Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB.

Miguel B Coelho,Eduardo Eyras,Christopher Wj Smith,Nicolás Bellora,Melis Kayikci,Martina Hallegger,Jan Attig,Julian König,Jernej Ule

doi:10.15252/embj.201489852

Abstract

Matrin3 is an RNA- and DNA-binding nuclear matrix protein found to be associated with neural and muscular degenerative diseases. A number of possible functions of Matrin3 have been suggested, but no widespread role in RNA metabolism has yet been clearly demonstrated. We identified Matrin3 by its interaction with the second RRM domain of the splicing regulator PTB. Using a combination of RNAi knockdown, transcriptome profiling and iCLIP, we find that Matrin3 is a regulator of hundreds of alternative splicing events, principally acting as a splicing repressor with only a small proportion of targeted events being co-regulated by PTB. In contrast to other splicing regulators, Matrin3 binds to an extended region within repressed exons and flanking introns with no sharply defined peaks. The identification of this clear molecular function of Matrin3 should help to clarify the molecular pathology of ALS and other diseases caused by mutations of Matrin3.

Highlights

Alternative splicing (AS) provides multi-cellular eukaryotes with a proteomic capacity that far exceeds the number of genes (Nilsen & Graveley, 2010)
PTB RRM2 was fused to GST in wild-type (WT) and Y247Q mutant form, which impairs interaction with Raver1 PRI peptides (Joshi et al, 2011) (Fig 1A), and used as bait to pull down interacting proteins from HeLa nuclear extracts
Matrin3 has long been suspected to play a role in RNA metabolism due to the presence of RNA-binding domains and its interactions with multiple other RNA-binding proteins, some with known roles in splicing regulation and other RNA processing roles (Polydorides et al, 2000; Zeitz et al, 2009; Salton et al, 2011)

Summary

Introduction

Alternative splicing (AS) provides multi-cellular eukaryotes with a proteomic capacity that far exceeds the number of genes (Nilsen & Graveley, 2010). Regulation of AS is dictated primarily by RNA-binding proteins (RBPs) that can bind to specific RNA sequence elements and which can act as either activators of repressors (Coelho & Smith, 2014). RNA-binding proteins remain the key ‘readers’ of splicing codes (Barash et al, 2010). RBPs typically have one or more RNAbinding domains, and exhibit varying degrees of specificity, usually recognizing sequence motifs of ~3–5 nt (Ray et al, 2013). While much has been learned about the action of individual RBPs binding to their cognate binding sites, the combinatorial nature of splicing regulation has led to an increased focus on the ways in which groups of regulatory proteins can act together (Barash et al, 2010; Campbell et al, 2012; Zhang et al, 2013; Cereda et al, 2014)

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Results

Conclusion