PT - JOURNAL ARTICLE AU - Anil Raj AU - Sidney H. Wang AU - Heejung Shim AU - Arbel Harpak AU - Yang I. Li AU - Brett Englemann AU - Matthew Stephens AU - Yoav Gilad AU - Jonathan K. Pritchard TI - Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling AID - 10.1101/031617 DP - 2015 Jan 01 TA - bioRxiv PG - 031617 4099 - http://biorxiv.org/content/early/2015/11/25/031617.short 4100 - http://biorxiv.org/content/early/2015/11/25/031617.full AB - Accurate annotation of protein coding regions is essential for understanding how genetic information is translated into biological functions. Here we describe riboHMM, a new method that uses ribosome footprint data along with gene expression and sequence information to accurately infer translated sequences. We applied our method to human lymphoblastoid cell lines and identified 7,273 previously unannotated coding sequences, including 2,442 translated upstream open reading frames. We observed an enrichment of harringtonine-treated ribosome footprints at the inferred initiation sites, validating many of the novel coding sequences. The novel sequences exhibit significant signatures of selective constraint in the reading frames of the inferred proteins, suggesting that many of these are functional. Nearly 40% of bicistronic transcripts showed significant negative correlation in the levels of translation of their two coding sequences, suggesting a key regulatory role for these novel translated sequences. Our work significantly expands the set of known coding regions in humans.