A DCL3 dicing code within Pol IV-RDR2 transcripts diversifies the siRNA pool guiding RNA-directed DNA methylation

• Published in: eLife Vol. 11
• Main Authors: Loffer, Andrew, Singh, Jasleen, Fukudome, Akihito, Mishra, Vibhor, Wang, Feng, Pikaard, Craig S
• Format: Journal Article
• Language: English
• Published: England eLife Sciences Publications Ltd 31.01.2022; eLife Sciences Publications, Ltd
• Subjects: Arabidopsis - genetics; Arabidopsis Proteins - genetics; Arabidopsis Proteins - metabolism; Biosynthesis; Chromosomes and Gene Expression; Coverage; Deoxyribonucleic acid; dicer endonuclease; dicer-like 3; DNA; DNA methylation; DNA viruses; DNA-directed RNA polymerase; Gene Expression Regulation, Plant; Genetics and Genomics; Hypotheses; Proteins; Ribonuclease III - genetics; Ribonuclease III - metabolism; RNA polymerase; RNA silencing; RNA, Small Interfering - genetics; RNA, Small Interfering - metabolism; RNA-Dependent RNA Polymerase; RNA-directed DNA methylation; RNA-directed RNA polymerase; siRNA; siRNA biogenesis; Transcription; Transcription, Genetic; dicer-like 3; genetics; A. thaliana; siRNA biogenesis; chromosomes; genomics; RNA polymerase; RNA silencing; RNA-directed DNA methylation; dicer endonuclease; gene expression
• ISSN: 2050-084X; 2050-084X
• DOI: 10.7554/elife.73260

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.