TY - JOUR TI - Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling AU - Raj, Anil AU - Wang, Sidney H AU - Shim, Heejung AU - Harpak, Arbel AU - Li, Yang I AU - Engelmann, Brett AU - Stephens, Matthew AU - Gilad, Yoav AU - Pritchard, Jonathan K A2 - Ingolia, Nicholas T VL - 5 PY - 2016 DA - 2016/05/27 SP - e13328 C1 - eLife 2016;5:e13328 DO - 10.7554/eLife.13328 UR - https://doi.org/10.7554/eLife.13328 AB - 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. KW - ribosome profiling KW - translation KW - hidden Markov models KW - upstream ORF KW - noncoding RNA JF - eLife SN - 2050-084X PB - eLife Sciences Publications, Ltd ER -