---
_id: '14826'
abstract:
- lang: eng
  text: The plant-signaling molecule auxin triggers fast and slow cellular responses
    across land plants and algae. The nuclear auxin pathway mediates gene expression
    and controls growth and development in land plants, but this pathway is absent
    from algal sister groups. Several components of rapid responses have been identified
    in Arabidopsis, but it is unknown if these are part of a conserved mechanism.
    We recently identified a fast, proteome-wide phosphorylation response to auxin.
    Here, we show that this response occurs across 5 land plant and algal species
    and converges on a core group of shared targets. We found conserved rapid physiological
    responses to auxin in the same species and identified rapidly accelerated fibrosarcoma
    (RAF)-like protein kinases as central mediators of auxin-triggered phosphorylation
    across species. Genetic analysis connects this kinase to both auxin-triggered
    protein phosphorylation and rapid cellular response, thus identifying an ancient
    mechanism for fast auxin responses in the green lineage.
acknowledgement: 'We are grateful to Asuka Shitaku and Eri Koide for generating and
  sharing the Marchantia PRAF-mCitrine line and Peng-Cheng Wang for sharing the Arabidopsis
  raf mutant. We are grateful to our team members for discussions and helpful advice.
  This work was supported by funding from the Netherlands Organization for Scientific
  Research (NWO): VICI grant 865.14.001 and ENW-KLEIN OCENW.KLEIN.027 grants to D.W.;
  VENI grant VI.VENI.212.003 to A.K.; the European Research Council AdG DIRNDL (contract
  number 833867) to D.W.; CoG CATCH to J.S.; StG CELLONGATE (contract 803048) to M.F.;
  and AdG ETAP (contract 742985) to J.F.; MEXT KAKENHI grant number JP19H05675 to
  T.K.; JSPS KAKENHI grant number JP20H03275 to R.N.; Takeda Science Foundation to
  R.N.; and the Austrian Science Fund (FWF, P29988) to J.F.'
article_processing_charge: Yes (in subscription journal)
article_type: original
author:
- first_name: Andre
  full_name: Kuhn, Andre
  last_name: Kuhn
- first_name: Mark
  full_name: Roosjen, Mark
  last_name: Roosjen
- first_name: Sumanth
  full_name: Mutte, Sumanth
  last_name: Mutte
- first_name: Shiv Mani
  full_name: Dubey, Shiv Mani
  last_name: Dubey
- first_name: Vanessa Polet
  full_name: Carrillo Carrasco, Vanessa Polet
  last_name: Carrillo Carrasco
- first_name: Sjef
  full_name: Boeren, Sjef
  last_name: Boeren
- first_name: Aline
  full_name: Monzer, Aline
  id: 2DB5D88C-D7B3-11E9-B8FD-7907E6697425
  last_name: Monzer
- first_name: Jasper
  full_name: Koehorst, Jasper
  last_name: Koehorst
- first_name: Takayuki
  full_name: Kohchi, Takayuki
  last_name: Kohchi
- first_name: Ryuichi
  full_name: Nishihama, Ryuichi
  last_name: Nishihama
- first_name: Matyas
  full_name: Fendrych, Matyas
  id: 43905548-F248-11E8-B48F-1D18A9856A87
  last_name: Fendrych
  orcid: 0000-0002-9767-8699
- first_name: Joris
  full_name: Sprakel, Joris
  last_name: Sprakel
- first_name: Jiří
  full_name: Friml, Jiří
  id: 4159519E-F248-11E8-B48F-1D18A9856A87
  last_name: Friml
  orcid: 0000-0002-8302-7596
- first_name: Dolf
  full_name: Weijers, Dolf
  last_name: Weijers
citation:
  ama: Kuhn A, Roosjen M, Mutte S, et al. RAF-like protein kinases mediate a deeply
    conserved, rapid auxin response. <i>Cell</i>. 2024;187(1):130-148.e17. doi:<a
    href="https://doi.org/10.1016/j.cell.2023.11.021">10.1016/j.cell.2023.11.021</a>
  apa: Kuhn, A., Roosjen, M., Mutte, S., Dubey, S. M., Carrillo Carrasco, V. P., Boeren,
    S., … Weijers, D. (2024). RAF-like protein kinases mediate a deeply conserved,
    rapid auxin response. <i>Cell</i>. Elsevier. <a href="https://doi.org/10.1016/j.cell.2023.11.021">https://doi.org/10.1016/j.cell.2023.11.021</a>
  chicago: Kuhn, Andre, Mark Roosjen, Sumanth Mutte, Shiv Mani Dubey, Vanessa Polet
    Carrillo Carrasco, Sjef Boeren, Aline Monzer, et al. “RAF-like Protein Kinases
    Mediate a Deeply Conserved, Rapid Auxin Response.” <i>Cell</i>. Elsevier, 2024.
