Binding to RNA regulates Set1 function

Cell Discovery
Pierre LucianoVincent Géli

Abstract

The Set1 family of histone H3 lysine 4 (H3K4) methyltransferases is highly conserved from yeast to human. Here we show that the Set1 complex (Set1C) directly binds RNA in vitro through the regions that comprise the double RNA recognition motifs (dRRM) and N-SET domain within Set1 and its subunit Spp1. To investigate the functional relevance of RNA binding, we performed UV RNA crosslinking (CRAC) for Set1 and RNA polymerase II in parallel with ChIP-seq experiments. Set1 binds nascent transcripts through its dRRM. RNA binding is important to define the appropriate topology of Set1C distribution along transcription units and correlates with the efficient deposition of the H3K4me3 mark. In addition, we uncovered that Set1 binds to different classes of RNAs to levels that largely exceed the levels of binding to the general population of transcripts, suggesting the Set1 persists on these RNAs after transcription. This class includes RNAs derived from SET1, Ty1 retrotransposons, specific transcription factors genes and snRNAs (small nuclear RNAs). We propose that Set1 modulates adaptive responses, as exemplified by the post-transcriptional inhibition of Ty1 retrotransposition.

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Citations

Apr 5, 2018·Nucleic Acids Research·Beth R WattsLidia Vasiljeva
Jul 8, 2020·International Journal of Molecular Sciences·Joan Serrano-QuílezSusana Rodríguez-Navarro
Mar 3, 2019·Cells·Meagan Jezek, Erin M Green
May 3, 2020·Nature Communications·Hyun Jin BaeStephen Buratowski
Jul 25, 2018·The Journal of Cell Biology·Zsolt KarányiLóránt Székvölgyi
Jul 6, 2021·The Journal of Biological Chemistry·Ryan J Separovich, Marc R Wilkins

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Datasets Mentioned

BETA
GSE104486
GSE104485

Methods Mentioned

BETA
ChIP-seq
electrophoretic mobility shift assay
ChIP
electrophoretic
PCR
electrophoresis
Assay

Software Mentioned

Bedtools
FasQC
ngs
makeTagDirectory
HOMER
makeUCSCfile
pyCRAC
fastx
pyFastqDuplicateRemover
BedGraphs

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