The RNAs of RNA-directed DNA methylation
Open accessAbstract
RNA-directed chromatin modification that includes cytosine methylation silences transposable elements in both plants and mammals, contributing to genome defense and stability. In Arabidopsis thaliana, most RNA-directed DNA methylation (RdDM) is guided by small RNAs derived from double-stranded precursors synthesized at cytosine-methylated loci by nuclear multisubunit RNA Polymerase IV (Pol IV), in close partnership with the RNA-dependent RNA polymerase, RDR2. These small RNAs help keep transposons transcriptionally inactive. However, if transposons escape silencing, and are transcribed by multisubunit RNA polymerase II (Pol II), their mRNAs can be recognized and degraded, generating small RNAs that can also guide initial DNA methylation, thereby enabling subsequent Pol IV-RDR2 recruitment. In both pathways, the small RNAs find their target sites by interacting with longer noncoding RNAs synthesized by multisubunit RNA Polymerase V (Pol V). Despite a decade of progress, numerous questions remain concerning the initiation, synthesis, processing, size and features of the RNAs that drive RdDM. Here, we review recent insights, questions and controversies concerning RNAs produced by Pols IV and V, and their functions in RdDM. We also provide new data concerning Pol V transcript 5' and 3' ends. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Plants make small RNAs from double-stranded precursors using dedicated polymerases; these RNAs target DNA methylation and H3K9 methylation machinery.
“Plants produce small RNAs derived from double-stranded precursors, which are synthesized by dedicated polymerases and target DNA methylation and the H3K9 methylation machinery 71 .”
From Advances in epigenetics link genetics to the environment and disease (2019) · cites this paper as [71]
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Sorted by citations
Advances in epigenetics link genetics to the environment and disease
Cavalli, G., & Heard, E. (2019) · Nature · doi:10.1038/s41586-019-1411-0 · Cited by 1,509 · see citing works
- Authors
- Wendte, J. M., & Pikaard, C. S.
- Affiliations
- Indiana University Bloomington (US)
- Howard Hughes Medical Institute (US)
- Corresponding author
- Pikaard, Craig S.
- Venue
- Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms
- Publisher
- Elsevier BV
- Published
- 2017-01
- Volume
- 1860
- Issue
- 1
- Pages
- 140-148
- ISSN
- 1874-9399 (ISSN-L)
- PMC
- PMC5203809
- OpenAlex
- W2510741342
- Cited by
- 140
- References
- 110
- Citations by year
- 2026: 3 · 2025: 6 · 2024: 9 · 2023: 11 · 2022: 17 · 2021: 18 · 2020: 14 · 2019: 24 · 2018: 16 · 2017: 19 · 2016: 1
- FWCI
- 1.81
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (GM077590, T32GM007757)
- National Institute of General Medical Sciences (F31GM116346)
- Gordon and Betty Moore Foundation
- Howard Hughes Medical Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
- Keywords
- RNA-directed DNA methylation, RNA polymerase IV, RNA polymerase V, RNA polymerase II, RDR2, small RNA, transposon silencing, cytosine methylation, Arabidopsis thaliana, non-coding RNA, genome defense
- MeSH terms
- Amino Acid Sequence, Chromatin, DNA-Directed RNA Polymerases, Arabidopsis, Gene Expression Regulation, Plant, RNA, Plant, DNA Methylation, Arabidopsis Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
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