    <a href="https://doi.org/10.1016/j.cell.2023.11.021">https://doi.org/10.1016/j.cell.2023.11.021</a>.
  ieee: A. Kuhn <i>et al.</i>, “RAF-like protein kinases mediate a deeply conserved,
    rapid auxin response,” <i>Cell</i>, vol. 187, no. 1. Elsevier, p. 130–148.e17,
    2024.
  ista: Kuhn A, Roosjen M, Mutte S, Dubey SM, Carrillo Carrasco VP, Boeren S, Monzer
    A, Koehorst J, Kohchi T, Nishihama R, Fendrych M, Sprakel J, Friml J, Weijers
    D. 2024. RAF-like protein kinases mediate a deeply conserved, rapid auxin response.
    Cell. 187(1), 130–148.e17.
  mla: Kuhn, Andre, et al. “RAF-like Protein Kinases Mediate a Deeply Conserved, Rapid
    Auxin Response.” <i>Cell</i>, vol. 187, no. 1, Elsevier, 2024, p. 130–148.e17,
    doi:<a href="https://doi.org/10.1016/j.cell.2023.11.021">10.1016/j.cell.2023.11.021</a>.
  short: A. Kuhn, M. Roosjen, S. Mutte, S.M. Dubey, V.P. Carrillo Carrasco, S. Boeren,
    A. Monzer, J. Koehorst, T. Kohchi, R. Nishihama, M. Fendrych, J. Sprakel, J. Friml,
    D. Weijers, Cell 187 (2024) 130–148.e17.
date_created: 2024-01-17T12:45:40Z
date_published: 2024-01-04T00:00:00Z
date_updated: 2024-01-22T13:43:40Z
day: '04'
ddc:
- '580'
department:
- _id: JiFr
doi: 10.1016/j.cell.2023.11.021
ec_funded: 1
external_id:
  pmid:
  - '38128538'
file:
- access_level: open_access
  checksum: 06fd236a9ee0b46ccb05f44695bfc34b
  content_type: application/pdf
  creator: dernst
  date_created: 2024-01-22T13:41:41Z
  date_updated: 2024-01-22T13:41:41Z
  file_id: '14874'
  file_name: 2024_Cell_Kuhn.pdf
  file_size: 13194060
  relation: main_file
  success: 1
file_date_updated: 2024-01-22T13:41:41Z
has_accepted_license: '1'
intvolume: '       187'
issue: '1'
keyword:
- General Biochemistry
- Genetics and Molecular Biology
language:
- iso: eng
license: https://creativecommons.org/licenses/by-nc/4.0/
month: '01'
oa: 1
oa_version: Published Version
page: 130-148.e17
pmid: 1
project:
- _id: 261099A6-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '742985'
  name: Tracing Evolution of Auxin Transport and Polarity in Plants
- _id: 262EF96E-B435-11E9-9278-68D0E5697425
  call_identifier: FWF
  grant_number: P29988
  name: RNA-directed DNA methylation in plant development
publication: Cell
publication_identifier:
  eissn:
  - 1097-4172
  issn:
  - 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: RAF-like protein kinases mediate a deeply conserved, rapid auxin response
tmp:
  image: /images/cc_by_nc.png
  legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode
  name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)
  short: CC BY-NC (4.0)
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 187
year: '2024'
...
---
_id: '10573'
abstract:
- lang: eng
  text: How tissues acquire complex shapes is a fundamental question in biology and
    regenerative medicine. Zebrafish semicircular canals form from invaginations in
    the otic epithelium (buds) that extend and fuse to form the hubs of each canal.
