_name: Kaneshiro
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: 'Buchwalter A, Kaneshiro JM, Hetzer M. Coaching from the sidelines: The nuclear
periphery in genome regulation. Nature Reviews Genetics. 2019;20(1):39-50.
doi:10.1038/s41576-018-0063-5'
apa: 'Buchwalter, A., Kaneshiro, J. M., & Hetzer, M. (2019). Coaching from the
sidelines: The nuclear periphery in genome regulation. Nature Reviews Genetics.
Springer Nature. https://doi.org/10.1038/s41576-018-0063-5'
chicago: 'Buchwalter, Abigail, Jeanae M. Kaneshiro, and Martin Hetzer. “Coaching
from the Sidelines: The Nuclear Periphery in Genome Regulation.” Nature Reviews
Genetics. Springer Nature, 2019. https://doi.org/10.1038/s41576-018-0063-5.'
ieee: 'A. Buchwalter, J. M. Kaneshiro, and M. Hetzer, “Coaching from the sidelines:
The nuclear periphery in genome regulation,” Nature Reviews Genetics, vol.
20, no. 1. Springer Nature, pp. 39–50, 2019.'
ista: 'Buchwalter A, Kaneshiro JM, Hetzer M. 2019. Coaching from the sidelines:
The nuclear periphery in genome regulation. Nature Reviews Genetics. 20(1), 39–50.'
mla: 'Buchwalter, Abigail, et al. “Coaching from the Sidelines: The Nuclear Periphery
in Genome Regulation.” Nature Reviews Genetics, vol. 20, no. 1, Springer
Nature, 2019, pp. 39–50, doi:10.1038/s41576-018-0063-5.'
short: A. Buchwalter, J.M. Kaneshiro, M. Hetzer, Nature Reviews Genetics 20 (2019)
39–50.
date_created: 2022-04-07T07:44:45Z
date_published: 2019-01-01T00:00:00Z
date_updated: 2022-07-18T08:31:42Z
day: '01'
doi: 10.1038/s41576-018-0063-5
extern: '1'
external_id:
pmid:
- '30356165'
intvolume: ' 20'
issue: '1'
keyword:
- Genetics (clinical)
- Genetics
- Molecular Biology
language:
- iso: eng
month: '01'
oa_version: None
page: 39-50
pmid: 1
publication: Nature Reviews Genetics
publication_identifier:
eissn:
- 1471-0064
issn:
- 1471-0056
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: 'Coaching from the sidelines: The nuclear periphery in genome regulation'
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 20
year: '2019'
...
---
_id: '11060'
abstract:
- lang: eng
text: The inner nuclear membrane (INM) is a subdomain of the endoplasmic reticulum
(ER) that is gated by the nuclear pore complex. It is unknown whether proteins
of the INM and ER are degraded through shared or distinct pathways in mammalian
cells. We applied dynamic proteomics to profile protein half-lives and report
that INM and ER residents turn over at similar rates, indicating that the INM’s
unique topology is not a barrier to turnover. Using a microscopy approach, we
observed that the proteasome can degrade INM proteins in situ. However, we also
uncovered evidence for selective, vesicular transport-mediated turnover of a single
INM protein, emerin, that is potentiated by ER stress. Emerin is rapidly cleared
from the INM by a mechanism that requires emerin’s LEM domain to mediate vesicular
trafficking to lysosomes. This work demonstrates that the INM can be dynamically
remodeled in response to environmental inputs.
article_number: e49796
article_processing_charge: No
article_type: original
author:
- first_name: Abigail
full_name: Buchwalter, Abigail
last_name: Buchwalter
- first_name: Roberta
full_name: Schulte, Roberta
last_name: Schulte
- first_name: Hsiao
full_name: Tsai, Hsiao
last_name: Tsai
- first_name: Juliana
full_name: Capitanio, Juliana
last_name: Capitanio
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. Selective clearance
of the inner nuclear membrane protein emerin by vesicular transport during ER
stress. eLife. 2019;8. doi:10.7554/elife.49796
apa: Buchwalter, A., Schulte, R., Tsai, H., Capitanio, J., & Hetzer, M. (2019).
Selective clearance of the inner nuclear membrane protein emerin by vesicular
transport during ER stress. ELife. eLife Sciences Publications. https://doi.org/10.7554/elife.49796
chicago: Buchwalter, Abigail, Roberta Schulte, Hsiao Tsai, Juliana Capitanio, and
Martin Hetzer. “Selective Clearance of the Inner Nuclear Membrane Protein Emerin
by Vesicular Transport during ER Stress.” ELife. eLife Sciences Publications,
2019. https://doi.org/10.7554/elife.49796.
ieee: A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, and M. Hetzer, “Selective
clearance of the inner nuclear membrane protein emerin by vesicular transport
during ER stress,” eLife, vol. 8. eLife Sciences Publications, 2019.
ista: Buchwalter A, Schulte R, Tsai H, Capitanio J, Hetzer M. 2019. Selective clearance
of the inner nuclear membrane protein emerin by vesicular transport during ER
stress. eLife. 8, e49796.
mla: Buchwalter, Abigail, et al. “Selective Clearance of the Inner Nuclear Membrane
Protein Emerin by Vesicular Transport during ER Stress.” ELife, vol. 8,
e49796, eLife Sciences Publications, 2019, doi:10.7554/elife.49796.
short: A. Buchwalter, R. Schulte, H. Tsai, J. Capitanio, M. Hetzer, ELife 8 (2019).
date_created: 2022-04-07T07:45:02Z
date_published: 2019-10-10T00:00:00Z
date_updated: 2023-05-31T06:36:22Z
day: '10'
ddc:
- '570'
doi: 10.7554/elife.49796
extern: '1'
external_id:
pmid:
- '31599721'
file:
- access_level: open_access
checksum: 1e8672a1e9c3dc0a2d3d0dad89673616
content_type: application/pdf
creator: dernst
date_created: 2022-04-08T08:18:01Z
date_updated: 2022-04-08T08:18:01Z
file_id: '11138'
file_name: 2019_eLife_Buchwalter.pdf
file_size: 6984654
relation: main_file
success: 1
file_date_updated: 2022-04-08T08:18:01Z
has_accepted_license: '1'
intvolume: ' 8'
keyword:
- General Immunology and Microbiology
- General Biochemistry
- Genetics and Molecular Biology
- General Medicine
- General Neuroscience
language:
- iso: eng
month: '10'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
related_material:
record:
- id: '13079'
relation: research_data
status: public
scopus_import: '1'
status: public
title: Selective clearance of the inner nuclear membrane protein emerin by vesicular
transport during ER stress
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: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 8
year: '2019'
...
---
_id: '8405'
abstract:
- lang: eng
text: Atomic-resolution structure determination is crucial for understanding protein
function. Cryo-EM and NMR spectroscopy both provide structural information, but
currently cryo-EM does not routinely give access to atomic-level structural data,
and, generally, NMR structure determination is restricted to small (<30 kDa) proteins.
We introduce an integrated structure determination approach that simultaneously
uses NMR and EM data to overcome the limits of each of these methods. The approach
enables structure determination of the 468 kDa large dodecameric aminopeptidase
TET2 to a precision and accuracy below 1 Å by combining secondary-structure information
obtained from near-complete magic-angle-spinning NMR assignments of the 39 kDa-large
subunits, distance restraints from backbone amides and ILV methyl groups, and
a 4.1 Å resolution EM map. The resulting structure exceeds current standards of
NMR and EM structure determination in terms of molecular weight and precision.
