Literature DB >> 24514441

Emerging evidence for functional peptides encoded by short open reading frames.

Shea J Andrews1, Joseph A Rothnagel1.   

Abstract

Short open reading frames (sORFs) are a common feature of all genomes, but their coding potential has mostly been disregarded, partly because of the difficulty in determining whether these sequences are translated. Recent innovations in computing, proteomics and high-throughput analyses of translation start sites have begun to address this challenge and have identified hundreds of putative coding sORFs. The translation of some of these has been confirmed, although the contribution of their peptide products to cellular functions remains largely unknown. This Review examines this hitherto overlooked component of the proteome and considers potential roles for sORF-encoded peptides.

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Year:  2014        PMID: 24514441     DOI: 10.1038/nrg3520

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  120 in total

1.  Polyamine regulation of ribosome pausing at the upstream open reading frame of S-adenosylmethionine decarboxylase.

Authors:  G L Law; A Raney; C Heusner; D R Morris
Journal:  J Biol Chem       Date:  2001-08-06       Impact factor: 5.157

Review 2.  Nature, nurture, or chance: stochastic gene expression and its consequences.

Authors:  Arjun Raj; Alexander van Oudenaarden
Journal:  Cell       Date:  2008-10-17       Impact factor: 41.582

3.  Drosophila Pgc protein inhibits P-TEFb recruitment to chromatin in primordial germ cells.

Authors:  Kazuko Hanyu-Nakamura; Hiroko Sonobe-Nojima; Akie Tanigawa; Paul Lasko; Akira Nakamura
Journal:  Nature       Date:  2008-01-16       Impact factor: 49.962

4.  Thrombopoietin production is inhibited by a translational mechanism.

Authors:  N Ghilardi; A Wiestner; R C Skoda
Journal:  Blood       Date:  1998-12-01       Impact factor: 22.113

Review 5.  RNA-Seq: a revolutionary tool for transcriptomics.

Authors:  Zhong Wang; Mark Gerstein; Michael Snyder
Journal:  Nat Rev Genet       Date:  2009-01       Impact factor: 53.242

6.  Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling.

Authors:  Nicholas T Ingolia; Sina Ghaemmaghami; John R S Newman; Jonathan S Weissman
Journal:  Science       Date:  2009-02-12       Impact factor: 47.728

7.  Observation of dually decoded regions of the human genome using ribosome profiling data.

Authors:  Audrey M Michel; Kingshuk Roy Choudhury; Andrew E Firth; Nicholas T Ingolia; John F Atkins; Pavel V Baranov
Journal:  Genome Res       Date:  2012-05-16       Impact factor: 9.043

8.  The reality of pervasive transcription.

Authors:  Michael B Clark; Paulo P Amaral; Felix J Schlesinger; Marcel E Dinger; Ryan J Taft; John L Rinn; Chris P Ponting; Peter F Stadler; Kevin V Morris; Antonin Morillon; Joel S Rozowsky; Mark B Gerstein; Claes Wahlestedt; Yoshihide Hayashizaki; Piero Carninci; Thomas R Gingeras; John S Mattick
Journal:  PLoS Biol       Date:  2011-07-12       Impact factor: 8.029

9.  Identification of novel conserved peptide uORF homology groups in Arabidopsis and rice reveals ancient eukaryotic origin of select groups and preferential association with transcription factor-encoding genes.

Authors:  Celine A Hayden; Richard A Jorgensen
Journal:  BMC Biol       Date:  2007-07-30       Impact factor: 7.431

10.  HSPC300 and its role in neuronal connectivity.

Authors:  Abrar Qurashi; H Bahar Sahin; Pilar Carrera; Alexis Gautreau; Annette Schenck; Angela Giangrande
Journal:  Neural Dev       Date:  2007-09-25       Impact factor: 3.842

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  218 in total

Review 1.  Long non-coding RNAs in corticogenesis: deciphering the non-coding code of the brain.

Authors:  Julieta Aprea; Federico Calegari
Journal:  EMBO J       Date:  2015-10-29       Impact factor: 11.598

2.  An upstream open reading frame is essential for feedback regulation of ascorbate biosynthesis in Arabidopsis.

Authors:  William A Laing; Marcela Martínez-Sánchez; Michele A Wright; Sean M Bulley; Di Brewster; Andrew P Dare; Maysoon Rassam; Daisy Wang; Roy Storey; Richard C Macknight; Roger P Hellens
Journal:  Plant Cell       Date:  2015-02-27       Impact factor: 11.277

3.  Modulation of Shoot Phosphate Level and Growth by PHOSPHATE1 Upstream Open Reading Frame.

Authors:  Rodrigo S Reis; Jules Deforges; Tatiana Sokoloff; Yves Poirier
Journal:  Plant Physiol       Date:  2020-04-23       Impact factor: 8.340

4.  Deep transcriptome annotation enables the discovery and functional characterization of cryptic small proteins.

Authors:  Sondos Samandi; Annie V Roy; Vivian Delcourt; Jean-François Lucier; Jules Gagnon; Maxime C Beaudoin; Benoît Vanderperre; Marc-André Breton; Julie Motard; Jean-François Jacques; Mylène Brunelle; Isabelle Gagnon-Arsenault; Isabelle Fournier; Aida Ouangraoua; Darel J Hunting; Alan A Cohen; Christian R Landry; Michelle S Scott; Xavier Roucou
Journal:  Elife       Date:  2017-10-30       Impact factor: 8.140

5.  A micropeptide encoded by a putative long noncoding RNA regulates muscle performance.

Authors:  Douglas M Anderson; Kelly M Anderson; Chi-Lun Chang; Catherine A Makarewich; Benjamin R Nelson; John R McAnally; Prasad Kasaragod; John M Shelton; Jen Liou; Rhonda Bassel-Duby; Eric N Olson
Journal:  Cell       Date:  2015-01-29       Impact factor: 41.582

Review 6.  Encoding activities of non-coding RNAs.

Authors:  Yanan Pang; Chuanbin Mao; Shanrong Liu
Journal:  Theranostics       Date:  2018-03-28       Impact factor: 11.556

Review 7.  A helicase links upstream ORFs and RNA structure.

Authors:  Eckhard Jankowsky; Ulf-Peter Guenther
Journal:  Curr Genet       Date:  2018-11-27       Impact factor: 3.886

8.  Translation of small open reading frames within unannotated RNA transcripts in Saccharomyces cerevisiae.

Authors:  Jenna E Smith; Juan R Alvarez-Dominguez; Nicholas Kline; Nathan J Huynh; Sarah Geisler; Wenqian Hu; Jeff Coller; Kristian E Baker
Journal:  Cell Rep       Date:  2014-06-12       Impact factor: 9.423

9.  OCCAM: prediction of small ORFs in bacterial genomes by means of a target-decoy database approach and machine learning techniques.

Authors:  Fabio R Cerqueira; Ana Tereza Ribeiro Vasconcelos
Journal:  Database (Oxford)       Date:  2020-01-01       Impact factor: 3.451

Review 10.  Discovery and characterization of smORF-encoded bioactive polypeptides.

Authors:  Alan Saghatelian; Juan Pablo Couso
Journal:  Nat Chem Biol       Date:  2015-12       Impact factor: 15.040

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