    We find that conventional actomyosin-driven behaviors are not required. Instead,
    local secretion of hyaluronan, made by the enzymes uridine 5′-diphosphate dehydrogenase
    (ugdh) and hyaluronan synthase 3 (has3), drives canal morphogenesis. Charged hyaluronate
    polymers osmotically swell with water and generate isotropic extracellular pressure
    to deform the overlying epithelium into buds. The mechanical anisotropy needed
    to shape buds into tubes is conferred by a polarized distribution of actomyosin
    and E-cadherin-rich membrane tethers, which we term cytocinches. Most work on
    tissue morphogenesis ascribes actomyosin contractility as the driving force, while
    the extracellular matrix shapes tissues through differential stiffness. Our work
    inverts this expectation. Hyaluronate pressure shaped by anisotropic tissue stiffness
    may be a widespread mechanism for powering morphological change in organogenesis
    and tissue engineering.
acknowledgement: We thank Ian Swinburne, Sandy Nandagopal, and Toru Kawanishi for
  support, discussions, and reagents. We thank Vanessa Barone, Joseph Nasser, and
  members of the Megason lab for useful comments on the manuscript and general feedback.
  We are grateful to the Heisenberg and Knaut labs for transgenic fish. Diagrams on
  the right in the graphical abstract were created using BioRender. This work was
  supported by NIH R01DC015478 and NIH R01GM107733 to S.G.M. A.M. was supported by
  Human Frontiers Science Program LTF and NIH K99HD098918.
article_processing_charge: No
article_type: original
author:
- first_name: Akankshi
  full_name: Munjal, Akankshi
  last_name: Munjal
- first_name: Edouard B
  full_name: Hannezo, Edouard B
  id: 3A9DB764-F248-11E8-B48F-1D18A9856A87
  last_name: Hannezo
  orcid: 0000-0001-6005-1561
- first_name: Tony Y.C.
  full_name: Tsai, Tony Y.C.
  last_name: Tsai
- first_name: Timothy J.
  full_name: Mitchison, Timothy J.
  last_name: Mitchison
- first_name: Sean G.
  full_name: Megason, Sean G.
  last_name: Megason
citation:
  ama: Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. Extracellular hyaluronate
    pressure shaped by cellular tethers drives tissue morphogenesis. <i>Cell</i>.
    2021;184(26):6313-6325.e18. doi:<a href="https://doi.org/10.1016/j.cell.2021.11.025">10.1016/j.cell.2021.11.025</a>
  apa: Munjal, A., Hannezo, E. B., Tsai, T. Y. C., Mitchison, T. J., &#38; Megason,
    S. G. (2021). Extracellular hyaluronate pressure shaped by cellular tethers drives
    tissue morphogenesis. <i>Cell</i>. Elsevier ; Cell Press. <a href="https://doi.org/10.1016/j.cell.2021.11.025">https://doi.org/10.1016/j.cell.2021.11.025</a>
  chicago: Munjal, Akankshi, Edouard B Hannezo, Tony Y.C. Tsai, Timothy J. Mitchison,
    and Sean G. Megason. “Extracellular Hyaluronate Pressure Shaped by Cellular Tethers
    Drives Tissue Morphogenesis.” <i>Cell</i>. Elsevier ; Cell Press, 2021. <a href="https://doi.org/10.1016/j.cell.2021.11.025">https://doi.org/10.1016/j.cell.2021.11.025</a>.
  ieee: A. Munjal, E. B. Hannezo, T. Y. C. Tsai, T. J. Mitchison, and S. G. Megason,
    “Extracellular hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis,”
    <i>Cell</i>, vol. 184, no. 26. Elsevier ; Cell Press, p. 6313–6325.e18, 2021.
  ista: Munjal A, Hannezo EB, Tsai TYC, Mitchison TJ, Megason SG. 2021. Extracellular
    hyaluronate pressure shaped by cellular tethers drives tissue morphogenesis. Cell.
    184(26), 6313–6325.e18.
  mla: Munjal, Akankshi, et al. “Extracellular Hyaluronate Pressure Shaped by Cellular
    Tethers Drives Tissue Morphogenesis.” <i>Cell</i>, vol. 184, no. 26, Elsevier ;
    Cell Press, 2021, p. 6313–6325.e18, doi:<a href="https://doi.org/10.1016/j.cell.2021.11.025">10.1016/j.cell.2021.11.025</a>.
  short: A. Munjal, E.B. Hannezo, T.Y.C. Tsai, T.J. Mitchison, S.G. Megason, Cell
    184 (2021) 6313–6325.e18.
date_created: 2021-12-26T23:01:26Z
date_published: 2021-12-22T00:00:00Z
date_updated: 2023-08-17T06:28:25Z
day: '22'
department:
- _id: EdHa
doi: 10.1016/j.cell.2021.11.025
external_id:
  isi:
  - '000735387500002'
intvolume: '       184'
isi: 1
issue: '26'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://www.biorxiv.org/content/10.1101/2020.09.28.316042
month: '12'
oa: 1
oa_version: Preprint
page: 6313-6325.e18
publication: Cell
publication_identifier:
  eissn:
  - 1097-4172
  issn:
  - 0092-8674
publication_status: published
publisher: Elsevier ; Cell Press
quality_controlled: '1'
scopus_import: '1'
status: public
title: Extracellular hyaluronate pressure shaped by cellular tethers drives tissue
  morphogenesis
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 184
year: '2021'
...
---
_id: '7001'
acknowledged_ssus:
- _id: PreCl
- _id: Bio
article_processing_charge: No
article_type: original
author:
- first_name: Cornelia
  full_name: Schwayer, Cornelia
  id: 3436488C-F248-11E8-B48F-1D18A9856A87
  last_name: Schwayer
  orcid: 0000-0001-5130-2226
- first_name: Shayan
  full_name: Shamipour, Shayan
  id: 40B34FE2-F248-11E8-B48F-1D18A9856A87
  last_name: Shamipour
- first_name: Kornelija
  full_name: Pranjic-Ferscha, Kornelija
  id: 4362B3C2-F248-11E8-B48F-1D18A9856A87
  last_name: Pranjic-Ferscha
- first_name: Alexandra
  full_name: Schauer, Alexandra
  id: 30A536BA-F248-11E8-B48F-1D18A9856A87
  last_name: Schauer
  orcid: 0000-0001-7659-9142
- first_name: M
  full_name: Balda, M
  last_name: Balda
- first_name: M
  full_name: Tada, M
  last_name: Tada
- first_name: K
  full_name: Matter, K
  last_name: Matter
- first_name: Carl-Philipp J
  full_name: Heisenberg, Carl-Philipp J
  id: 39427864-F248-11E8-B48F-1D18A9856A87
  last_name: Heisenberg
  orcid: 0000-0002-0912-4566
citation:
  ama: Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight
    junctions depends on ZO-1 phase separation and flow. <i>Cell</i>. 2019;179(4):937-952.e18.
    doi:<a href="https://doi.org/10.1016/j.cell.2019.10.006">10.1016/j.cell.2019.10.006</a>
  apa: Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada,
    M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends
    on ZO-1 phase separation and flow. <i>Cell</i>. Cell Press. <a href="https://doi.org/10.1016/j.cell.2019.10.006">https://doi.org/10.1016/j.cell.2019.10.006</a>
  chicago: Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra
    Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation
    of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” <i>Cell</i>. Cell
    Press, 2019. <a href="https://doi.org/10.1016/j.cell.2019.10.006">https://doi.org/10.1016/j.cell.2019.10.006</a>.
  ieee: C. Schwayer <i>et al.</i>, “Mechanosensation of tight junctions depends on
    ZO-1 phase separation and flow,” <i>Cell</i>, vol. 179, no. 4. Cell Press, p.
    937–952.e18, 2019.
  ista: Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter
    K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1
    phase separation and flow. Cell. 179(4), 937–952.e18.
  mla: Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on
    ZO-1 Phase Separation and Flow.” <i>Cell</i>, vol. 179, no. 4, Cell Press, 2019,
    p. 937–952.e18, doi:<a href="https://doi.org/10.1016/j.cell.2019.10.006">10.1016/j.cell.2019.10.006</a>.
  short: C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada,
    K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18.
