Global analysis of Upf1 in mESCs reveals expanded scope of nonsense-mediated mRNA decay

ABSTRACT: Nonsense-mediated mRNA decay (NMD) is a conserved RNA surveillance pathway that is an important modulator of disease pathology and is required for embryonic development. Despite significant research effort, the rules that govern NMD remain incompletely understood. Here we used a combined¬ approach, integrating RNA-Seq, ribosome footprinting, and CLIP-Seq analysis of the essential NMD factor Upf1, to provide a more complete picture of the role of NMD in modulating gene expression in murine embryonic stem cells (mESCs). We show that presence of an exon-exon junction ?50 nucleotides (nt) downstream of a termination codon (dEJ) contributes to NMD independently of 3' UTR length, but has stronger effects in genes with shorter 3' UTRs. We also map translated upstream open reading frames (uORFs

ORGANISM(S): Mus musculus

SUBMITTER: Jessica Hurt 

PROVIDER: E-GEOD-41785 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress