A DCL3 dicing code within Pol IV-RDR2 transcripts diversifies the siRNA pool guiding RNA-directed DNA methylation
- Indiana University Bloomington, United States
- Howard Hughes Medical Institute, Indiana University, United States
Abstract
In plants, selfish genetic elements including retrotransposons and DNA viruses are transcriptionally silenced by RNA-directed DNA methylation. Guiding the process are short interfering RNAs (siRNAs) cut by DICER-LIKE 3 (DCL3) from double-stranded precursors of ~30 bp that are synthesized by NUCLEAR RNA POLYMERASE IV (Pol IV) and RNA-DEPENDENT RNA POLYMERASE 2 (RDR2). We show that Pol IV's choice of initiating nucleotide, RDR2's initiation 1-2 nt internal to Pol IV transcript ends and RDR2's terminal transferase activity collectively yield a code that influences which precursor end is diced and whether 24 or 23 nt siRNAs are produced. By diversifying the size, sequence, and strand specificity of siRNAs derived from a given precursor, alternative patterns of DCL3 dicing allow for maximal siRNA coverage at methylated target loci.
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All data generated or analysed during this study are included in the manuscript and supporting file; Source Data files have been provided for all figures.
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Author details
Funding
National Institutes of Health (GM077590)
- Craig S Pikaard
Howard Hughes Medical Institute (Investigator:Pikaard)
- Akihito Fukudome
- Vibhor Mishra
- Feng Wang
- Craig S Pikaard
Indiana University Foundation (Carlos O. Miller Graduate Student Fellowship)
- Andrew Loffer
- Jasleen Singh
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2022, Loffer et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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A DCL3 dicing code within Pol IV-RDR2 transcripts diversifies the siRNA pool guiding RNA-directed DNA methylation
eLife 11:e73260.
https://doi.org/10.7554/eLife.73260
