Evidence map›Paper›PMID 40579456›Full record

ArticleNature cell biology2025

REM transcription factors and GDE1 shape the DNA methylation landscape through the recruitment of RNA polymerase IV transcription complexes.

Zhongshou Wu, Yan Xue, Shuya Wang, Yuan-Hsin Shih, Zhenhui Zhong, Suhua Feng, Jonathan Draper, Allen Lu, Carsten A Hoeke, Jihui Sha and 4 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nature cell biology, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.

0numbers the graph read from it
0cells of the map it votes in
8citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

8 citing papers in PubMed.

  1. Review
  2. Article
  3. Article
  4. A fungal natural product that inhibits plant cellulose biosynthesis by disrupting cellulose synthase complexes.Proceedings of the National Academy of Sciences of the United States of America · 2026
    Article
  5. Article
  6. Article
  7. Article
  8. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors.

Zhongshou WuState Key Laboratory of Rice Biological Breeding, Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou, China.
Yan XueDepartment of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.
Shuya WangDepartment of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.
Yuan-Hsin ShihDepartment of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.
Zhenhui ZhongDepartment of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0002-8438-0375
Suhua FengDepartment of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.
Jonathan DraperDepartment of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0009-0006-1767-5735
Allen LuDepartment of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.
Carsten A HoekeDepartment of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0009-0008-2581-2319
Jihui ShaDepartment of Biological Chemistry, University of California at Los Angeles, Los Angeles, CA, USA.ORCID http://orcid.org/0000-0002-7358-1606
Lu LiDepartment of Biological Chemistry, University of California at Los Angeles, Los Angeles, CA, USA.
James WohlschlegelDepartment of Biological Chemistry, University of California at Los Angeles, Los Angeles, CA, USA.
Keqiang WuInstitute of Plant Biology, National Taiwan University, Taipei, Taiwan.ORCID http://orcid.org/0000-0002-5791-3594
Steven E JacobsenDepartment of Molecular, Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA, USA. jacobsen@ucla.edu.ORCID http://orcid.org/0000-0001-9483-138X

Funding

Epigenetic gene regulation in ArabidopsisR35GM130272 · NIGMS · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI JACOBSEN, STEVEN E · 2019 to 2023
$1.6M
Howard Hughes Medical Institute (HHMI) PJ100000343NIGMS NIH HHS R35 GM130272
6 · The paper itself

Abstract

In plants, the maintenance of DNA methylation is controlled by several self-reinforcing loops involving histone methylation and non-coding RNAs. However, how methylation is initially patterned at specific genomic loci is largely unknown. Here we describe four Arabidopsis REM transcription factors, VDD, VAL, REM12 and REM13, that recognize specific sequence regions and, together with the protein GENETICS DETERMINES EPIGENETICS1 (GDE1), recruit RNA polymerase IV transcription complexes. This targeted recruitment leads to the production of 24-nucleotide small interfering RNAs that guide DNA methylation to specific genomic sites in plant female reproductive tissues. In the absence of GDE1, polymerase IV transcription complexes are directed to loci bound by an alternative transcription factor, REM8, highlighting the role of REM transcription factors and GDE1 proteins as positional cues for epigenetic modulation. These findings establish a direct connection between sequence-specific transcription factors and the spatial regulation of siRNA production and DNA methylation, offering new insights into the genetic control of epigenetic patterning.

Indexed as

ArabidopsisArabidopsis ProteinsDNA-Directed RNA PolymerasesDNA MethylationTranscription FactorsTranscription, GeneticEpigenesis, GeneticGene Expression Regulation, PlantRNA, Small InterferingArabidopsis ProteinsDNA-Directed RNA PolymerasesRNA polymerase IV, ArabidopsisRNA, Small InterferingTranscription Factors

Identifiers

PMID40579456
PMCPMC12270911

What OpenQuestion holds

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LicenceCC BY
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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.