Literature DB >> 24468696

Ribosome profiling: new views of translation, from single codons to genome scale.

Nicholas T Ingolia1.   

Abstract

Genome-wide analyses of gene expression have so far focused on the abundance of mRNA species as measured either by microarray or, more recently, by RNA sequencing. However, neither approach provides information on protein synthesis, which is the true end point of gene expression. Ribosome profiling is an emerging technique that uses deep sequencing to monitor in vivo translation. Studies using ribosome profiling have already provided new insights into the identity and the amount of proteins that are produced by cells, as well as detailed views into the mechanism of protein synthesis itself.

Mesh:

Substances:

Year:  2014        PMID: 24468696     DOI: 10.1038/nrg3645

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


  65 in total

Review 1.  lincRNAs: genomics, evolution, and mechanisms.

Authors:  Igor Ulitsky; David P Bartel
Journal:  Cell       Date:  2013-07-03       Impact factor: 41.582

Review 2.  Synonymous but not the same: the causes and consequences of codon bias.

Authors:  Joshua B Plotkin; Grzegorz Kudla
Journal:  Nat Rev Genet       Date:  2010-11-23       Impact factor: 53.242

3.  Assessing gene-level translational control from ribosome profiling.

Authors:  Adam B Olshen; Andrew C Hsieh; Craig R Stumpf; Richard A Olshen; Davide Ruggero; Barry S Taylor
Journal:  Bioinformatics       Date:  2013-09-18       Impact factor: 6.937

4.  Mammalian microRNAs predominantly act to decrease target mRNA levels.

Authors:  Huili Guo; Nicholas T Ingolia; Jonathan S Weissman; David P Bartel
Journal:  Nature       Date:  2010-08-12       Impact factor: 49.962

5.  Genome-wide ribosome profiling reveals complex translational regulation in response to oxidative stress.

Authors:  Maxim V Gerashchenko; Alexei V Lobanov; Vadim N Gladyshev
Journal:  Proc Natl Acad Sci U S A       Date:  2012-10-08       Impact factor: 11.205

Review 6.  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

7.  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

8.  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

9.  edgeR: a Bioconductor package for differential expression analysis of digital gene expression data.

Authors:  Mark D Robinson; Davis J McCarthy; Gordon K Smyth
Journal:  Bioinformatics       Date:  2009-11-11       Impact factor: 6.937

10.  Extensive transcriptional heterogeneity revealed by isoform profiling.

Authors:  Vicent Pelechano; Wu Wei; Lars M Steinmetz
Journal:  Nature       Date:  2013-04-24       Impact factor: 49.962

View more
  258 in total

1.  Beyond the Linear Genome: Paired-End Sequencing as a Biophysical Tool.

Authors:  Viviana I Risca; William J Greenleaf
Journal:  Trends Cell Biol       Date:  2015-10-01       Impact factor: 20.808

Review 2.  Augmented genetic decoding: global, local and temporal alterations of decoding processes and codon meaning.

Authors:  Pavel V Baranov; John F Atkins; Martina M Yordanova
Journal:  Nat Rev Genet       Date:  2015-08-11       Impact factor: 53.242

3.  The mTORC1/4E-BP pathway coordinates hemoglobin production with L-leucine availability.

Authors:  Jacky Chung; Daniel E Bauer; Alireza Ghamari; Christopher P Nizzi; Kathryn M Deck; Paul D Kingsley; Yvette Y Yien; Nicholas C Huston; Caiyong Chen; Iman J Schultz; Arthur J Dalton; Johannes G Wittig; James Palis; Stuart H Orkin; Harvey F Lodish; Richard S Eisenstein; Alan B Cantor; Barry H Paw
Journal:  Sci Signal       Date:  2015-04-14       Impact factor: 8.192

4.  Cell-type specific polysome profiling from mammalian tissues.

Authors:  Joseph Seimetz; Waqar Arif; Sushant Bangru; Mikel Hernaez; Auinash Kalsotra
Journal:  Methods       Date:  2018-11-27       Impact factor: 3.608

5.  Deciphering poxvirus gene expression by RNA sequencing and ribosome profiling.

Authors:  Zhilong Yang; Shuai Cao; Craig A Martens; Stephen F Porcella; Zhi Xie; Ming Ma; Ben Shen; Bernard Moss
Journal:  J Virol       Date:  2015-04-22       Impact factor: 5.103

6.  Reduced pachytene piRNAs and translation underlie spermiogenic arrest in Maelstrom mutant mice.

Authors:  Julio Castañeda; Pavol Genzor; Godfried W van der Heijden; Ali Sarkeshik; John R Yates; Nicholas T Ingolia; Alex Bortvin
Journal:  EMBO J       Date:  2014-07-25       Impact factor: 11.598

7.  Rationally designed, heterologous S. cerevisiae transcripts expose novel expression determinants.

Authors:  Tuval Ben-Yehezkel; Shimshi Atar; Hadas Zur; Alon Diament; Eli Goz; Tzipy Marx; Rafael Cohen; Alexandra Dana; Anna Feldman; Ehud Shapiro; Tamir Tuller
Journal:  RNA Biol       Date:  2015       Impact factor: 4.652

8.  Transcriptome-wide Interrogation of the Functional Intronome by Spliceosome Profiling.

Authors:  Weijun Chen; Jill Moore; Hakan Ozadam; Hennady P Shulha; Nicholas Rhind; Zhiping Weng; Melissa J Moore
Journal:  Cell       Date:  2018-05-03       Impact factor: 41.582

Review 9.  Probing the mechanisms underlying human diseases in making ribosomes.

Authors:  Katherine I Farley; Susan J Baserga
Journal:  Biochem Soc Trans       Date:  2016-08-15       Impact factor: 5.407

Review 10.  Proteome complexity and the forces that drive proteome imbalance.

Authors:  J Wade Harper; Eric J Bennett
Journal:  Nature       Date:  2016-09-15       Impact factor: 49.962

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.