Interrogating the degradation pathways of unstable mRNAs with XRN1-resistant sequences.

Abstract:

:The turnover of messenger RNAs (mRNAs) is a key regulatory step of gene expression in eukaryotic cells. Due to the complexity of the mammalian degradation machinery, the contribution of decay factors to the directionality of mRNA decay is poorly understood. Here we characterize a molecular tool to interrogate mRNA turnover via the detection of XRN1-resistant decay fragments (xrFrag). Using nonsense-mediated mRNA decay (NMD) as a model pathway, we establish xrFrag analysis as a robust indicator of accelerated 5'-3' mRNA decay. In tethering assays, monitoring xrFrag accumulation allows to distinguish decapping and endocleavage activities from deadenylation. Moreover, xrFrag analysis of mRNA degradation induced by miRNAs, AU-rich elements (AREs) as well as the 3' UTRs of cytokine mRNAs reveals the contribution of 5'-3' decay and endonucleolytic cleavage. Our work uncovers formerly unrecognized modes of mRNA turnover and establishes xrFrag as a powerful tool for RNA decay analyses.

journal_name

Nat Commun

journal_title

Nature communications

authors

Boehm V,Gerbracht JV,Marx MC,Gehring NH

doi

10.1038/ncomms13691

subject

Has Abstract

pub_date

2016-12-05 00:00:00

pages

13691

issn

2041-1723

pii

ncomms13691

journal_volume

7

pub_type

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