Importantly, the approach is successful even in cases where only medium-resolution
cryo-EM data are available.
article_number: '2697'
article_processing_charge: No
article_type: original
author:
- first_name: Diego F.
full_name: Gauto, Diego F.
last_name: Gauto
- first_name: Leandro F.
full_name: Estrozi, Leandro F.
last_name: Estrozi
- first_name: Charles D.
full_name: Schwieters, Charles D.
last_name: Schwieters
- first_name: Gregory
full_name: Effantin, Gregory
last_name: Effantin
- first_name: Pavel
full_name: Macek, Pavel
last_name: Macek
- first_name: Remy
full_name: Sounier, Remy
last_name: Sounier
- first_name: Astrid C.
full_name: Sivertsen, Astrid C.
last_name: Sivertsen
- first_name: Elena
full_name: Schmidt, Elena
last_name: Schmidt
- first_name: Rime
full_name: Kerfah, Rime
last_name: Kerfah
- first_name: Guillaume
full_name: Mas, Guillaume
last_name: Mas
- first_name: Jacques-Philippe
full_name: Colletier, Jacques-Philippe
last_name: Colletier
- first_name: Peter
full_name: Güntert, Peter
last_name: Güntert
- first_name: Adrien
full_name: Favier, Adrien
last_name: Favier
- first_name: Guy
full_name: Schoehn, Guy
last_name: Schoehn
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
- first_name: Jerome
full_name: Boisbouvier, Jerome
last_name: Boisbouvier
citation:
ama: Gauto DF, Estrozi LF, Schwieters CD, et al. Integrated NMR and cryo-EM atomic-resolution
structure determination of a half-megadalton enzyme complex. Nature Communications.
2019;10. doi:10.1038/s41467-019-10490-9
apa: Gauto, D. F., Estrozi, L. F., Schwieters, C. D., Effantin, G., Macek, P., Sounier,
R., … Boisbouvier, J. (2019). Integrated NMR and cryo-EM atomic-resolution structure
determination of a half-megadalton enzyme complex. Nature Communications.
Springer Nature. https://doi.org/10.1038/s41467-019-10490-9
chicago: Gauto, Diego F., Leandro F. Estrozi, Charles D. Schwieters, Gregory Effantin,
Pavel Macek, Remy Sounier, Astrid C. Sivertsen, et al. “Integrated NMR and Cryo-EM
Atomic-Resolution Structure Determination of a Half-Megadalton Enzyme Complex.”
Nature Communications. Springer Nature, 2019. https://doi.org/10.1038/s41467-019-10490-9.
ieee: D. F. Gauto et al., “Integrated NMR and cryo-EM atomic-resolution structure
determination of a half-megadalton enzyme complex,” Nature Communications,
vol. 10. Springer Nature, 2019.
ista: Gauto DF, Estrozi LF, Schwieters CD, Effantin G, Macek P, Sounier R, Sivertsen
AC, Schmidt E, Kerfah R, Mas G, Colletier J-P, Güntert P, Favier A, Schoehn G,
Schanda P, Boisbouvier J. 2019. Integrated NMR and cryo-EM atomic-resolution structure
determination of a half-megadalton enzyme complex. Nature Communications. 10,
2697.
mla: Gauto, Diego F., et al. “Integrated NMR and Cryo-EM Atomic-Resolution Structure
Determination of a Half-Megadalton Enzyme Complex.” Nature Communications,
vol. 10, 2697, Springer Nature, 2019, doi:10.1038/s41467-019-10490-9.
short: D.F. Gauto, L.F. Estrozi, C.D. Schwieters, G. Effantin, P. Macek, R. Sounier,
A.C. Sivertsen, E. Schmidt, R. Kerfah, G. Mas, J.-P. Colletier, P. Güntert, A.
Favier, G. Schoehn, P. Schanda, J. Boisbouvier, Nature Communications 10 (2019).
date_created: 2020-09-17T10:28:25Z
date_published: 2019-06-19T00:00:00Z
date_updated: 2021-01-12T08:19:03Z
day: '19'
doi: 10.1038/s41467-019-10490-9
extern: '1'
external_id:
pmid:
- '31217444'
intvolume: ' 10'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-019-10490-9
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
status: public
title: Integrated NMR and cryo-EM atomic-resolution structure determination of a half-megadalton
enzyme complex
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 10
year: '2019'
...
---
_id: '9060'
abstract:
- lang: eng
text: Molecular motors are essential to the living, generating fluctuations that
boost transport and assist assembly. Active colloids, that consume energy to move,
hold similar potential for man-made materials controlled by forces generated from
within. Yet, their use as a powerhouse in materials science lacks. Here we show
a massive acceleration of the annealing of a monolayer of passive beads by moderate
addition of self-propelled microparticles. We rationalize our observations with
a model of collisions that drive active fluctuations and activate the annealing.
The experiment is quantitatively compared with Brownian dynamic simulations that
further unveil a dynamical transition in the mechanism of annealing. Active dopants
travel uniformly in the system or co-localize at the grain boundaries as a result
of the persistence of their motion. Our findings uncover the potential of internal
activity to control materials and lay the groundwork for the rise of materials
science beyond equilibrium.
article_number: '3380'
article_processing_charge: No
article_type: original
arxiv: 1
author:
- first_name: Sophie
full_name: Ramananarivo, Sophie
last_name: Ramananarivo
- first_name: Etienne
full_name: Ducrot, Etienne
last_name: Ducrot
- first_name: Jérémie A
full_name: Palacci, Jérémie A
id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d
last_name: Palacci
orcid: 0000-0002-7253-9465
citation:
ama: Ramananarivo S, Ducrot E, Palacci JA. Activity-controlled annealing of colloidal
monolayers. Nature Communications. 2019;10(1). doi:10.1038/s41467-019-11362-y
apa: Ramananarivo, S., Ducrot, E., & Palacci, J. A. (2019). Activity-controlled
annealing of colloidal monolayers. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-019-11362-y
chicago: Ramananarivo, Sophie, Etienne Ducrot, and Jérémie A Palacci. “Activity-Controlled
Annealing of Colloidal Monolayers.” Nature Communications. Springer Nature,
2019. https://doi.org/10.1038/s41467-019-11362-y.
ieee: S. Ramananarivo, E. Ducrot, and J. A. Palacci, “Activity-controlled annealing
of colloidal monolayers,” Nature Communications, vol. 10, no. 1. Springer
Nature, 2019.
ista: Ramananarivo S, Ducrot E, Palacci JA. 2019. Activity-controlled annealing
of colloidal monolayers. Nature Communications. 10(1), 3380.
mla: Ramananarivo, Sophie, et al. “Activity-Controlled Annealing of Colloidal Monolayers.”
Nature Communications, vol. 10, no. 1, 3380, Springer Nature, 2019, doi:10.1038/s41467-019-11362-y.
short: S. Ramananarivo, E. Ducrot, J.A. Palacci, Nature Communications 10 (2019).
date_created: 2021-02-02T13:43:36Z
date_published: 2019-07-29T00:00:00Z
date_updated: 2023-02-23T13:47:59Z
day: '29'
ddc:
- '530'
doi: 10.1038/s41467-019-11362-y
extern: '1'
external_id:
arxiv:
- '1909.07382'
pmid:
- '31358762'
file:
- access_level: open_access
checksum: 70c6e5d6fbea0932b0669505ab6633ec
content_type: application/pdf
creator: cziletti
date_created: 2021-02-02T13:47:21Z
date_updated: 2021-02-02T13:47:21Z
file_id: '9061'
file_name: 2019_NatureComm_Ramananarivo.pdf
file_size: 2820337
relation: main_file
success: 1
file_date_updated: 2021-02-02T13:47:21Z
has_accepted_license: '1'
intvolume: ' 10'
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
- General Physics and Astronomy
- General Chemistry
language:
- iso: eng
month: '07'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Activity-controlled annealing of colloidal monolayers
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: D865714E-FA4E-11E9-B85B-F5C5E5697425
volume: 10
year: '2019'
...
---
_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: '10880'
abstract:
- lang: eng
text: Acquisition of evolutionary novelties is a fundamental process for adapting
to the external environment and invading new niches and results in the diversification
of life, which we can see in the world today. How such novel phenotypic traits
are acquired in the course of evolution and are built up in developing embryos
has been a central question in biology. Whole-genome duplication (WGD) is a process
of genome doubling that supplies raw genetic materials and increases genome complexity.
Recently, it has been gradually revealed that WGD and subsequent fate changes
of duplicated genes can facilitate phenotypic evolution. Here, we review the current
understanding of the relationship between WGD and the acquisition of evolutionary
novelties. We show some examples of this link and discuss how WGD and subsequent
duplicated genes can facilitate phenotypic evolution as well as when such genomic
doubling can be advantageous for adaptation.
acknowledgement: This work was supported by JSPS overseas research fellowships (Y.M.)
and SENSHIN Medical Research Foundation (K.K.T.).
article_processing_charge: No
article_type: original
author:
- first_name: Moriyama
full_name: Yuuta, Moriyama
id: 4968E7C8-F248-11E8-B48F-1D18A9856A87
last_name: Yuuta
orcid: 0000-0002-2853-8051
- first_name: Kazuko
full_name: Koshiba-Takeuchi, Kazuko
last_name: Koshiba-Takeuchi
citation:
ama: Yuuta M, Koshiba-Takeuchi K. Significance of whole-genome duplications on the
emergence of evolutionary novelties. Briefings in Functional Genomics.
