The 3′ processing of antisense RNAs physically links to chromatin-based transcriptional control

Xiaofeng Fang,Zhe Wu,Oleg Raitskin,Kimberly Webb,Philipp Voigt,Tiancong Lu,Martin Howard,Caroline Dean

doi:10.1073/pnas.2007268117

Xiaofeng Fang, Zhe Wu + Show 6 more

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https://doi.org/10.1073/pnas.2007268117

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Abstract

Noncoding RNA plays essential roles in transcriptional control and chromatin silencing. At Arabidopsis thaliana FLC, antisense transcription quantitatively influences transcriptional output, but the mechanism by which this occurs is still unclear. Proximal polyadenylation of the antisense transcripts by FCA, an RNA-binding protein that physically interacts with RNA 3' processing factors, reduces FLC transcription. This process genetically requires FLD, a homolog of the H3K4 demethylase LSD1. However, the mechanism linking RNA processing to FLD function had not been established. Here, we show that FLD tightly associates with LUMINIDEPENDENS (LD) and SET DOMAIN GROUP 26 (SDG26) in vivo, and, together, they prevent accumulation of monomethylated H3K4 (H3K4me1) over the FLC gene body. SDG26 interacts with the RNA 3' processing factor FY (WDR33), thus linking activities for proximal polyadenylation of the antisense transcripts to FLD/LD/SDG26-associated H3K4 demethylation. We propose this demethylation antagonizes an active transcription module, thus reducing H3K36me3 accumulation and increasing H3K27me3. Consistent with this view, we show that Polycomb Repressive Complex 2 (PRC2) silencing is genetically required by FCA to repress FLC Overall, our work provides insights into RNA-mediated chromatin silencing.

Highlights

Noncoding RNA plays essential roles in transcriptional control and chromatin silencing
Studying the quantitative transcriptional regulation of the A. thaliana floral repressor FLOWERING LOCUS C (FLC) has led us into dissection of how alternative processing of antisense transcripts regulates local chromatin environment and transcriptional output [7]
We find that dynamic interactions between RNA-binding proteins, 3′ processing factors, and the chromatin modifiers FLOWERING LOCUS D (FLD)/LD/ SET DOMAIN GROUP 26 (SDG26) result in a chromatin state associated with low transcriptional initiation and slow elongation, marked by low H3K4me1, low H3K36me3, and high H3K27me3

Summary

Introduction

Noncoding RNA plays essential roles in transcriptional control and chromatin silencing. Proximal polyadenylation of the antisense transcripts by FCA, an RNA-binding protein that physically interacts with RNA 3′ processing factors, reduces FLC transcription. This process genetically requires FLD, a homolog of the H3K4 demethylase LSD1. In a second less well understood mechanism at FLC, transcription is quantitatively regulated by COOLAIR antisense transcript processing linked to chromatin regulation This is mediated by a set of genes grouped into the autonomous floral pathway (some of which are putative equivalents of SPEN), which have widespread transcriptional functions in the Arabidopsis genome through RNA-mediated chromatin pathways [7]. The autonomous pathway component FCA is an RNA-binding protein that mediates alternative 3′ end processing of COOLAIR

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