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Literature DB >> 29224064

An Integrated Polysome Profiling and Ribosome Profiling Method to Investigate In Vivo Translatome.

Abstract

Recent advances in global translatome analysis technologies enable us to understand how translational regulation of gene expression modulates cellular functions. In this chapter, we present an integrated method to measure various aspects of translatome by polysome profiling and ribosome profiling using purified B cells. We standardized our protocols to directly compare the results from these two approaches. Parallel assessment of translatome with these two approaches can generate a comprehensive picture on how translational regulation determines protein output.

Entities: CellLine Chemical Disease Gene Species

Keywords: Polysome profiling; Ribo-seq; Ribosome profiling; Translational regulation of gene expression; Translatome

Mesh：

Substances：
Proteins
RNA, Messenger

Year: 2018 PMID： 29224064 PMCID： PMC6314483 DOI： 10.1007/978-1-4939-7514-3_1

Source DB: PubMed Journal: Methods Mol Biol ISSN： 1064-3745

18 in total

1. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae.

Authors: Yoav Arava; Yulei Wang; John D Storey; Chih Long Liu; Patrick O Brown; Daniel Herschlag
Journal: Proc Natl Acad Sci U S A Date: 2003-03-26 Impact factor: 11.205

Review 2. Ribosome profiling: new views of translation, from single codons to genome scale.

Authors: Nicholas T Ingolia
Journal: Nat Rev Genet Date: 2014-01-28 Impact factor: 53.242

3. Cotranslational response to proteotoxic stress by elongation pausing of ribosomes.

Authors: Botao Liu; Yan Han; Shu-Bing Qian
Journal: Mol Cell Date: 2013-01-03 Impact factor: 17.970

4. Dom34 rescues ribosomes in 3' untranslated regions.

Authors: Nicholas R Guydosh; Rachel Green
Journal: Cell Date: 2014-02-27 Impact factor: 41.582

5. MicroRNA-17~92 plays a causative role in lymphomagenesis by coordinating multiple oncogenic pathways.

Authors: Hyun Yong Jin; Hiroyo Oda; Maoyi Lai; Rebecca L Skalsky; Kelly Bethel; Jovan Shepherd; Seung Goo Kang; Wen-Hsien Liu; Mohsen Sabouri-Ghomi; Bryan R Cullen; Klaus Rajewsky; Changchun Xiao
Journal: EMBO J Date: 2013-08-06 Impact factor: 11.598

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. A network of multiple regulatory layers shapes gene expression in fission yeast.

Authors: Daniel H Lackner; Traude H Beilharz; Samuel Marguerat; Juan Mata; Stephen Watt; Falk Schubert; Thomas Preiss; Jürg Bähler
Journal: Mol Cell Date: 2007-04-13 Impact factor: 17.970

8. Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments.

Authors: Liana F Lareau; Dustin H Hite; Gregory J Hogan; Patrick O Brown
Journal: Elife Date: 2014-05-09 Impact factor: 8.140

9. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments.

Authors: Nicholas T Ingolia; Gloria A Brar; Silvia Rouskin; Anna M McGeachy; Jonathan S Weissman
Journal: Nat Protoc Date: 2012-07-26 Impact factor: 13.491

An Integrated Polysome Profiling and Ribosome Profiling Method to Investigate In Vivo Translatome.

1. Genome-wide analysis of mRNA translation profiles in Saccharomyces cerevisiae.

Review 2. Ribosome profiling: new views of translation, from single codons to genome scale.

3. Cotranslational response to proteotoxic stress by elongation pausing of ribosomes.

4. Dom34 rescues ribosomes in 3' untranslated regions.

5. MicroRNA-17~92 plays a causative role in lymphomagenesis by coordinating multiple oncogenic pathways.

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

7. A network of multiple regulatory layers shapes gene expression in fission yeast.

8. Distinct stages of the translation elongation cycle revealed by sequencing ribosome-protected mRNA fragments.

9. The ribosome profiling strategy for monitoring translation in vivo by deep sequencing of ribosome-protected mRNA fragments.

10. Translational regulation of specific mRNAs controls feedback inhibition and survival during macrophage activation.

Review 1. The effects of codon bias and optimality on mRNA and protein regulation.

2. Translating Ribosome Affinity Purification (TRAP) of Cell Type-specific mRNA from Mouse Brain Lysates.

3. Fluorescent Polysome Profiling in Caenorhabditis elegans.

4. Polysome Profiling without Gradient Makers or Fractionation Systems.

Review 5. Non-coding RNAs in malaria infection.