2018;17(5):329-338. doi:10.1093/bfgp/ely007
apa: Yuuta, M., & Koshiba-Takeuchi, K. (2018). Significance of whole-genome
duplications on the emergence of evolutionary novelties. Briefings in Functional
Genomics. Oxford University Press. https://doi.org/10.1093/bfgp/ely007
chicago: Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome
Duplications on the Emergence of Evolutionary Novelties.” Briefings in Functional
Genomics. Oxford University Press, 2018. https://doi.org/10.1093/bfgp/ely007.
ieee: M. Yuuta and K. Koshiba-Takeuchi, “Significance of whole-genome duplications
on the emergence of evolutionary novelties,” Briefings in Functional Genomics,
vol. 17, no. 5. Oxford University Press, pp. 329–338, 2018.
ista: Yuuta M, Koshiba-Takeuchi K. 2018. Significance of whole-genome duplications
on the emergence of evolutionary novelties. Briefings in Functional Genomics.
17(5), 329–338.
mla: Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome
Duplications on the Emergence of Evolutionary Novelties.” Briefings in Functional
Genomics, vol. 17, no. 5, Oxford University Press, 2018, pp. 329–38, doi:10.1093/bfgp/ely007.
short: M. Yuuta, K. Koshiba-Takeuchi, Briefings in Functional Genomics 17 (2018)
329–338.
date_created: 2022-03-18T12:40:35Z
date_published: 2018-09-01T00:00:00Z
date_updated: 2023-09-19T15:11:22Z
day: '01'
department:
- _id: CaHe
doi: 10.1093/bfgp/ely007
external_id:
isi:
- '000456054400004'
pmid:
- '29579140'
intvolume: ' 17'
isi: 1
issue: '5'
keyword:
- Genetics
- Molecular Biology
- Biochemistry
- General Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1093/bfgp/ely007
month: '09'
oa: 1
oa_version: Published Version
page: 329-338
pmid: 1
publication: Briefings in Functional Genomics
publication_identifier:
eissn:
- 2041-2657
issn:
- 2041-2649
publication_status: published
publisher: Oxford University Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Significance of whole-genome duplications on the emergence of evolutionary
novelties
type: journal_article
user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1
volume: 17
year: '2018'
...
---
_id: '11063'
abstract:
- lang: eng
text: The total number of nuclear pore complexes (NPCs) per nucleus varies greatly
between different cell types and is known to change during cell differentiation
and cell transformation. However, the underlying mechanisms that control how many
nuclear transport channels are assembled into a given nuclear envelope remain
unclear. Here, we report that depletion of the NPC basket protein Tpr, but not
Nup153, dramatically increases the total NPC number in various cell types. This
negative regulation of Tpr occurs via a phosphorylation cascade of extracellular
signal-regulated kinase (ERK), the central kinase of the mitogen-activated protein
kinase (MAPK) pathway. Tpr serves as a scaffold for ERK to phosphorylate the nucleoporin
(Nup) Nup153, which is critical for early stages of NPC biogenesis. Our results
reveal a critical role of the Nup Tpr in coordinating signal transduction pathways
during cell proliferation and the dynamic organization of the nucleus.
article_processing_charge: No
article_type: original
author:
- first_name: Asako
full_name: McCloskey, Asako
last_name: McCloskey
- first_name: Arkaitz
full_name: Ibarra, Arkaitz
last_name: Ibarra
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: McCloskey A, Ibarra A, Hetzer M. Tpr regulates the total number of nuclear
pore complexes per cell nucleus. Genes & Development. 2018;32(19-20):1321-1331.
doi:10.1101/gad.315523.118
apa: McCloskey, A., Ibarra, A., & Hetzer, M. (2018). Tpr regulates the total
number of nuclear pore complexes per cell nucleus. Genes & Development.
Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.315523.118
chicago: McCloskey, Asako, Arkaitz Ibarra, and Martin Hetzer. “Tpr Regulates the
Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development.
Cold Spring Harbor Laboratory, 2018. https://doi.org/10.1101/gad.315523.118.
ieee: A. McCloskey, A. Ibarra, and M. Hetzer, “Tpr regulates the total number of
nuclear pore complexes per cell nucleus,” Genes & Development, vol.
32, no. 19–20. Cold Spring Harbor Laboratory, pp. 1321–1331, 2018.
ista: McCloskey A, Ibarra A, Hetzer M. 2018. Tpr regulates the total number of nuclear
pore complexes per cell nucleus. Genes & Development. 32(19–20), 1321–1331.
mla: McCloskey, Asako, et al. “Tpr Regulates the Total Number of Nuclear Pore Complexes
per Cell Nucleus.” Genes & Development, vol. 32, no. 19–20, Cold Spring
Harbor Laboratory, 2018, pp. 1321–31, doi:10.1101/gad.315523.118.
short: A. McCloskey, A. Ibarra, M. Hetzer, Genes & Development 32 (2018) 1321–1331.
date_created: 2022-04-07T07:45:30Z
date_published: 2018-09-18T00:00:00Z
date_updated: 2022-07-18T08:32:32Z
day: '18'
doi: 10.1101/gad.315523.118
extern: '1'
external_id:
pmid:
- '30228202'
intvolume: ' 32'
issue: 19-20
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/gad.315523.118
month: '09'
oa: 1
oa_version: Published Version
page: 1321-1331
pmid: 1
publication: Genes & Development
publication_identifier:
issn:
- 0890-9369
- 1549-5477
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: Tpr regulates the total number of nuclear pore complexes per cell nucleus
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 32
year: '2018'
...
---
_id: '8436'
abstract:
- lang: eng
text: The exchange of metabolites between the mitochondrial matrix and the cytosol
depends on β-barrel channels in the outer membrane and α-helical carrier proteins
in the inner membrane. The essential translocase of the inner membrane (TIM) chaperones
escort these proteins through the intermembrane space, but the structural and
mechanistic details remain elusive. We have used an integrated structural biology
approach to reveal the functional principle of TIM chaperones. Multiple clamp-like
binding sites hold the mitochondrial membrane proteins in a translocation-competent
elongated form, thus mimicking characteristics of co-translational membrane insertion.
The bound preprotein undergoes conformational dynamics within the chaperone binding
clefts, pointing to a multitude of dynamic local binding events. Mutations in
these binding sites cause cell death or growth defects associated with impairment
of carrier and β-barrel protein biogenesis. Our work reveals how a single mitochondrial
“transfer-chaperone” system is able to guide α-helical and β-barrel membrane proteins
in a “nascent chain-like” conformation through a ribosome-free compartment.
article_processing_charge: No
article_type: original
author:
- first_name: Katharina
full_name: Weinhäupl, Katharina
last_name: Weinhäupl
- first_name: Caroline
full_name: Lindau, Caroline
last_name: Lindau
- first_name: Audrey
full_name: Hessel, Audrey
last_name: Hessel
- first_name: Yong
full_name: Wang, Yong
last_name: Wang
- first_name: Conny
full_name: Schütze, Conny
last_name: Schütze
- first_name: Tobias
full_name: Jores, Tobias
last_name: Jores
- first_name: Laura
full_name: Melchionda, Laura
last_name: Melchionda
- first_name: Birgit
full_name: Schönfisch, Birgit
last_name: Schönfisch
- first_name: Hubert
full_name: Kalbacher, Hubert
last_name: Kalbacher
- first_name: Beate
full_name: Bersch, Beate
last_name: Bersch
- first_name: Doron
full_name: Rapaport, Doron
last_name: Rapaport
- first_name: Martha
full_name: Brennich, Martha
last_name: Brennich
- first_name: Kresten
full_name: Lindorff-Larsen, Kresten
last_name: Lindorff-Larsen
- first_name: Nils
full_name: Wiedemann, Nils
last_name: Wiedemann
- first_name: Paul
full_name: Schanda, Paul
id: 7B541462-FAF6-11E9-A490-E8DFE5697425
last_name: Schanda
orcid: 0000-0002-9350-7606
citation:
ama: Weinhäupl K, Lindau C, Hessel A, et al. Structural basis of membrane protein
chaperoning through the mitochondrial intermembrane space. Cell. 2018;175(5):1365-1379.e25.
doi:10.1016/j.cell.2018.10.039
apa: Weinhäupl, K., Lindau, C., Hessel, A., Wang, Y., Schütze, C., Jores, T., …
Schanda, P. (2018). Structural basis of membrane protein chaperoning through the
mitochondrial intermembrane space. Cell. Elsevier. https://doi.org/10.1016/j.cell.2018.10.039
chicago: Weinhäupl, Katharina, Caroline Lindau, Audrey Hessel, Yong Wang, Conny
Schütze, Tobias Jores, Laura Melchionda, et al. “Structural Basis of Membrane
Protein Chaperoning through the Mitochondrial Intermembrane Space.” Cell.