date_created: 2019-11-12T12:51:06Z
date_published: 2019-10-31T00:00:00Z
date_updated: 2024-03-25T23:30:21Z
day: '31'
ddc:
- '570'
department:
- _id: CaHe
- _id: BjHo
doi: 10.1016/j.cell.2019.10.006
ec_funded: 1
external_id:
  isi:
  - '000493898000012'
  pmid:
  - '31675500'
file:
- access_level: open_access
  checksum: 33dac4bb77ee630e2666e936b4d57980
  content_type: application/pdf
  creator: dernst
  date_created: 2020-10-21T07:09:45Z
  date_updated: 2020-10-21T07:09:45Z
  file_id: '8684'
  file_name: 2019_Cell_Schwayer_accepted.pdf
  file_size: 8805878
  relation: main_file
  success: 1
file_date_updated: 2020-10-21T07:09:45Z
has_accepted_license: '1'
intvolume: '       179'
isi: 1
issue: '4'
language:
- iso: eng
month: '10'
oa: 1
oa_version: Submitted Version
page: 937-952.e18
pmid: 1
project:
- _id: 260F1432-B435-11E9-9278-68D0E5697425
  call_identifier: H2020
  grant_number: '742573'
  name: Interaction and feedback between cell mechanics and fate specification in
    vertebrate gastrulation
publication: Cell
publication_identifier:
  eissn:
  - 1097-4172
  issn:
  - 0092-8674
publication_status: published
publisher: Cell Press
quality_controlled: '1'
related_material:
  link:
  - description: News auf IST Website
    relation: press_release
    url: https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/
  record:
  - id: '7186'
    relation: dissertation_contains
    status: public
  - id: '8350'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: Mechanosensation of tight junctions depends on ZO-1 phase separation and flow
type: journal_article
user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8
volume: 179
year: '2019'
...
---
_id: '6877'
article_processing_charge: No
article_type: original
author:
- first_name: Aglaja
  full_name: Kopf, Aglaja
  id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87
  last_name: Kopf
  orcid: 0000-0002-2187-6656
- first_name: Michael K
  full_name: Sixt, Michael K
  id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87
  last_name: Sixt
  orcid: 0000-0002-6620-9179
citation:
  ama: Kopf A, Sixt MK. The neural crest pitches in to remove apoptotic debris. <i>Cell</i>.
    2019;179(1):51-53. doi:<a href="https://doi.org/10.1016/j.cell.2019.08.047">10.1016/j.cell.2019.08.047</a>
  apa: Kopf, A., &#38; Sixt, M. K. (2019). The neural crest pitches in to remove apoptotic
    debris. <i>Cell</i>. Elsevier. <a href="https://doi.org/10.1016/j.cell.2019.08.047">https://doi.org/10.1016/j.cell.2019.08.047</a>
  chicago: Kopf, Aglaja, and Michael K Sixt. “The Neural Crest Pitches in to Remove
    Apoptotic Debris.” <i>Cell</i>. Elsevier, 2019. <a href="https://doi.org/10.1016/j.cell.2019.08.047">https://doi.org/10.1016/j.cell.2019.08.047</a>.
  ieee: A. Kopf and M. K. Sixt, “The neural crest pitches in to remove apoptotic debris,”
    <i>Cell</i>, vol. 179, no. 1. Elsevier, pp. 51–53, 2019.
  ista: Kopf A, Sixt MK. 2019. The neural crest pitches in to remove apoptotic debris.
    Cell. 179(1), 51–53.
  mla: Kopf, Aglaja, and Michael K. Sixt. “The Neural Crest Pitches in to Remove Apoptotic
    Debris.” <i>Cell</i>, vol. 179, no. 1, Elsevier, 2019, pp. 51–53, doi:<a href="https://doi.org/10.1016/j.cell.2019.08.047">10.1016/j.cell.2019.08.047</a>.
  short: A. Kopf, M.K. Sixt, Cell 179 (2019) 51–53.
date_created: 2019-09-15T22:00:46Z
date_published: 2019-09-19T00:00:00Z
date_updated: 2024-03-25T23:30:22Z
day: '19'
department:
- _id: MiSi
doi: 10.1016/j.cell.2019.08.047
external_id:
  isi:
  - '000486618500011'
  pmid:
  - '31539498'
intvolume: '       179'
isi: 1
issue: '1'
language:
- iso: eng
month: '09'
oa_version: None
page: 51-53
pmid: 1
publication: Cell
publication_identifier:
  eissn:
  - 1097-4172
  issn:
  - 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
related_material:
  record:
  - id: '6891'
    relation: dissertation_contains
    status: public
scopus_import: '1'
status: public
title: The neural crest pitches in to remove apoptotic debris
type: journal_article
user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87
volume: 179
year: '2019'
...
