Literature DB >> 33765278

Poly-A Tailing and Adaptor Ligation Methods for Ribo-Seq Library Construction.

Jingfan Qiu1, Shu-Bing Qian2.   

Abstract

Ribosome profiling is a powerful technique that enables researchers to monitor translational events across the transcriptome. It provides a snapshot of ribosome positions and density across the transcriptome at a sub-codon resolution. Here we describe the whole procedure of profiling ribosome footprints in mammalian cells. Two methods for Ribo-seq library construction are introduced, and their advantages and disadvantages are compared. There is a room for further improvement of Ribo-seq in terms of the amount of starting material, the duration of library construction, and the resolution of sequencing results.

Entities:  

Keywords:  Codon; Deep sequencing; Ribo-seq; Translation; mRNA

Mesh:

Substances:

Year:  2021        PMID: 33765278     DOI: 10.1007/978-1-0716-1150-0_10

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


  12 in total

1.  Ribosome profiling of mouse embryonic stem cells reveals the complexity and dynamics of mammalian proteomes.

Authors:  Nicholas T Ingolia; Liana F Lareau; Jonathan S Weissman
Journal:  Cell       Date:  2011-11-03       Impact factor: 41.582

Review 2.  Ribosome profiling reveals the what, when, where and how of protein synthesis.

Authors:  Gloria A Brar; Jonathan S Weissman
Journal:  Nat Rev Mol Cell Biol       Date:  2015-10-14       Impact factor: 94.444

3.  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

4.  Capture and Amplification by Tailing and Switching (CATS). An ultrasensitive ligation-independent method for generation of DNA libraries for deep sequencing from picogram amounts of DNA and RNA.

Authors:  Andrey Turchinovich; Harald Surowy; Andrius Serva; Marc Zapatka; Peter Lichter; Barbara Burwinkel
Journal:  RNA Biol       Date:  2014-06-12       Impact factor: 4.652

5.  Cycloheximide can distort measurements of mRNA levels and translation efficiency.

Authors:  Daniel A Santos; Lei Shi; Benjamin P Tu; Jonathan S Weissman
Journal:  Nucleic Acids Res       Date:  2019-06-04       Impact factor: 16.971

6.  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

7.  Decoding human cytomegalovirus.

Authors:  Noam Stern-Ginossar; Ben Weisburd; Annette Michalski; Vu Thuy Khanh Le; Marco Y Hein; Sheng-Xiong Huang; Ming Ma; Ben Shen; Shu-Bing Qian; Hartmut Hengel; Matthias Mann; Nicholas T Ingolia; Jonathan S Weissman
Journal:  Science       Date:  2012-11-23       Impact factor: 47.728

8.  Quantitative profiling of initiating ribosomes in vivo.

Authors:  Xiangwei Gao; Ji Wan; Botao Liu; Ming Ma; Ben Shen; Shu-Bing Qian
Journal:  Nat Methods       Date:  2014-12-08       Impact factor: 28.547

9.  Translation inhibitors cause abnormalities in ribosome profiling experiments.

Authors:  Maxim V Gerashchenko; Vadim N Gladyshev
Journal:  Nucleic Acids Res       Date:  2014-07-23       Impact factor: 16.971

10.  Ligation-free ribosome profiling of cell type-specific translation in the brain.

Authors:  Nicholas Hornstein; Daniela Torres; Sohani Das Sharma; Guomei Tang; Peter Canoll; Peter A Sims
Journal:  Genome Biol       Date:  2016-07-05       Impact factor: 13.583

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