Elsevier, 2018. https://doi.org/10.1016/j.cell.2018.10.039.
ieee: K. Weinhäupl et al., “Structural basis of membrane protein chaperoning
through the mitochondrial intermembrane space,” Cell, vol. 175, no. 5.
Elsevier, p. 1365–1379.e25, 2018.
ista: Weinhäupl K, Lindau C, Hessel A, Wang Y, Schütze C, Jores T, Melchionda L,
Schönfisch B, Kalbacher H, Bersch B, Rapaport D, Brennich M, Lindorff-Larsen K,
Wiedemann N, Schanda P. 2018. Structural basis of membrane protein chaperoning
through the mitochondrial intermembrane space. Cell. 175(5), 1365–1379.e25.
mla: Weinhäupl, Katharina, et al. “Structural Basis of Membrane Protein Chaperoning
through the Mitochondrial Intermembrane Space.” Cell, vol. 175, no. 5,
Elsevier, 2018, p. 1365–1379.e25, doi:10.1016/j.cell.2018.10.039.
short: K. Weinhäupl, C. Lindau, A. Hessel, Y. Wang, C. Schütze, T. Jores, L. Melchionda,
B. Schönfisch, H. Kalbacher, B. Bersch, D. Rapaport, M. Brennich, K. Lindorff-Larsen,
N. Wiedemann, P. Schanda, Cell 175 (2018) 1365–1379.e25.
date_created: 2020-09-18T10:04:39Z
date_published: 2018-11-15T00:00:00Z
date_updated: 2021-01-12T08:19:15Z
day: '15'
doi: 10.1016/j.cell.2018.10.039
extern: '1'
intvolume: ' 175'
issue: '5'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
month: '11'
oa_version: None
page: 1365-1379.e25
publication: Cell
publication_identifier:
issn:
- 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
status: public
title: Structural basis of membrane protein chaperoning through the mitochondrial
intermembrane space
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 175
year: '2018'
...
---
_id: '13374'
abstract:
- lang: eng
text: Confining molecules to volumes only slightly larger than the molecules themselves
can profoundly alter their properties. Molecular switches—entities that can be
toggled between two or more forms upon exposure to an external stimulus—often
require conformational freedom to isomerize. Therefore, placing these switches
in confined spaces can render them non-operational. To preserve the switchability
of these species under confinement, we work with a water-soluble coordination
cage that is flexible enough to adapt its shape to the conformation of the encapsulated
guest. We show that owing to its flexibility, the cage is not only capable of
accommodating—and solubilizing in water—several light-responsive spiropyran-based
molecular switches, but, more importantly, it also provides an environment suitable
for the efficient, reversible photoisomerization of the bound guests. Our findings
pave the way towards studying various molecular switching processes in confined
environments.
article_number: '641'
article_processing_charge: No
article_type: original
author:
- first_name: Dipak
full_name: Samanta, Dipak
last_name: Samanta
- first_name: Daria
full_name: Galaktionova, Daria
last_name: Galaktionova
- first_name: Julius
full_name: Gemen, Julius
last_name: Gemen
- first_name: Linda J. W.
full_name: Shimon, Linda J. W.
last_name: Shimon
- first_name: Yael
full_name: Diskin-Posner, Yael
last_name: Diskin-Posner
- first_name: Liat
full_name: Avram, Liat
last_name: Avram
- first_name: Petr
full_name: Král, Petr
last_name: Král
- first_name: Rafal
full_name: Klajn, Rafal
id: 8e84690e-1e48-11ed-a02b-a1e6fb8bb53b
last_name: Klajn
citation:
ama: Samanta D, Galaktionova D, Gemen J, et al. Reversible chromism of spiropyran
in the cavity of a flexible coordination cage. Nature Communications. 2018;9.
doi:10.1038/s41467-017-02715-6
apa: Samanta, D., Galaktionova, D., Gemen, J., Shimon, L. J. W., Diskin-Posner,
Y., Avram, L., … Klajn, R. (2018). Reversible chromism of spiropyran in the cavity
of a flexible coordination cage. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-017-02715-6
chicago: Samanta, Dipak, Daria Galaktionova, Julius Gemen, Linda J. W. Shimon, Yael
Diskin-Posner, Liat Avram, Petr Král, and Rafal Klajn. “Reversible Chromism of
Spiropyran in the Cavity of a Flexible Coordination Cage.” Nature Communications.
Springer Nature, 2018. https://doi.org/10.1038/s41467-017-02715-6.
ieee: D. Samanta et al., “Reversible chromism of spiropyran in the cavity
of a flexible coordination cage,” Nature Communications, vol. 9. Springer
Nature, 2018.
ista: Samanta D, Galaktionova D, Gemen J, Shimon LJW, Diskin-Posner Y, Avram L,
Král P, Klajn R. 2018. Reversible chromism of spiropyran in the cavity of a flexible
coordination cage. Nature Communications. 9, 641.
mla: Samanta, Dipak, et al. “Reversible Chromism of Spiropyran in the Cavity of
a Flexible Coordination Cage.” Nature Communications, vol. 9, 641, Springer
Nature, 2018, doi:10.1038/s41467-017-02715-6.
short: D. Samanta, D. Galaktionova, J. Gemen, L.J.W. Shimon, Y. Diskin-Posner, L.
Avram, P. Král, R. Klajn, Nature Communications 9 (2018).
date_created: 2023-08-01T09:39:32Z
date_published: 2018-02-13T00:00:00Z
date_updated: 2023-08-07T10:54:05Z
day: '13'
doi: 10.1038/s41467-017-02715-6
extern: '1'
external_id:
pmid:
- '29440687'
intvolume: ' 9'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-017-02715-6
month: '02'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
related_material:
link:
- relation: erratum
url: https://doi.org/10.1038/s41467-018-03701-2
scopus_import: '1'
status: public
title: Reversible chromism of spiropyran in the cavity of a flexible coordination
cage
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '14284'
abstract:
- lang: eng
text: Pore-forming toxins (PFT) are virulence factors that transform from soluble
to membrane-bound states. The Yersinia YaxAB system represents a family of binary
α-PFTs with orthologues in human, insect, and plant pathogens, with unknown structures.
YaxAB was shown to be cytotoxic and likely involved in pathogenesis, though the
molecular basis for its two-component lytic mechanism remains elusive. Here, we
present crystal structures of YaxA and YaxB, together with a cryo-electron microscopy
map of the YaxAB complex. Our structures reveal a pore predominantly composed
of decamers of YaxA–YaxB heterodimers. Both subunits bear membrane-active moieties,
but only YaxA is capable of binding to membranes by itself. YaxB can subsequently
be recruited to membrane-associated YaxA and induced to present its lytic transmembrane
helices. Pore formation can progress by further oligomerization of YaxA–YaxB dimers.
