Transcriptomics,Genomics

Dataset Information

164

A High Resolution Profile of NMD Substrates in Yeast


ABSTRACT: We report a high resolution catalouge of NMD substrates using RNA-Seq. We discovered several hundred new substrates for NMD. Using published ribosome footprint profiling data, we measured ribosome densities of normal-looking NMD substrates and non-NMD substrates. NMD substrates exhibited a striking difference in normalized ribosome occupancy in wild-type and UPF1 cells. We also found that normal looking NMD substrates have higher ratio of out of frame reads, lower codon optimalites and a higher propensity to have long stretches of non-optimal codons. Overall design: Total RNA profilies of 7 different yeast strains grown in rich media.

INSTRUMENT(S): Illumina HiSeq 4000 (Saccharomyces cerevisiae)

SUBMITTER: Allan Jacobson  

PROVIDER: GSE86428 | GEO | 2016-12-02

SECONDARY ACCESSION(S): PRJNA341846

REPOSITORIES: GEO

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Publications

High-resolution profiling of NMD targets in yeast reveals translational fidelity as a basis for substrate selection.

Celik Alper A   Baker Richard R   He Feng F   Jacobson Allan A  

RNA (New York, N.Y.) 20170216 5


Nonsense-mediated mRNA decay (NMD) plays an important role in eukaryotic gene expression, yet the scope and the defining features of NMD-targeted transcripts remain elusive. To address these issues, we reevaluated the genome-wide expression of annotated transcripts in yeast cells harboring deletions of the UPF1, UPF2, or UPF3 genes. Our new RNA-seq analyses confirm previous results of microarray studies, but also uncover hundreds of new NMD-regulated transcripts that had escaped previous detecti  ...[more]

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