Raj et al. 2015 (PRJNA303958)

General Details

Title Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling.
Organism
Number of Samples 2
Release Date 2015/11/22 00:00
Sequencing Types
Protocol Details

Study Links

Repository Details

SRA SRP066598
ENA SRP066598
GEO GSE75290
BioProject PRJNA303958

Publication

Title
Authors Raj A,Wang SH,Shim H,Harpak A,Li YI,Engelmann B,Stephens M,Gilad Y,Pritchard JK
Journal eLife
Publication Date 2016 May 27
Abstract Accurate annotation of protein coding regions is essential for understanding how genetic information is translated into function. We describe riboHMM, a new method that uses ribosome footprint data to accurately infer translated sequences. Applying riboHMM to human lymphoblastoid cell lines, we identified 7273 novel coding sequences, including 2442 translated upstream open reading frames. We observed an enrichment of footprints at inferred initiation sites after drug-induced arrest of translation initiation, validating many of the novel coding sequences. The novel proteins exhibit significant selective constraint in the inferred reading frames, suggesting that many are functional. Moreover, ~40% of bicistronic transcripts showed negative correlation in the translation levels of their two coding sequences, suggesting a potential regulatory role for these novel regions. Despite known limitations of mass spectrometry to detect protein expressed at low level, we estimated a 14% validation rate. Our work significantly expands the set of known coding regions in humans.
PMC PMC4940163
PMID 27232982
DOI
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)
SRR2954800 PRJNA303958 Homo sapiens GM19204 Ribo-Seq
SRR2954801 PRJNA303958 Homo sapiens GM19238 Ribo-Seq
Run Accession Study Accession Scientific Name Cell Line Library Type Treatment GWIPS-viz Trips-Viz Reads BAM BigWig (F) BigWig (R)

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