Our results allow for a comparison between pore assemblies belonging to the wider
ClyA-like family of α-PFTs, highlighting diverse pore architectures.
article_number: '1806'
article_processing_charge: No
article_type: original
author:
- first_name: Bastian
full_name: Bräuning, Bastian
last_name: Bräuning
- first_name: Eva
full_name: Bertosin, Eva
last_name: Bertosin
- first_name: Florian M
full_name: Praetorius, Florian M
id: dfec9381-4341-11ee-8fd8-faa02bba7d62
last_name: Praetorius
- first_name: Christian
full_name: Ihling, Christian
last_name: Ihling
- first_name: Alexandra
full_name: Schatt, Alexandra
last_name: Schatt
- first_name: Agnes
full_name: Adler, Agnes
last_name: Adler
- first_name: Klaus
full_name: Richter, Klaus
last_name: Richter
- first_name: Andrea
full_name: Sinz, Andrea
last_name: Sinz
- first_name: Hendrik
full_name: Dietz, Hendrik
last_name: Dietz
- first_name: Michael
full_name: Groll, Michael
last_name: Groll
citation:
ama: Bräuning B, Bertosin E, Praetorius FM, et al. Structure and mechanism of the
two-component α-helical pore-forming toxin YaxAB. Nature Communications.
2018;9. doi:10.1038/s41467-018-04139-2
apa: Bräuning, B., Bertosin, E., Praetorius, F. M., Ihling, C., Schatt, A., Adler,
A., … Groll, M. (2018). Structure and mechanism of the two-component α-helical
pore-forming toxin YaxAB. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04139-2
chicago: Bräuning, Bastian, Eva Bertosin, Florian M Praetorius, Christian Ihling,
Alexandra Schatt, Agnes Adler, Klaus Richter, Andrea Sinz, Hendrik Dietz, and
Michael Groll. “Structure and Mechanism of the Two-Component α-Helical Pore-Forming
Toxin YaxAB.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04139-2.
ieee: B. Bräuning et al., “Structure and mechanism of the two-component α-helical
pore-forming toxin YaxAB,” Nature Communications, vol. 9. Springer Nature,
2018.
ista: Bräuning B, Bertosin E, Praetorius FM, Ihling C, Schatt A, Adler A, Richter
K, Sinz A, Dietz H, Groll M. 2018. Structure and mechanism of the two-component
α-helical pore-forming toxin YaxAB. Nature Communications. 9, 1806.
mla: Bräuning, Bastian, et al. “Structure and Mechanism of the Two-Component α-Helical
Pore-Forming Toxin YaxAB.” Nature Communications, vol. 9, 1806, Springer
Nature, 2018, doi:10.1038/s41467-018-04139-2.
short: B. Bräuning, E. Bertosin, F.M. Praetorius, C. Ihling, A. Schatt, A. Adler,
K. Richter, A. Sinz, H. Dietz, M. Groll, Nature Communications 9 (2018).
date_created: 2023-09-06T12:07:33Z
date_published: 2018-05-04T00:00:00Z
date_updated: 2023-11-07T11:46:12Z
day: '04'
doi: 10.1038/s41467-018-04139-2
extern: '1'
external_id:
pmid:
- '29728606'
intvolume: ' 9'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-018-04139-2
month: '05'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Structure and mechanism of the two-component α-helical pore-forming toxin YaxAB
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 9
year: '2018'
...
---
_id: '11065'
abstract:
- lang: eng
text: Premature aging disorders provide an opportunity to study the mechanisms that
drive aging. In Hutchinson-Gilford progeria syndrome (HGPS), a mutant form of
the nuclear scaffold protein lamin A distorts nuclei and sequesters nuclear proteins.
We sought to investigate protein homeostasis in this disease. Here, we report
a widespread increase in protein turnover in HGPS-derived cells compared to normal
cells. We determine that global protein synthesis is elevated as a consequence
of activated nucleoli and enhanced ribosome biogenesis in HGPS-derived fibroblasts.
Depleting normal lamin A or inducing mutant lamin A expression are each sufficient
to drive nucleolar expansion. We further show that nucleolar size correlates with
donor age in primary fibroblasts derived from healthy individuals and that ribosomal
RNA production increases with age, indicating that nucleolar size and activity
can serve as aging biomarkers. While limiting ribosome biogenesis extends lifespan
in several systems, we show that increased ribosome biogenesis and activity are
a hallmark of premature aging.
article_number: '328'
article_processing_charge: No
article_type: original
author:
- first_name: Abigail
full_name: Buchwalter, Abigail
last_name: Buchwalter
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Buchwalter A, Hetzer M. Nucleolar expansion and elevated protein translation
in premature aging. Nature Communications. 2017;8. doi:10.1038/s41467-017-00322-z
apa: Buchwalter, A., & Hetzer, M. (2017). Nucleolar expansion and elevated protein
translation in premature aging. Nature Communications. Springer Nature.
https://doi.org/10.1038/s41467-017-00322-z
chicago: Buchwalter, Abigail, and Martin Hetzer. “Nucleolar Expansion and Elevated
Protein Translation in Premature Aging.” Nature Communications. Springer
Nature, 2017. https://doi.org/10.1038/s41467-017-00322-z.
ieee: A. Buchwalter and M. Hetzer, “Nucleolar expansion and elevated protein translation
in premature aging,” Nature Communications, vol. 8. Springer Nature, 2017.
ista: Buchwalter A, Hetzer M. 2017. Nucleolar expansion and elevated protein translation
in premature aging. Nature Communications. 8, 328.
mla: Buchwalter, Abigail, and Martin Hetzer. “Nucleolar Expansion and Elevated Protein
Translation in Premature Aging.” Nature Communications, vol. 8, 328, Springer
Nature, 2017, doi:10.1038/s41467-017-00322-z.
short: A. Buchwalter, M. Hetzer, Nature Communications 8 (2017).
date_created: 2022-04-07T07:45:50Z
date_published: 2017-08-30T00:00:00Z
date_updated: 2022-07-18T08:33:03Z
day: '30'
doi: 10.1038/s41467-017-00322-z
extern: '1'
external_id:
pmid:
- '28855503'
intvolume: ' 8'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/s41467-017-00322-z
month: '08'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
issn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nucleolar expansion and elevated protein translation in premature aging
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 8
year: '2017'
...
---
_id: '11066'
abstract:
- lang: eng
text: Recent studies have shown that a subset of nucleoporins (Nups) can detach
from the nuclear pore complex and move into the nuclear interior to regulate transcription.
One such dynamic Nup, called Nup98, has been implicated in gene activation in
healthy cells and has been shown to drive leukemogenesis when mutated in patients
with acute myeloid leukemia (AML). Here we show that in hematopoietic cells, Nup98
binds predominantly to transcription start sites to recruit the Wdr82–Set1A/COMPASS
(complex of proteins associated with Set1) complex, which is required for deposition
of the histone 3 Lys4 trimethyl (H3K4me3)-activating mark. Depletion of Nup98
or Wdr82 abolishes Set1A recruitment to chromatin and subsequently ablates H3K4me3
at adjacent promoters. Furthermore, expression of a Nup98 fusion protein implicated
in aggressive AML causes mislocalization of H3K4me3 at abnormal regions and up-regulation
of associated genes. Our findings establish a function of Nup98 in hematopoietic
gene activation and provide mechanistic insight into which Nup98 leukemic fusion
proteins promote AML.
article_processing_charge: No
article_type: original
author:
- first_name: Tobias M.
full_name: Franks, Tobias M.
last_name: Franks
- first_name: Asako
full_name: McCloskey, Asako
last_name: McCloskey
- first_name: Maxim Nikolaievich
full_name: Shokhirev, Maxim Nikolaievich
last_name: Shokhirev
- first_name: Chris
full_name: Benner, Chris
last_name: Benner
- first_name: Annie
full_name: Rathore, Annie
last_name: Rathore
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Franks TM, McCloskey A, Shokhirev MN, Benner C, Rathore A, Hetzer M. Nup98
recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation
in hematopoietic progenitor cells. Genes & Development. 2017;31(22):2222-2234.
doi:10.1101/gad.306753.117
apa: Franks, T. M., McCloskey, A., Shokhirev, M. N., Benner, C., Rathore, A., &
Hetzer, M. (2017). Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters
to regulate H3K4 trimethylation in hematopoietic progenitor cells. Genes &
Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.306753.117
chicago: Franks, Tobias M., Asako McCloskey, Maxim Nikolaievich Shokhirev, Chris
Benner, Annie Rathore, and Martin Hetzer. “Nup98 Recruits the Wdr82–Set1A/COMPASS
Complex to Promoters to Regulate H3K4 Trimethylation in Hematopoietic Progenitor
Cells.” Genes & Development. Cold Spring Harbor Laboratory, 2017. https://doi.org/10.1101/gad.306753.117.
ieee: T. M. Franks, A. McCloskey, M. N. Shokhirev, C. Benner, A. Rathore, and M.
