title: Thousands of novel translated open reading frames in humans inferred by ribosome footprint profiling.
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.
authors.affiliation: Department of Genetics, Stanford University, Stanford, United States.
authors.forename: Anil
authors.identifier: 0000-0003-4412-0883
authors.initials: A
authors.lastname: Raj
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.
authors.forename: Sidney H
authors.initials: SH
authors.lastname: Wang
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.
authors.forename: Heejung
authors.initials: H
authors.lastname: Shim
authors.affiliation: Department of Biology, Stanford University, Stanford, United States.
authors.forename: Arbel
authors.initials: A
authors.lastname: Harpak
authors.affiliation: Department of Genetics, Stanford University, Stanford, United States.
authors.forename: Yang I
authors.identifier: 0000-0002-0736-251X
authors.initials: YI
authors.lastname: Li
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.
authors.forename: Brett
authors.identifier: 0000-0002-9845-6668
authors.initials: B
authors.lastname: Engelmann
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.|Department of Statistics, University of Chicago, Chicago, United States.
authors.forename: Matthew
authors.initials: M
authors.lastname: Stephens
authors.affiliation: Department of Human Genetics, University of Chicago, Chicago, United States.
authors.forename: Yoav
authors.initials: Y
authors.lastname: Gilad
authors.affiliation: Department of Genetics, Stanford University, Stanford, United States.|Department of Biology, Stanford University, Stanford, United States.|Howard Hughes Medical Institute, Stanford University, Stanford, United States.
authors.forename: Jonathan K
authors.initials: JK
authors.lastname: Pritchard
mesh_terms: D002460:Cell Line; D006801:Humans; D008214:Lymphocytes / Q000502:physiology; D008967:Molecular Biology / Q000379:methods*; D016366:Open Reading Frames; D014176:Protein Biosynthesis; D012270:Ribosomes / Q000378:metabolism*
keywords: computational biology; evolutionary biology; genomics; hidden Markov models; human; noncoding RNA; ribosome profiling; systems biology; translation; upstream ORF