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Pervasive functional translation of noncanonical human open reading frames

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Science  06 Mar 2020:
Vol. 367, Issue 6482, pp. 1140-1146
DOI: 10.1126/science.aay0262

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Expanding the human proteome

Using mass spectrometry, ribosome profiling, and several CRISPR-based screens, Chen et al. identified hundreds of previously uncharacterized functional micropeptides in the human genome (see the Perspective by Wei and Guo). Protein translation outside of annotated open reading frames (ORFs) in messenger RNAs and within ORFs in long noncoding RNAs is pervasive. A functional screen using CRISPR-Cas9 with single-cell transcriptomics suggested critical roles for hundreds of micropeptides. Micropeptides encoded by multiple short, upstream ORFs form stable protein complexes with the downstream canonical proteins encoded on the same messenger RNAs.

Science, this issue p. 1140; see also p. 1074

Abstract

Ribosome profiling has revealed pervasive but largely uncharacterized translation outside of canonical coding sequences (CDSs). In this work, we exploit a systematic CRISPR-based screening strategy to identify hundreds of noncanonical CDSs that are essential for cellular growth and whose disruption elicits specific, robust transcriptomic and phenotypic changes in human cells. Functional characterization of the encoded microproteins reveals distinct cellular localizations, specific protein binding partners, and hundreds of microproteins that are presented by the human leukocyte antigen system. We find multiple microproteins encoded in upstream open reading frames, which form stable complexes with the main, canonical protein encoded on the same messenger RNA, thereby revealing the use of functional bicistronic operons in mammals. Together, our results point to a family of functional human microproteins that play critical and diverse cellular roles.

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