Literature DB >> 22705790

Large-scale mapping of branchpoints in human pre-mRNA transcripts in vivo.

Allison J Taggart1, Alec M DeSimone, Janice S Shih, Madeleine E Filloux, William G Fairbrother.   

Abstract

We present the first large-scale identification of lariats-the transient branched introns that are released as a byproduct of pre-mRNA splicing. The locations of the branchpoints in these introns provide insight into the early steps of splicing. From this data set, we have developed a comprehensive model of 3' splice-site selection, identified new mechanisms of alternative splicing and mapped the distribution of splicing factors around branchpoints.

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Year:  2012        PMID： 22705790      PMCID： PMC3465671          DOI： 10.1038/nsmb.2327

Source DB:  PubMed          Journal:  Nat Struct Mol Biol        ISSN： 1545-9985            Impact factor:   15.369


  20 in total

1.  Evidence for a linear search in bimolecular 3' splice site AG selection.

Authors:  S Chen; K Anderson; M J Moore
Journal:  Proc Natl Acad Sci U S A       Date:  2000-01-18       Impact factor: 11.205

2.  Multiple sequence alignment with the Clustal series of programs.

Authors:  Ramu Chenna; Hideaki Sugawara; Tadashi Koike; Rodrigo Lopez; Toby J Gibson; Desmond G Higgins; Julie D Thompson
Journal:  Nucleic Acids Res       Date:  2003-07-01       Impact factor: 16.971

3.  Sfold web server for statistical folding and rational design of nucleic acids.

Authors:  Ye Ding; Chi Yu Chan; Charles E Lawrence
Journal:  Nucleic Acids Res       Date:  2004-07-01       Impact factor: 16.971

4.  WebLogo: a sequence logo generator.

Authors:  Gavin E Crooks; Gary Hon; John-Marc Chandonia; Steven E Brenner
Journal:  Genome Res       Date:  2004-06       Impact factor: 9.043

5.  Precise branch point mapping and quantification of splicing intermediates.

Authors:  J Vogel; W R Hess; T Börner
Journal:  Nucleic Acids Res       Date:  1997-05-15       Impact factor: 16.971

6.  Scanning from an independently specified branch point defines the 3' splice site of mammalian introns.

Authors:  C W Smith; E B Porro; J G Patton; B Nadal-Ginard
Journal:  Nature       Date:  1989-11-16       Impact factor: 49.962

7.  Early commitment of yeast pre-mRNA to the spliceosome pathway.

Authors:  P Legrain; B Seraphin; M Rosbash
Journal:  Mol Cell Biol       Date:  1988-09       Impact factor: 4.272

8.  Scanning and competition between AGs are involved in 3' splice site selection in mammalian introns.

Authors:  C W Smith; T T Chu; B Nadal-Ginard
Journal:  Mol Cell Biol       Date:  1993-08       Impact factor: 4.272

9.  Human Gene Mutation Database (HGMD): 2003 update.

Authors:  Peter D Stenson; Edward V Ball; Matthew Mort; Andrew D Phillips; Jacqueline A Shiel; Nick S T Thomas; Shaun Abeysinghe; Michael Krawczak; David N Cooper
Journal:  Hum Mutat       Date:  2003-06       Impact factor: 4.878

10.  Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins.

Authors:  Stephanie C Huelga; Anthony Q Vu; Justin D Arnold; Tiffany Y Liang; Patrick P Liu; Bernice Y Yan; John Paul Donohue; Lily Shiue; Shawn Hoon; Sydney Brenner; Manuel Ares; Gene W Yeo
Journal:  Cell Rep       Date:  2012-02-23       Impact factor: 9.423
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  58 in total

1.  Genome-wide discovery of human splicing branchpoints.

Authors:  Tim R Mercer; Michael B Clark; Stacey B Andersen; Marion E Brunck; Wilfried Haerty; Joanna Crawford; Ryan J Taft; Lars K Nielsen; Marcel E Dinger; John S Mattick
Journal:  Genome Res       Date:  2015-01-05       Impact factor: 9.043

2.  Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites.

Authors:  Ying Liu; Zhongzheng Cao; Yinan Wang; Yu Guo; Ping Xu; Pengfei Yuan; Zhiheng Liu; Yuan He; Wensheng Wei
Journal:  Nat Biotechnol       Date:  2018-11-05       Impact factor: 54.908

3.  A Comprehensive Map of Intron Branchpoints and Lariat RNAs in Plants.

Authors:  Xiaotuo Zhang; Yong Zhang; Taiyun Wang; Ziwei Li; Jinping Cheng; Haoran Ge; Qi Tang; Kun Chen; Li Liu; Chenyu Lu; Junqiang Guo; Binglian Zheng; Yun Zheng
Journal:  Plant Cell       Date:  2019-03-20       Impact factor: 11.277

4.  SF1 Phosphorylation Enhances Specific Binding to U2AF65 and Reduces Binding to 3'-Splice-Site RNA.

Authors:  Rakesh Chatrikhi; Wenhua Wang; Ankit Gupta; Sarah Loerch; Alexandre Maucuer; Clara L Kielkopf
Journal:  Biophys J       Date:  2016-12-20       Impact factor: 4.033

5.  Identification of common genetic variants controlling transcript isoform variation in human whole blood.

Authors:  Xiaoling Zhang; Roby Joehanes; Brian H Chen; Tianxiao Huan; Saixia Ying; Peter J Munson; Andrew D Johnson; Daniel Levy; Christopher J O'Donnell
Journal:  Nat Genet       Date:  2015-02-16       Impact factor: 38.330

6.  Global donor and acceptor splicing site kinetics in human cells.

Authors:  Leonhard Wachutka; Livia Caizzi; Julien Gagneur; Patrick Cramer
Journal:  Elife       Date:  2019-04-26       Impact factor: 8.140

7.  Defective splicing of the RB1 transcript is the dominant cause of retinoblastomas.

Authors:  Kamil J Cygan; Rachel Soemedi; Christy L Rhine; Abraham Profeta; Eileen L Murphy; Michael F Murray; William G Fairbrother
Journal:  Hum Genet       Date:  2017-08-05       Impact factor: 4.132

8.  A Method to Predict the Structure and Stability of RNA/RNA Complexes.

Authors:  Xiaojun Xu; Shi-Jie Chen
Journal:  Methods Mol Biol       Date:  2016

9.  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

10.  Lariat sequencing in a unicellular yeast identifies regulated alternative splicing of exons that are evolutionarily conserved with humans.

Authors:  Ali R Awan; Amanda Manfredo; Jeffrey A Pleiss
Journal:  Proc Natl Acad Sci U S A       Date:  2013-07-16       Impact factor: 11.205
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