E-GEOD-60095 - Ribosome Profiling Reveals Pervasive Translation Outside of Annotated Protein-Coding Genes

Status
Released on 21 August 2014, last updated on 22 August 2014
Organism
Homo sapiens, Mus musculus
Samples (4)
Protocols (3)
Description
Ribosome profiling suggests that ribosomes occupy many regions of the transcriptome thought to be non-coding, including 5' UTRs and lncRNAs. Apparent ribosome footprints outside of protein-coding regions raise the possibility of artifacts unrelated to translation, particularly when they occupy multiple, overlapping open reading frames (ORFs). Here we show hallmarks of translation in these footprints: co-purification with the large ribosomal subunit, response to drugs targeting elongation, trinucleotide periodicity, and initiation at early AUGs. We develop a metric for distinguishing between 80S footprints and nonribosomal sources using footprint size distributions, which validates the vast majority of footprints outside of coding regions. We present evidence for polypeptide production beyond annotated genes, including induction of immune responses following human cytomegalovirus (HCMV) infection. Translation is pervasive on cytosolic transcripts outside of conserved reading frames, and direct detection of this expanded universe of translated products enables efforts to understand how cells manage and exploit its consequences. Ribosome profiling to verify that true ribosome footprints shift in response to different elongation inhibitors (CHX vs Emetine) and co-purify with an affinity-tagged large ribosomal subunit (bound vs input)
Experiment types
other, RNA-seq of coding RNA 
Contacts
Gaëlle J Talhouarne, Gloria A Brar, Jonathan S Weissman, Mark R Wills, Michael S Harris, Nicholas T Ingolia, Noam Stern-Ginossar, Sarah E Jackson
MINSEQE
Exp. designProtocolsVariablesProcessedSeq. reads
Files
Investigation descriptionE-GEOD-60095.idf.txt
Sample and data relationshipE-GEOD-60095.sdrf.txt
Processed data (1)E-GEOD-60095.processed.1.zip
Links