---
_id: '9458'
abstract:
- lang: eng
  text: Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes.
    Their genomes are typically depleted of CG dinucleotides because of imperfect
    repair of deaminated methylcytosines. Here, we extensively survey diverse species
    lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless
    frequently present and catalyzed by a different DNA methyltransferase family,
    Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years
    ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered
    methylation occurs at unprecedented densities and directly disfavors nucleosomes,
    contributing to nucleosome positioning between clusters. Dense methylation is
    enabled by a regime of genomic sequence evolution that enriches CG dinucleotides
    and drives the highest CG frequencies known. Species with linker methylation have
    small, transcriptionally active nuclei that approach the physical limits of chromatin
    compaction. These features constitute a previously unappreciated genome architecture,
    in which dense methylation influences nucleosome positions, likely facilitating
    nuclear processes under extreme spatial constraints.
article_processing_charge: No
article_type: original
author:
- first_name: Jason T.
  full_name: Huff, Jason T.
  last_name: Huff
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
citation:
  ama: Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome
    positioning in diverse eukaryotes. <i>Cell</i>. 2014;156(6):1286-1297. doi:<a
    href="https://doi.org/10.1016/j.cell.2014.01.029">10.1016/j.cell.2014.01.029</a>
  apa: Huff, J. T., &#38; Zilberman, D. (2014). Dnmt1-independent CG methylation contributes
    to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. Elsevier. <a href="https://doi.org/10.1016/j.cell.2014.01.029">https://doi.org/10.1016/j.cell.2014.01.029</a>
  chicago: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation
    Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>. Elsevier,
    2014. <a href="https://doi.org/10.1016/j.cell.2014.01.029">https://doi.org/10.1016/j.cell.2014.01.029</a>.
  ieee: J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes
    to nucleosome positioning in diverse eukaryotes,” <i>Cell</i>, vol. 156, no. 6.
    Elsevier, pp. 1286–1297, 2014.
  ista: Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to
    nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.
  mla: Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes
    to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>, vol. 156, no. 6,
    Elsevier, 2014, pp. 1286–97, doi:<a href="https://doi.org/10.1016/j.cell.2014.01.029">10.1016/j.cell.2014.01.029</a>.
  short: J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.
date_created: 2021-06-04T12:00:16Z
date_published: 2014-03-13T00:00:00Z
date_updated: 2021-12-14T08:22:36Z
day: '13'
department:
- _id: DaZi
doi: 10.1016/j.cell.2014.01.029
extern: '1'
external_id:
  pmid:
  - '24630728'
intvolume: '       156'
issue: '6'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1016/j.cell.2014.01.029
month: '03'
oa: 1
oa_version: Published Version
page: 1286-1297
pmid: 1
publication: Cell
publication_identifier:
  eissn:
  - 1097-4172
  issn:
  - 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse
  eukaryotes
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 156
year: '2014'
...
---
_id: '9459'
abstract:
- lang: eng
  text: Nucleosome remodelers of the DDM1/Lsh family are required for DNA methylation
    of transposable elements, but the reason for this is unknown. How DDM1 interacts
    with other methylation pathways, such as small-RNA-directed DNA methylation (RdDM),
    which is thought to mediate plant asymmetric methylation through DRM enzymes,
    is also unclear. Here, we show that most asymmetric methylation is facilitated
    by DDM1 and mediated by the methyltransferase CMT2 separately from RdDM. We find
    that heterochromatic sequences preferentially require DDM1 for DNA methylation
    and that this preference depends on linker histone H1. RdDM is instead inhibited
    by heterochromatin and absolutely requires the nucleosome remodeler DRD1. Together,
    DDM1 and RdDM mediate nearly all transposon methylation and collaborate to repress
    transposition and regulate the methylation and expression of genes. Our results
    indicate that DDM1 provides DNA methyltransferases access to H1-containing heterochromatin
    to allow stable silencing of transposable elements in cooperation with the RdDM
    pathway.