Hetzer, “Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate
H3K4 trimethylation in hematopoietic progenitor cells,” Genes & Development,
vol. 31, no. 22. Cold Spring Harbor Laboratory, pp. 2222–2234, 2017.
ista: Franks TM, McCloskey A, Shokhirev MN, Benner C, Rathore A, Hetzer M. 2017.
Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4 trimethylation
in hematopoietic progenitor cells. Genes & Development. 31(22), 2222–2234.
mla: Franks, Tobias M., et al. “Nup98 Recruits the Wdr82–Set1A/COMPASS Complex to
Promoters to Regulate H3K4 Trimethylation in Hematopoietic Progenitor Cells.”
Genes & Development, vol. 31, no. 22, Cold Spring Harbor Laboratory,
2017, pp. 2222–34, doi:10.1101/gad.306753.117.
short: T.M. Franks, A. McCloskey, M.N. Shokhirev, C. Benner, A. Rathore, M. Hetzer,
Genes & Development 31 (2017) 2222–2234.
date_created: 2022-04-07T07:45:59Z
date_published: 2017-12-21T00:00:00Z
date_updated: 2022-07-18T08:33:05Z
day: '21'
doi: 10.1101/gad.306753.117
extern: '1'
external_id:
pmid:
- '29269482'
intvolume: ' 31'
issue: '22'
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/gad.306753.117
month: '12'
oa: 1
oa_version: Published Version
page: 2222-2234
pmid: 1
publication: Genes & Development
publication_identifier:
issn:
- 0890-9369
- 1549-5477
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nup98 recruits the Wdr82–Set1A/COMPASS complex to promoters to regulate H3K4
trimethylation in hematopoietic progenitor cells
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 31
year: '2017'
...
---
_id: '11067'
abstract:
- lang: eng
text: Neural progenitor cells (NeuPCs) possess a unique nuclear architecture that
changes during differentiation. Nucleoporins are linked with cell-type-specific
gene regulation, coupling physical changes in nuclear structure to transcriptional
output; but, whether and how they coordinate with key fate-determining transcription
factors is unclear. Here we show that the nucleoporin Nup153 interacts with Sox2
in adult NeuPCs, where it is indispensable for their maintenance and controls
neuronal differentiation. Genome-wide analyses show that Nup153 and Sox2 bind
and co-regulate hundreds of genes. Binding of Nup153 to gene promoters or transcriptional
end sites correlates with increased or decreased gene expression, respectively,
and inhibiting Nup153 expression alters open chromatin configurations at its target
genes, disrupts genomic localization of Sox2, and promotes differentiation in
vitro and a gliogenic fate switch in vivo. Together, these findings reveal that
nuclear structural proteins may exert bimodal transcriptional effects to control
cell fate.
article_processing_charge: No
article_type: original
author:
- first_name: Tomohisa
full_name: Toda, Tomohisa
last_name: Toda
- first_name: Jonathan Y.
full_name: Hsu, Jonathan Y.
last_name: Hsu
- first_name: Sara B.
full_name: Linker, Sara B.
last_name: Linker
- first_name: Lauren
full_name: Hu, Lauren
last_name: Hu
- first_name: Simon T.
full_name: Schafer, Simon T.
last_name: Schafer
- first_name: Jerome
full_name: Mertens, Jerome
last_name: Mertens
- first_name: Filipe V.
full_name: Jacinto, Filipe V.
last_name: Jacinto
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
- first_name: Fred H.
full_name: Gage, Fred H.
last_name: Gage
citation:
ama: Toda T, Hsu JY, Linker SB, et al. Nup153 interacts with Sox2 to enable bimodal
gene regulation and maintenance of neural progenitor cells. Cell Stem Cell.
2017;21(5):618-634.e7. doi:10.1016/j.stem.2017.08.012
apa: Toda, T., Hsu, J. Y., Linker, S. B., Hu, L., Schafer, S. T., Mertens, J., …
Gage, F. H. (2017). Nup153 interacts with Sox2 to enable bimodal gene regulation
and maintenance of neural progenitor cells. Cell Stem Cell. Elsevier. https://doi.org/10.1016/j.stem.2017.08.012
chicago: Toda, Tomohisa, Jonathan Y. Hsu, Sara B. Linker, Lauren Hu, Simon T. Schafer,
Jerome Mertens, Filipe V. Jacinto, Martin Hetzer, and Fred H. Gage. “Nup153 Interacts
with Sox2 to Enable Bimodal Gene Regulation and Maintenance of Neural Progenitor
Cells.” Cell Stem Cell. Elsevier, 2017. https://doi.org/10.1016/j.stem.2017.08.012.
ieee: T. Toda et al., “Nup153 interacts with Sox2 to enable bimodal gene
regulation and maintenance of neural progenitor cells,” Cell Stem Cell,
vol. 21, no. 5. Elsevier, p. 618–634.e7, 2017.
ista: Toda T, Hsu JY, Linker SB, Hu L, Schafer ST, Mertens J, Jacinto FV, Hetzer
M, Gage FH. 2017. Nup153 interacts with Sox2 to enable bimodal gene regulation
and maintenance of neural progenitor cells. Cell Stem Cell. 21(5), 618–634.e7.
mla: Toda, Tomohisa, et al. “Nup153 Interacts with Sox2 to Enable Bimodal Gene Regulation
and Maintenance of Neural Progenitor Cells.” Cell Stem Cell, vol. 21, no.
5, Elsevier, 2017, p. 618–634.e7, doi:10.1016/j.stem.2017.08.012.
short: T. Toda, J.Y. Hsu, S.B. Linker, L. Hu, S.T. Schafer, J. Mertens, F.V. Jacinto,
M. Hetzer, F.H. Gage, Cell Stem Cell 21 (2017) 618–634.e7.
date_created: 2022-04-07T07:46:12Z
date_published: 2017-11-02T00:00:00Z
date_updated: 2022-07-18T08:33:07Z
day: '02'
doi: 10.1016/j.stem.2017.08.012
extern: '1'
external_id:
pmid:
- '28919367'
intvolume: ' 21'
issue: '5'
keyword:
- Cell Biology
- Genetics
- Molecular Medicine
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1016/j.stem.2017.08.012
month: '11'
oa: 1
oa_version: Published Version
page: 618-634.e7
pmid: 1
publication: Cell Stem Cell
publication_identifier:
issn:
- 1934-5909
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nup153 interacts with Sox2 to enable bimodal gene regulation and maintenance
of neural progenitor cells
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 21
year: '2017'
...
---
_id: '14005'
abstract:
- lang: eng
text: Strong-field photoelectron holography and laser-induced electron diffraction
(LIED) are two powerful emerging methods for probing the ultrafast dynamics of
molecules. However, both of them have remained restricted to static systems and
to nuclear dynamics induced by strong-field ionization. Here we extend these promising
methods to image purely electronic valence-shell dynamics in molecules using photoelectron
holography. In the same experiment, we use LIED and photoelectron holography simultaneously,
to observe coupled electronic-rotational dynamics taking place on similar timescales.
These results offer perspectives for imaging ultrafast dynamics of molecules on
femtosecond to attosecond timescales.
article_number: '15651'
article_processing_charge: No
article_type: original
author:
- first_name: Samuel G.
full_name: Walt, Samuel G.
last_name: Walt
- first_name: Niraghatam
full_name: Bhargava Ram, Niraghatam
last_name: Bhargava Ram
- first_name: Marcos
full_name: Atala, Marcos
last_name: Atala
- first_name: Nikolay I
full_name: Shvetsov-Shilovski, Nikolay I
last_name: Shvetsov-Shilovski
- first_name: Aaron
full_name: von Conta, Aaron
last_name: von Conta
- first_name: Denitsa Rangelova
full_name: Baykusheva, Denitsa Rangelova
id: 71b4d059-2a03-11ee-914d-dfa3beed6530
last_name: Baykusheva
- first_name: Manfred
full_name: Lein, Manfred
last_name: Lein
- first_name: Hans Jakob
full_name: Wörner, Hans Jakob
last_name: Wörner
citation:
ama: Walt SG, Bhargava Ram N, Atala M, et al. Dynamics of valence-shell electrons
and nuclei probed by strong-field holography and rescattering. Nature Communications.
