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3' UTR length and mRNP composition determine endocleavage efficiencies at termination codons

ABSTRACT: We aimed to study the cleavage sites of nonsense-mediated mRNA decay (NMD) substrates. Therefore, we depleted the major exoribonuclease XRN1 in human cell culture, which degrades the 3' fragments generated by SMG6-mediated endonucleolytic cleavage. Different reporter mRNAs or endogenous NMD targets were investigated and the 3' fragments were cloned, amplified and subsequently subjected to high throughput sequencing.

INSTRUMENT(S): Illumina HiSeq 2500

ORGANISM(S): Homo sapiens

SUBMITTER: Volker Boehm

PROVIDER: E-MTAB-2907 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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3' UTR length and messenger ribonucleoprotein composition determine endocleavage efficiencies at termination codons.

Boehm Volker V Haberman Nejc N Ottens Franziska F Ule Jernej J Gehring Niels H NH

Cell reports 20141009 2

Nonsense-mediated mRNA decay (NMD) degrades different classes of mRNAs, including transcripts with premature termination codons (PTCs). The NMD factor SMG6 initiates degradation of substrate mRNAs by endonucleolytic cleavage. Here, we aim to delineate the cascade of NMD-activating events that culminate in endocleavage. We report that long 3' UTRs elicit SMG6-mediated endonucleolytic degradation. The presence of an exon-junction complex (EJC) within the 3' UTR strongly stimulates endocleavage in ...[more]

PMID: 25310981

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