Evidence map›Paper›PMID 31329950›Full record

ArticleNucleic acids research2019

The Pol IV largest subunit CTD quantitatively affects siRNA levels guiding RNA-directed DNA methylation.

Jered M Wendte, Jeremy R Haag, Olga M Pontes, Jasleen Singh, Sara Metcalf, Craig S Pikaard

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Nucleic acids research, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing 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

5 citing papers in PubMed.

  1. The plant siRNA landscape.The Plant cell · 2024
    Review
  2. Review
  3. The epiallelic potential of transposable elements and its evolutionary significance in plants.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2021
    Review
  4. Epigenomic landscape and epigenetic regulation in maize.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020
    Review
  5. Review
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

6 authors.

Jered M WendteDepartment of Biology, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA.
Jeremy R HaagDepartment of Biology, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA.
Olga M PontesDivision of Biology and Biomedical Sciences, Washington University, St Louis, MO 63130, USA.
Jasleen SinghDepartment of Biology, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA.
Sara MetcalfDepartment of Biology, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA.
Craig S PikaardDepartment of Biology, Indiana University, 915 E. Third Street, Bloomington, IN 47405, USA.

Funding

TRAINING IN GENETICST32GM007757 · NIGMS · TRUSTEES OF INDIANA UNIVERSITY · PI KUMAR, JUSTIN P · 1985 to 2014
$8.1M
Roles of RNA Polymerases IV and V in siRNA-mediated gene silencingR01GM077590 · NIGMS · WASHINGTON UNIVERSITY · PI PIKAARD, CRAIG STUART · 2006 to 2020
$3.5M
lncRNA Processing and Function in Transcriptional Gene SilencingF31GM116346 · NIGMS · TRUSTEES OF INDIANA UNIVERSITY · PI WENDTE, JERED M · 2015 to 2016
$55k
NIGMS NIH HHS F31 GM116346NIGMS NIH HHS R01 GM077590NIGMS NIH HHS T32 GM007757
6 · The paper itself

Abstract

In plants, nuclear multisubunit RNA polymerases IV and V are RNA Polymerase II-related enzymes that synthesize non-coding RNAs for RNA-directed DNA methylation (RdDM) and transcriptional gene silencing. Here, we tested the importance of the C-terminal domain (CTD) of Pol IV's largest subunit given that the Pol II CTD mediates multiple aspects of Pol II transcription. We show that the CTD is dispensable for Pol IV catalytic activity and Pol IV termination-dependent activation of RNA-DEPENDENT RNA POLYMERASE 2, which partners with Pol IV to generate dsRNA precursors of the 24 nt siRNAs that guide RdDM. However, 24 nt siRNA levels decrease ∼80% when the CTD is deleted. RNA-dependent cytosine methylation is also reduced, but only ∼20%, suggesting that siRNA levels typically exceed the levels needed for methylation of most loci. Pol IV-dependent loci affected by loss of the CTD are primarily located in chromosome arms, similar to loci dependent CLSY1/2 or SHH1, which are proteins implicated in Pol IV recruitment. However, deletion of the CTD does not phenocopy clsy or shh1 mutants, consistent with the CTD affecting post-recruitment aspects of Pol IV activity at target loci.

Indexed as

ArabidopsisArabidopsis ProteinsCytosineDNA-Directed RNA PolymerasesDNA MethylationGene Expression Regulation, PlantGene SilencingGenetic LociHomeodomain ProteinsIntracellular Signaling Peptides and ProteinsMethyltransferasesPlants, Genetically ModifiedProtein DomainsProtein SubunitsRNA-Dependent RNA PolymeraseRNA, Small InterferingArabidopsis ProteinsCLASSY1 protein, ArabidopsisCytosineDNA-Directed RNA PolymerasesDRM2 protein, ArabidopsisHomeodomain ProteinsIntracellular Signaling Peptides and ProteinsMethyltransferasesNRPD1A protein, ArabidopsisProtein SubunitsRDR2 protein, ArabidopsisRNA-Dependent RNA PolymeraseRNA polymerase IV, ArabidopsisRNA polymerase V, ArabidopsisRNA, Small InterferingSHH1 protein, Arabidopsis

Identifiers

PMID31329950
PMCPMC6753486

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.