2017;8. doi:10.1038/ncomms15651
apa: Walt, S. G., Bhargava Ram, N., Atala, M., Shvetsov-Shilovski, N. I., von Conta,
A., Baykusheva, D. R., … Wörner, H. J. (2017). Dynamics of valence-shell electrons
and nuclei probed by strong-field holography and rescattering. Nature Communications.
Springer Nature. https://doi.org/10.1038/ncomms15651
chicago: Walt, Samuel G., Niraghatam Bhargava Ram, Marcos Atala, Nikolay I Shvetsov-Shilovski,
Aaron von Conta, Denitsa Rangelova Baykusheva, Manfred Lein, and Hans Jakob Wörner.
“Dynamics of Valence-Shell Electrons and Nuclei Probed by Strong-Field Holography
and Rescattering.” Nature Communications. Springer Nature, 2017. https://doi.org/10.1038/ncomms15651.
ieee: S. G. Walt et al., “Dynamics of valence-shell electrons and nuclei
probed by strong-field holography and rescattering,” Nature Communications,
vol. 8. Springer Nature, 2017.
ista: Walt SG, Bhargava Ram N, Atala M, Shvetsov-Shilovski NI, von Conta A, Baykusheva
DR, Lein M, Wörner HJ. 2017. Dynamics of valence-shell electrons and nuclei probed
by strong-field holography and rescattering. Nature Communications. 8, 15651.
mla: Walt, Samuel G., et al. “Dynamics of Valence-Shell Electrons and Nuclei Probed
by Strong-Field Holography and Rescattering.” Nature Communications, vol.
8, 15651, Springer Nature, 2017, doi:10.1038/ncomms15651.
short: S.G. Walt, N. Bhargava Ram, M. Atala, N.I. Shvetsov-Shilovski, A. von Conta,
D.R. Baykusheva, M. Lein, H.J. Wörner, Nature Communications 8 (2017).
date_created: 2023-08-10T06:36:09Z
date_published: 2017-06-15T00:00:00Z
date_updated: 2023-08-22T08:26:06Z
day: '15'
doi: 10.1038/ncomms15651
extern: '1'
external_id:
pmid:
- '28643771'
intvolume: ' 8'
keyword:
- General Physics and Astronomy
- General Biochemistry
- Genetics and Molecular Biology
- General Chemistry
- Multidisciplinary
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1038/ncomms15651
month: '06'
oa: 1
oa_version: Published Version
pmid: 1
publication: Nature Communications
publication_identifier:
eissn:
- 2041-1723
publication_status: published
publisher: Springer Nature
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dynamics of valence-shell electrons and nuclei probed by strong-field holography
and rescattering
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 8
year: '2017'
...
---
_id: '10370'
abstract:
- lang: eng
text: Eukaryotic cells are densely packed with macromolecular complexes and intertwining
organelles, continually transported and reshaped. Intriguingly, organelles avoid
clashing and entangling with each other in such limited space. Mitochondria form
extensive networks constantly remodeled by fission and fusion. Here, we show that
mitochondrial fission is triggered by mechanical forces. Mechano-stimulation of
mitochondria – via encounter with motile intracellular pathogens, via external
pressure applied by an atomic force microscope, or via cell migration across uneven
microsurfaces – results in the recruitment of the mitochondrial fission machinery,
and subsequent division. We propose that MFF, owing to affinity for narrow mitochondria,
acts as a membrane-bound force sensor to recruit the fission machinery to mechanically
strained sites. Thus, mitochondria adapt to the environment by sensing and responding
to biomechanical cues. Our findings that mechanical triggers can be coupled to
biochemical responses in membrane dynamics may explain how organelles orderly
cohabit in the crowded cytoplasm.
article_number: e30292
article_processing_charge: No
article_type: original
author:
- first_name: Sebastian Carsten Johannes
full_name: Helle, Sebastian Carsten Johannes
last_name: Helle
- first_name: Qian
full_name: Feng, Qian
last_name: Feng
- first_name: Mathias J
full_name: Aebersold, Mathias J
last_name: Aebersold
- first_name: Luca
full_name: Hirt, Luca
last_name: Hirt
- first_name: Raphael R
full_name: Grüter, Raphael R
last_name: Grüter
- first_name: Afshin
full_name: Vahid, Afshin
last_name: Vahid
- first_name: Andrea
full_name: Sirianni, Andrea
last_name: Sirianni
- first_name: Serge
full_name: Mostowy, Serge
last_name: Mostowy
- first_name: Jess G
full_name: Snedeker, Jess G
last_name: Snedeker
- first_name: Anđela
full_name: Šarić, Anđela
id: bf63d406-f056-11eb-b41d-f263a6566d8b
last_name: Šarić
orcid: 0000-0002-7854-2139
- first_name: Timon
full_name: Idema, Timon
last_name: Idema
- first_name: Tomaso
full_name: Zambelli, Tomaso
last_name: Zambelli
- first_name: Benoît
full_name: Kornmann, Benoît
last_name: Kornmann
citation:
ama: Helle SCJ, Feng Q, Aebersold MJ, et al. Mechanical force induces mitochondrial
fission. eLife. 2017;6. doi:10.7554/elife.30292
apa: Helle, S. C. J., Feng, Q., Aebersold, M. J., Hirt, L., Grüter, R. R., Vahid,
A., … Kornmann, B. (2017). Mechanical force induces mitochondrial fission. ELife.
eLife Sciences Publications. https://doi.org/10.7554/elife.30292
chicago: Helle, Sebastian Carsten Johannes, Qian Feng, Mathias J Aebersold, Luca
Hirt, Raphael R Grüter, Afshin Vahid, Andrea Sirianni, et al. “Mechanical Force
Induces Mitochondrial Fission.” ELife. eLife Sciences Publications, 2017.
https://doi.org/10.7554/elife.30292.
ieee: S. C. J. Helle et al., “Mechanical force induces mitochondrial fission,”
eLife, vol. 6. eLife Sciences Publications, 2017.
ista: Helle SCJ, Feng Q, Aebersold MJ, Hirt L, Grüter RR, Vahid A, Sirianni A, Mostowy
S, Snedeker JG, Šarić A, Idema T, Zambelli T, Kornmann B. 2017. Mechanical force
induces mitochondrial fission. eLife. 6, e30292.
mla: Helle, Sebastian Carsten Johannes, et al. “Mechanical Force Induces Mitochondrial
Fission.” ELife, vol. 6, e30292, eLife Sciences Publications, 2017, doi:10.7554/elife.30292.
short: S.C.J. Helle, Q. Feng, M.J. Aebersold, L. Hirt, R.R. Grüter, A. Vahid, A.
Sirianni, S. Mostowy, J.G. Snedeker, A. Šarić, T. Idema, T. Zambelli, B. Kornmann,
ELife 6 (2017).
date_created: 2021-11-29T08:51:38Z
date_published: 2017-11-09T00:00:00Z
date_updated: 2021-11-29T09:28:14Z
day: '09'
ddc:
- '572'
doi: 10.7554/elife.30292
extern: '1'
external_id:
pmid:
- '29119945'
file:
- access_level: open_access
checksum: c35f42dcfb007f6d6c761a27e24c26d3
content_type: application/pdf
creator: cchlebak
date_created: 2021-11-29T09:07:41Z
date_updated: 2021-11-29T09:07:41Z
file_id: '10372'
file_name: 2017_eLife_Helle.pdf
file_size: 6120157
relation: main_file
success: 1
file_date_updated: 2021-11-29T09:07:41Z
has_accepted_license: '1'
intvolume: ' 6'
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://elifesciences.org/articles/30292
month: '11'
oa: 1
oa_version: Published Version
pmid: 1
publication: eLife
publication_identifier:
issn:
- 2050-084X
publication_status: published
publisher: eLife Sciences Publications
quality_controlled: '1'
scopus_import: '1'
status: public
title: Mechanical force induces mitochondrial fission
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: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 6
year: '2017'
...
