SWI2/SNF2 ATPase CHR2 remodels pri-miRNAs via Serrate to impede miRNA production

Abstract

Chromatin remodelling factors (CHRs) typically function to alter chromatin structure. CHRs also reside in ribonucleoprotein complexes, but little is known about their RNA-related functions. Here we show that CHR2 (also known as BRM), the ATPase subunit of the large switch/sucrose non-fermentable (SWI/SNF) complex, is a partner of the Microprocessor component Serrate (SE). CHR2 promotes the transcription of primary microRNA precursors (pri-miRNAs) while repressing miRNA accumulation in vivo. Direct interaction with SE is required for post-transcriptional inhibition of miRNA accumulation by CHR2 but not for its transcriptional activity. CHR2 can directly bind to and unwind pri-miRNAs and inhibit their processing, and this inhibition requires the remodelling and helicase activity of CHR2 in vitro and in vivo. Furthermore, the secondary structures of pri-miRNAs differed between wild-type Arabidopsis thaliana and chr2 mutants. We conclude that CHR2 accesses pri-miRNAs through SE and remodels their secondary structures, preventing downstream processing by DCL1 and HYL1. Our study uncovers pri-miRNAs as a substrate of CHR2, and an additional regulatory layer upstream of Microprocessor activity to control miRNA accumulation.

Improved TGIRT-seq methods for comprehensive transcriptome profiling with decreased adapter dimer formation and bias correction

“…An attractive feature of the TGIRT Total RNA-seq method is that it enables the comprehensive analysis of different RNA size classes in a single RNA-seq experiment, enabling applications such as comparison of mRNA codon usage with cellular tRNA levels (Bazzini et al 2016;Smith et al 2018), co-expression of small ncRNAs and mRNAs encoding components of RNP complexes (Boiven et al 2018), and analysis of tRNAs and tRNA fragments or mature, pre-, and pri-miRNA in the same RNA-seq Qin et al 2016;Burke et al 2016;Wang et al 2018). Previous work showed that the total RNA-seq protocol with TGIRT-III works well for quantitation of small RNAs down to ~60 nt (Boivin et al 2018), and the introduction of the NTT adapter in the present work substantially improves the representation of miRNAs in the datasets.…”

“…GsI-IIC RT (TGIRT-III) has been used for a variety of applications, including comprehensive profiling of whole-cell, exosomal and plasma RNAs Qin et al 2016;Shurtleff et al 2017;Boivin et al 2018); quantitative tRNA-seq based on the ability of the TGIRT enzyme to obtain full-length end-to-end reads of tRNAs with or without demethylase treatment (Shen et al 2015;Zheng et al 2015;Qin et al 2016); determination of tRNA aminoacylation levels (Evans et al 2017); high-throughput mapping of posttranscriptional modifications by distinctive patterns of misincorporation (Katibah et al 2014;Zheng et al 2015;Shen et al 2015;Shurtleff et al 2017;Li et al 2017;Safra et al 2017); identification of protein-bound RNAs by RIP-Seq or CLIP (Katibah et al 2014;Zarnegar et al 2016); and RNA-structure mapping by DMS-MaPseq (Zubradt et al 2017;Wang et al 2018) or SHAPE (Mohr et al 2018). A study comparing TGIRT-seq to benchmark TruSeq v3 datasets of rRNA depleted (ribodepleted) fragmented Universal Human Reference (UHR) RNA with External RNA Control Consortium (ERCC) spike-ins showed that TGIRT-seq: (i) better recapitulates the relative abundance of mRNAs and ERCC spike-ins; (ii) is more strand-specific;…”

Keep calm and carry on: miRNA biogenesis under stress

“…BRAHMA is the ATPase subunit of the large switch/sucrose non‐fermentable (SWI/SNF) complex, known by its broad role in the regulation of chromatin structure and transcription (reviewed in Clapier et al ., ). Recent studies have shown that BRAHMA interacts with SE and is able to alter the secondary structure of the miRNA primary transcripts, thus inhibiting their processing (Wang et al ., ). Interestingly, the interaction between BRAHMA and SE is required to modify the structure of the miRNA precursors, but it is not necessary for the transcriptional activity of BRAHMA (Wang et al ., ).…”

“…Recent studies have shown that BRAHMA interacts with SE and is able to alter the secondary structure of the miRNA primary transcripts, thus inhibiting their processing (Wang et al ., ). Interestingly, the interaction between BRAHMA and SE is required to modify the structure of the miRNA precursors, but it is not necessary for the transcriptional activity of BRAHMA (Wang et al ., ).…”

RSVdb: A comprehensive database of transcriptome RNA structure

“…This method can effectively detect the structure of mRNA in vivo at the transcriptome level. In recent years, an increasing number of studies have used this method or improved techniques, such as structure-seq, CIRS-seq, and DMS-MaPseq, to detect mRNA structures (12)(13)(14)(15)(16)(17)(18). Currently, there are several databases collecting in vivo mRNA structure information: RMDB (https://rmdb.stanford.edu/browse/), FoldAtlas (http://www.foldatlas.com/), and Structure Surfer (http://tesla.pcbi.upenn.edu/structuresurfer/) (19)(20)(21).…”