Ancient Origin and Recent Innovations of RNA Polymerase IV and V

Molecular Biology and Evolution
Yi HuangRebecca A Mosher

Abstract

Small RNA-mediated chromatin modification is a conserved feature of eukaryotes. In flowering plants, the short interfering (si)RNAs that direct transcriptional silencing are abundant and subfunctionalization has led to specialized machinery responsible for synthesis and action of these small RNAs. In particular, plants possess polymerase (Pol) IV and Pol V, multi-subunit homologs of the canonical DNA-dependent RNA Pol II, as well as specialized members of the RNA-dependent RNA Polymerase (RDR), Dicer-like (DCL), and Argonaute (AGO) families. Together these enzymes are required for production and activity of Pol IV-dependent (p4-)siRNAs, which trigger RNA-directed DNA methylation (RdDM) at homologous sequences. p4-siRNAs accumulate highly in developing endosperm, a specialized tissue found only in flowering plants, and are rare in nonflowering plants, suggesting that the evolution of flowers might coincide with the emergence of specialized RdDM machinery. Through comprehensive identification of RdDM genes from species representing the breadth of the land plant phylogeny, we describe the ancient origin of Pol IV and Pol V, suggesting that a nearly complete and functional RdDM pathway could have existed in the earliest land plants...Continue Reading

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Datasets Mentioned

BETA
SRR1531151

Methods Mentioned

BETA
RNAseq
AGO hook
PCR
RNA-seq

Software Mentioned

RADAR
Cladogram
iPlant Discovery Environment
PAML
RNAseq
RAxML
Geneious
BLASTP
BLAST
PRINSEQ

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