---
_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: '11070'
abstract:
- lang: eng
text: The organization of the genome in the three-dimensional space of the nucleus
is coupled with cell type-specific gene expression. However, how nuclear architecture
influences transcription that governs cell identity remains unknown. Here, we
show that nuclear pore complex (NPC) components Nup93 and Nup153 bind superenhancers
(SE), regulatory structures that drive the expression of key genes that specify
cell identity. We found that nucleoporin-associated SEs localize preferentially
to the nuclear periphery, and absence of Nup153 and Nup93 results in dramatic
transcriptional changes of SE-associated genes. Our results reveal a crucial role
of NPC components in the regulation of cell type-specifying genes and highlight
nuclear architecture as a regulatory layer of genome functions in cell fate.
article_processing_charge: No
article_type: original
author:
- first_name: Arkaitz
full_name: Ibarra, Arkaitz
last_name: Ibarra
- first_name: Chris
full_name: Benner, Chris
last_name: Benner
- first_name: Swati
full_name: Tyagi, Swati
last_name: Tyagi
- first_name: Jonah
full_name: Cool, Jonah
last_name: Cool
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Ibarra A, Benner C, Tyagi S, Cool J, Hetzer M. Nucleoporin-mediated regulation
of cell identity genes. Genes & Development. 2016;30(20):2253-2258.
doi:10.1101/gad.287417.116
apa: Ibarra, A., Benner, C., Tyagi, S., Cool, J., & Hetzer, M. (2016). Nucleoporin-mediated
regulation of cell identity genes. Genes & Development. Cold Spring
Harbor Laboratory. https://doi.org/10.1101/gad.287417.116
chicago: Ibarra, Arkaitz, Chris Benner, Swati Tyagi, Jonah Cool, and Martin Hetzer.
“Nucleoporin-Mediated Regulation of Cell Identity Genes.” Genes & Development.
Cold Spring Harbor Laboratory, 2016. https://doi.org/10.1101/gad.287417.116.
ieee: A. Ibarra, C. Benner, S. Tyagi, J. Cool, and M. Hetzer, “Nucleoporin-mediated
regulation of cell identity genes,” Genes & Development, vol. 30, no.
20. Cold Spring Harbor Laboratory, pp. 2253–2258, 2016.
ista: Ibarra A, Benner C, Tyagi S, Cool J, Hetzer M. 2016. Nucleoporin-mediated
regulation of cell identity genes. Genes & Development. 30(20), 2253–2258.
mla: Ibarra, Arkaitz, et al. “Nucleoporin-Mediated Regulation of Cell Identity Genes.”
Genes & Development, vol. 30, no. 20, Cold Spring Harbor Laboratory,
2016, pp. 2253–58, doi:10.1101/gad.287417.116.
short: A. Ibarra, C. Benner, S. Tyagi, J. Cool, M. Hetzer, Genes & Development
30 (2016) 2253–2258.
date_created: 2022-04-07T07:48:08Z
date_published: 2016-11-02T00:00:00Z
date_updated: 2022-07-18T08:33:49Z
day: '02'
doi: 10.1101/gad.287417.116
extern: '1'
external_id:
pmid:
- '27807035'
intvolume: ' 30'
issue: '20'
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/gad.287417.116
month: '11'
oa: 1
oa_version: Published Version
page: 2253-2258
pmid: 1
publication: Genes & Development
publication_identifier:
eissn:
- 1549-5477
issn:
- 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: Nucleoporin-mediated regulation of cell identity genes
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 30
year: '2016'
...
---
_id: '11071'
abstract:
- lang: eng
text: Nuclear pore complexes (NPCs) emerged as nuclear transport channels in eukaryotic
cells ∼1.5 billion years ago. While the primary role of NPCs is to regulate nucleo–cytoplasmic
transport, recent research suggests that certain NPC proteins have additionally
acquired the role of affecting gene expression at the nuclear periphery and in
the nucleoplasm in metazoans. Here we identify a widely expressed variant of the
transmembrane nucleoporin (Nup) Pom121 (named sPom121, for “soluble Pom121”) that
arose by genomic rearrangement before the divergence of hominoids. sPom121 lacks
the nuclear membrane-anchoring domain and thus does not localize to the NPC. Instead,
sPom121 colocalizes and interacts with nucleoplasmic Nup98, a previously identified
transcriptional regulator, at gene promoters to control transcription of its target
genes in human cells. Interestingly, sPom121 transcripts appear independently
in several mammalian species, suggesting convergent innovation of Nup-mediated
transcription regulation during mammalian evolution. Our findings implicate alternate
transcription initiation as a mechanism to increase the functional diversity of
NPC components.
article_processing_charge: No
article_type: original
author:
- first_name: Tobias M.
full_name: Franks, Tobias M.
last_name: Franks
- first_name: Chris
full_name: Benner, Chris
last_name: Benner
- first_name: Iñigo
full_name: Narvaiza, Iñigo
last_name: Narvaiza
- first_name: Maria C.N.
full_name: Marchetto, Maria C.N.
last_name: Marchetto
- first_name: Janet M.
full_name: Young, Janet M.
last_name: Young
- first_name: Harmit S.
full_name: Malik, Harmit S.
last_name: Malik
- first_name: Fred H.
full_name: Gage, Fred H.
last_name: Gage
- first_name: Martin W
full_name: HETZER, Martin W
id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed
last_name: HETZER
orcid: 0000-0002-2111-992X
citation:
ama: Franks TM, Benner C, Narvaiza I, et al. Evolution of a transcriptional regulator
from a transmembrane nucleoporin. Genes & Development. 2016;30(10):1155-1171.
doi:10.1101/gad.280941.116
apa: Franks, T. M., Benner, C., Narvaiza, I., Marchetto, M. C. N., Young, J. M.,
Malik, H. S., … Hetzer, M. (2016). Evolution of a transcriptional regulator from
a transmembrane nucleoporin. Genes & Development. Cold Spring Harbor
Laboratory. https://doi.org/10.1101/gad.280941.116
chicago: Franks, Tobias M., Chris Benner, Iñigo Narvaiza, Maria C.N. Marchetto,
Janet M. Young, Harmit S. Malik, Fred H. Gage, and Martin Hetzer. “Evolution of
a Transcriptional Regulator from a Transmembrane Nucleoporin.” Genes &
Development. Cold Spring Harbor Laboratory, 2016. https://doi.org/10.1101/gad.280941.116.
ieee: T. M. Franks et al., “Evolution of a transcriptional regulator from
a transmembrane nucleoporin,” Genes & Development, vol. 30, no. 10.
Cold Spring Harbor Laboratory, pp. 1155–1171, 2016.
ista: Franks TM, Benner C, Narvaiza I, Marchetto MCN, Young JM, Malik HS, Gage FH,
Hetzer M. 2016. Evolution of a transcriptional regulator from a transmembrane
nucleoporin. Genes & Development. 30(10), 1155–1171.
mla: Franks, Tobias M., et al. “Evolution of a Transcriptional Regulator from a
Transmembrane Nucleoporin.” Genes & Development, vol. 30, no. 10, Cold
Spring Harbor Laboratory, 2016, pp. 1155–71, doi:10.1101/gad.280941.116.
short: T.M. Franks, C. Benner, I. Narvaiza, M.C.N. Marchetto, J.M. Young, H.S. Malik,
F.H. Gage, M. Hetzer, Genes & Development 30 (2016) 1155–1171.
date_created: 2022-04-07T07:48:20Z
date_published: 2016-05-19T00:00:00Z
date_updated: 2022-07-18T08:33:50Z
day: '19'
doi: 10.1101/gad.280941.116
extern: '1'
external_id:
pmid:
- '27198230'
intvolume: ' 30'
issue: '10'
keyword:
- Developmental Biology
- Genetics
language:
- iso: eng
main_file_link:
- open_access: '1'
url: https://doi.org/10.1101/gad.280941.116
month: '05'
oa: 1
oa_version: Published Version
page: 1155-1171
pmid: 1
publication: Genes & Development
publication_identifier:
eissn:
- 1549-5477
issn:
- 0890-9369
publication_status: published
publisher: Cold Spring Harbor Laboratory
quality_controlled: '1'
scopus_import: '1'
status: public
title: Evolution of a transcriptional regulator from a transmembrane nucleoporin
type: journal_article
user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd
volume: 30
year: '2016'
...