article_processing_charge: No
article_type: original
author:
- first_name: Assaf
  full_name: Zemach, Assaf
  last_name: Zemach
- first_name: M. Yvonne
  full_name: Kim, M. Yvonne
  last_name: Kim
- first_name: Ping-Hung
  full_name: Hsieh, Ping-Hung
  last_name: Hsieh
- first_name: Devin
  full_name: Coleman-Derr, Devin
  last_name: Coleman-Derr
- first_name: Leor
  full_name: Eshed-Williams, Leor
  last_name: Eshed-Williams
- first_name: Ka
  full_name: Thao, Ka
  last_name: Thao
- first_name: Stacey L.
  full_name: Harmer, Stacey L.
  last_name: Harmer
- first_name: Daniel
  full_name: Zilberman, Daniel
  id: 6973db13-dd5f-11ea-814e-b3e5455e9ed1
  last_name: Zilberman
  orcid: 0000-0002-0123-8649
citation:
  ama: Zemach A, Kim MY, Hsieh P-H, et al. The Arabidopsis nucleosome remodeler DDM1
    allows DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>.
    2013;153(1):193-205. doi:<a href="https://doi.org/10.1016/j.cell.2013.02.033">10.1016/j.cell.2013.02.033</a>
  apa: Zemach, A., Kim, M. Y., Hsieh, P.-H., Coleman-Derr, D., Eshed-Williams, L.,
    Thao, K., … Zilberman, D. (2013). The Arabidopsis nucleosome remodeler DDM1 allows
    DNA methyltransferases to access H1-containing heterochromatin. <i>Cell</i>. Elsevier.
    <a href="https://doi.org/10.1016/j.cell.2013.02.033">https://doi.org/10.1016/j.cell.2013.02.033</a>
  chicago: Zemach, Assaf, M. Yvonne Kim, Ping-Hung Hsieh, Devin Coleman-Derr, Leor
    Eshed-Williams, Ka Thao, Stacey L. Harmer, and Daniel Zilberman. “The Arabidopsis
    Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing
    Heterochromatin.” <i>Cell</i>. Elsevier, 2013. <a href="https://doi.org/10.1016/j.cell.2013.02.033">https://doi.org/10.1016/j.cell.2013.02.033</a>.
  ieee: A. Zemach <i>et al.</i>, “The Arabidopsis nucleosome remodeler DDM1 allows
    DNA methyltransferases to access H1-containing heterochromatin,” <i>Cell</i>,
    vol. 153, no. 1. Elsevier, pp. 193–205, 2013.
  ista: Zemach A, Kim MY, Hsieh P-H, Coleman-Derr D, Eshed-Williams L, Thao K, Harmer
    SL, Zilberman D. 2013. The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases
    to access H1-containing heterochromatin. Cell. 153(1), 193–205.
  mla: Zemach, Assaf, et al. “The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA
    Methyltransferases to Access H1-Containing Heterochromatin.” <i>Cell</i>, vol.
    153, no. 1, Elsevier, 2013, pp. 193–205, doi:<a href="https://doi.org/10.1016/j.cell.2013.02.033">10.1016/j.cell.2013.02.033</a>.
  short: A. Zemach, M.Y. Kim, P.-H. Hsieh, D. Coleman-Derr, L. Eshed-Williams, K.
    Thao, S.L. Harmer, D. Zilberman, Cell 153 (2013) 193–205.
date_created: 2021-06-04T12:23:28Z
date_published: 2013-03-28T00:00:00Z
date_updated: 2021-12-14T08:25:35Z
day: '28'
department:
- _id: DaZi
doi: 10.1016/j.cell.2013.02.033
extern: '1'
external_id:
  pmid:
  - '23540698'
intvolume: '       153'
issue: '1'
language:
- iso: eng
main_file_link:
- open_access: '1'
  url: https://doi.org/10.1016/j.cell.2013.02.033
month: '03'
oa: 1
oa_version: Published Version
page: 193-205
pmid: 1
publication: Cell
publication_identifier:
  eissn:
  - 1097-4172
  issn:
  - 0092-8674
publication_status: published
publisher: Elsevier
quality_controlled: '1'
scopus_import: '1'
status: public
title: The Arabidopsis nucleosome remodeler DDM1 allows DNA methyltransferases to
  access H1-containing heterochromatin
type: journal_article
user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9
volume: 153
year: '2013'
...