A widespread sequence-specific mRNA decay pathway mediated by hnRNPs A1 and A2/B1.

Rene Geissler,Alfred Simkin,Jürgen Scheller,Doreen Floss,Elizabeth A Fogarty,Andrew Grimson,Ravi Patel

doi:10.1101/gad.277392.116

Rene Geissler, Alfred Simkin + Show 5 more

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https://doi.org/10.1101/gad.277392.116

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Abstract

3'-untranslated regions (UTRs) specify post-transcriptional fates of mammalian messenger RNAs (mRNAs), yet knowledge of the underlying sequences and mechanisms is largely incomplete. Here, we identify two related novel 3' UTR motifs in mammals that specify transcript degradation. These motifs are interchangeable and active only within 3' UTRs, where they are often preferentially conserved; furthermore, they are found in hundreds of transcripts, many encoding regulatory proteins. We found that degradation occurs via mRNA deadenylation, mediated by the CCR4-NOT complex. We purified trans factors that recognize the motifs and identified heterogeneous nuclear ribonucleoproteins (hnRNPs) A1 and A2/B1, which are required for transcript degradation, acting in a previously unknown manner. We used RNA sequencing (RNA-seq) to confirm hnRNP A1 and A2/B1 motif-dependent roles genome-wide, profiling cells depleted of these factors singly and in combination. Interestingly, the motifs are most active within the distal portion of 3' UTRs, suggesting that their role in gene regulation can be modulated by alternative processing, resulting in shorter 3' UTRs.

Highlights

Regulation of gene expression is central to the understanding of biological systems; while transcription is the predominant stage of regulation, consequential regulation acts on the other processes that together culminate in protein synthesis
GENES & DEVELOPMENT 30:1070–1085 Published by Cold Spring Harbor Laboratory Press; ISSN 0890-9369/16; www.genesdev.org cis and trans factors are known to regulate 3′ untranslated regions (UTRs), this knowledge is far from sufficient to explain the extensive variation in messenger RNAs (mRNAs) translation and stability across the transcriptome (Matoulkova et al 2012)
For each 8-nucleotide sequence, we calculated the number of conserved instances of the 8mer within mammalian 3′ UTRs together with an estimate of the number of conserved instances that we would expect if the 8mer were evolving without selection

Summary

Introduction

Regulation of gene expression is central to the understanding of biological systems; while transcription is the predominant stage of regulation, consequential regulation acts on the other processes that together culminate in protein synthesis. The collection of post-transcriptional events that act on mature messenger RNAs (mRNAs) are governed by regulatory cis-acting sequences within the 5′ and 3′ untranslated regions (UTRs), which recruit trans factors that largely control mRNA stability, localization, and translation. Target sites for miRNAs recruit a miRNA–protein complex, which binds 3′ UTRs in a sequence-specific manner and interacts with multiple decay and translation initiation factors to trigger transcript destabilization and translational repression (Bartel 2009; Braun et al 2011; Chekulaeva et al 2011; Fukao et al 2014). 3′ UTRs themselves are not static, with alternative cleavage and polyadenylation (APA) generating shorter and longer isoforms in different cellular environments (Mayr 2015) Taken together, these observations imply that detailed mechanistic descriptions of 3′ UTR-mediated activities are a prerequisite for understanding their roles in regulatory pathways

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