Integrated workflow for discovery of microprotein-coding small open reading frames

Kevin Cao; Yasamin Hajy Heydary; Gregory Tong; Thomas Farid Martinez

doi:10.1016/j.xpro.2023.102649

Integrated workflow for discovery of microprotein-coding small open reading frames

STAR Protoc. 2023 Dec 15;4(4):102649. doi: 10.1016/j.xpro.2023.102649. Epub 2023 Oct 23.

Authors

Kevin Cao¹, Yasamin Hajy Heydary¹, Gregory Tong¹, Thomas Farid Martinez²

Affiliations

¹ Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92617, USA.
² Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, CA 92617, USA; Department of Biological Chemistry, University of California, Irvine, Irvine, CA 92617, USA. Electronic address: t.martinez@uci.edu.

Abstract

Small open reading frame (smORF)-encoded microproteins, proteins containing less than 100-150 amino acids, are an emerging class of functional biomolecules. Here, we present a protocol for identifying translated smORFs in mammalian systems genome wide. We describe steps for generation of ribosome profiling (Ribo-seq) data, in silico translation of a transcriptome assembly to create an ORF database, and computational analysis of Ribo-seq to score individual smORFs for translation. Identification of translated smORFs is the first step to studying the functions of microproteins. For complete details on the use and execution of this protocol, please refer to Martinez et al.¹.

Keywords: Bioinformatics; Cell Biology; Cell Culture; Gene Expression; Genomics; Molecular Biology; RNAseq; Sequence Analysis; Sequencing.

MeSH terms

Animals
Genome
Mammals
Micropeptides*
Open Reading Frames / genetics
Proteins* / genetics
Workflow

Substances

Micropeptides
Proteins

Grants and funding

K01 CA249038/CA/NCI NIH HHS/United States