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

被引：3

作者：

Cao, Kevin ^{[1
]}

Heydary, Yasamin Hajy ^{[1
]}

Tong, Gregory ^{[1
]}

Martinez, Thomas Farid ^{[1
,2
]}

机构：

[1] Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92617 USA

[2] Univ Calif Irvine, Dept Biol Chem, Irvine, CA 92617 USA

来源：

STAR PROTOCOLS | 2023年 / 4卷 / 04期

关键词：

TRANSLATION;

D O I：

10.1016/j.xpro.2023.102649

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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

引用

页数：26

共 10 条

[1] Calviello L, 2016, NAT METHODS, V13, P165, DOI [10.1038/NMETH.3688, 10.1038/nmeth.3688]
[2] STAR: ultrafast universal RNA-seq aligner
Dobin, Alexander
Davis, Carrie A.
Schlesinger, Felix
Drenkow, Jorg
Zaleski, Chris
Jha, Sonali
Batut, Philippe
Chaisson, Mark
Gingeras, Thomas R.
[J]. BIOINFORMATICS, 2013, 29 (01) : 15 - 21
[3] Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities
Heinz, Sven
Benner, Christopher
Spann, Nathanael
Bertolino, Eric
Lin, Yin C.
Laslo, Peter
Cheng, Jason X.
Murre, Cornelis
Singh, Harinder
Glass, Christopher K.
[J]. MOLECULAR CELL, 2010, 38 (04) : 576 - 589
[4] Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling
Ingolia, Nicholas T.
Ghaemmaghami, Sina
Newman, John R. S.
Weissman, Jonathan S.
[J]. SCIENCE, 2009, 324 (5924) : 218 - 223
[5] Many lncRNAs, 5′UTRs, and pseudogenes are translated and some are likely to express functional proteins
Ji, Zhe
Song, Ruisheng
Regev, Aviv
Struhl, Kevin
[J]. ELIFE, 2015, 4
[6] The Sequence Alignment/Map format and SAMtools
Li, Heng
Handsaker, Bob
Wysoker, Alec
Fennell, Tim
Ruan, Jue
Homer, Nils
Marth, Gabor
Abecasis, Goncalo
Durbin, Richard
[J]. BIOINFORMATICS, 2009, 25 (16) : 2078 - 2079
[7] Profiling mouse brown and white adipocytes to identify metabolically relevant small ORFs and functional microproteins
Martinez, Thomas F.
Lyons-Abbott, Sally
Bookout, Angie L.
De Souza, Eduardo V.
Donaldson, Cynthia
Vaughan, Joan M.
Lau, Calvin
Abramov, Ariel
Baquero, Arian F.
Baquero, Karalee
Friedrich, Dave
Huard, Justin
Davis, Ray
Kim, Bong
Koch, Ty
Mercer, Aaron J.
Misquith, Ayesha
Murray, Sara A.
Perry, Sakara
Pino, Lindsay K.
Sanford, Christina
Simon, Alex
Zhang, Yu
Zipp, Garrett
Bizarro, Cristiano V.
Shokhirev, Maxim N.
Whittle, Andrew J.
Searle, Brian C.
MacCoss, Michael J.
Saghatelian, Alan
Barnes, Christopher A.
[J]. CELL METABOLISM, 2023, 35 (01) : 166 - +
[8] Accurate annotation of human protein-coding small open reading frames
Martinez, Thomas F.
Chu, Qian
Donaldson, Cynthia
Tan, Dan
Shokhirev, Maxim N.
Saghatelian, Alan
[J]. NATURE CHEMICAL BIOLOGY, 2020, 16 (04) : 458 - +
[9] Transcriptome-wide measurement of translation by ribosome profiling
McGlincy, Nicholas J.
Ingolia, Nicholas T.
[J]. METHODS, 2017, 126 : 112 - 129
[10] BEDTools: a flexible suite of utilities for comparing genomic features
Quinlan, Aaron R.
Hall, Ira M.
[J]. BIOINFORMATICS, 2010, 26 (06) : 841 - 842

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