Quality control of transcription start site selection by nonsense-mediated-mRNA decay.

Alain Jacquier,Laurence Ma,Cosmin Saveanu,Frank Feuerbach,Christophe Malabat

doi:10.7554/elife.06722

Abstract

Nonsense-mediated mRNA decay (NMD) is a translation-dependent RNA quality-control pathway targeting transcripts such as messenger RNAs harboring premature stop-codons or short upstream open reading frame (uORFs). Our transcription start sites (TSSs) analysis of Saccharomyces cerevisiae cells deficient for RNA degradation pathways revealed that about half of the pervasive transcripts are degraded by NMD, which provides a fail-safe mechanism to remove spurious transcripts that escaped degradation in the nucleus. Moreover, we found that the low specificity of RNA polymerase II TSSs selection generates, for 47% of the expressed genes, NMD-sensitive transcript isoforms carrying uORFs or starting downstream of the ATG START codon. Despite the low abundance of this last category of isoforms, their presence seems to constrain genomic sequences, as suggested by the significant bias against in-frame ATGs specifically found at the beginning of the corresponding genes and reflected by a depletion of methionines in the N-terminus of the encoded proteins.

Highlights

Recent advances in sequencing technologies led to the detection of a wealth of new RNA transcripts and revealed that eukaryotic genomes are pervasively transcribed
In the yeast S. cerevisiae, degradation-coupled transcription termination of pervasive transcripts relies on the Nrd1Nab3-Sen1 (NNS) complex, which interacts with the carboxy-terminal domain (CTD) of the RNA polymerase II (RNAPII) phosphorylated on serine 5 and triggers termination upon recognition of short sequences on the nascent RNA (Arigo et al, 2006; Thiebaut et al, 2006; Gudipati et al, 2008; Vasiljeva et al, 2008; Schulz et al, 2013)
Analysis of the cumulative 5′-end read counts per nucleotide around the start codon for all protein-coding genes showed that, genome-wide, 77% (2,190,211) of the reads obtained for tobacco acid pyrophosphatase (TAP)-treated samples could be mapped within a 200 nucleotide region upstream of the start codons with a maximum at around 30 nucleotides upstream from ATGs, while only 22% mapped to the same region when this treatment was omitted (Figure 1B)

Summary

Introduction

Recent advances in sequencing technologies led to the detection of a wealth of new RNA transcripts and revealed that eukaryotic genomes are pervasively transcribed. In the yeast S. cerevisiae, degradation-coupled transcription termination of pervasive transcripts relies on the Nrd1Nab3-Sen (NNS) complex, which interacts with the carboxy-terminal domain (CTD) of the RNA polymerase II (RNAPII) phosphorylated on serine 5 and triggers termination upon recognition of short sequences on the nascent RNA (Arigo et al, 2006; Thiebaut et al, 2006; Gudipati et al, 2008; Vasiljeva et al, 2008; Schulz et al, 2013)

Methods

Results

Conclusion