Literature DB >> 24378600

Genomics of alternative splicing: evolution, development and pathophysiology.

Eric R Gamazon1, Barbara E Stranger.   

Abstract

Alternative splicing is a major cellular mechanism in metazoans for generating proteomic diversity. A large proportion of protein-coding genes in multicellular organisms undergo alternative splicing, and in humans, it has been estimated that nearly 90 % of protein-coding genes-much larger than expected-are subject to alternative splicing. Genomic analyses of alternative splicing have illuminated its universal role in shaping the evolution of genomes, in the control of developmental processes, and in the dynamic regulation of the transcriptome to influence phenotype. Disruption of the splicing machinery has been found to drive pathophysiology, and indeed reprogramming of aberrant splicing can provide novel approaches to the development of molecular therapy. This review focuses on the recent progress in our understanding of alternative splicing brought about by the unprecedented explosive growth of genomic data and highlights the relevance of human splicing variation on disease and therapy.

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Year:  2014        PMID: 24378600     DOI: 10.1007/s00439-013-1411-3

Source DB:  PubMed          Journal:  Hum Genet        ISSN: 0340-6717            Impact factor:   4.132


  93 in total

1.  Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.

Authors:  Lucia A Hindorff; Praveen Sethupathy; Heather A Junkins; Erin M Ramos; Jayashri P Mehta; Francis S Collins; Teri A Manolio
Journal:  Proc Natl Acad Sci U S A       Date:  2009-05-27       Impact factor: 11.205

Review 2.  Alternative polyadenylation: a twist on mRNA 3' end formation.

Authors:  Carol S Lutz
Journal:  ACS Chem Biol       Date:  2008-09-26       Impact factor: 5.100

3.  Stem cell transcriptome profiling via massive-scale mRNA sequencing.

Authors:  Nicole Cloonan; Alistair R R Forrest; Gabriel Kolle; Brooke B A Gardiner; Geoffrey J Faulkner; Mellissa K Brown; Darrin F Taylor; Anita L Steptoe; Shivangi Wani; Graeme Bethel; Alan J Robertson; Andrew C Perkins; Stephen J Bruce; Clarence C Lee; Swati S Ranade; Heather E Peckham; Jonathan M Manning; Kevin J McKernan; Sean M Grimmond
Journal:  Nat Methods       Date:  2008-05-30       Impact factor: 28.547

4.  Analysis and design of RNA sequencing experiments for identifying isoform regulation.

Authors:  Yarden Katz; Eric T Wang; Edoardo M Airoldi; Christopher B Burge
Journal:  Nat Methods       Date:  2010-11-07       Impact factor: 28.547

5.  Human QKI, a potential regulator of mRNA expression of human oligodendrocyte-related genes involved in schizophrenia.

Authors:  Karolina Aberg; Peter Saetre; Niclas Jareborg; Elena Jazin
Journal:  Proc Natl Acad Sci U S A       Date:  2006-04-25       Impact factor: 11.205

6.  Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:  Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason D Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jörg Hackermüller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; Piero Carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard M Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos E Antonarakis; Yutao Fu; Eric D Green; Ulaş Karaöz; Adam Siepel; James Taylor; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory M Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Todd A Richmond; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Gonçalo R Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George M Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Journal:  Nature       Date:  2007-06-14       Impact factor: 49.962

7.  A postnatal switch of CELF and MBNL proteins reprograms alternative splicing in the developing heart.

Authors:  Auinash Kalsotra; Xinshu Xiao; Amanda J Ward; John C Castle; Jason M Johnson; Christopher B Burge; Thomas A Cooper
Journal:  Proc Natl Acad Sci U S A       Date:  2008-12-15       Impact factor: 11.205

Review 8.  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

9.  A user's guide to the encyclopedia of DNA elements (ENCODE).

Authors: 
Journal:  PLoS Biol       Date:  2011-04-19       Impact factor: 8.029

10.  The importance of identifying alternative splicing in vertebrate genome annotation.

Authors:  Adam Frankish; Jonathan M Mudge; Mark Thomas; Jennifer Harrow
Journal:  Database (Oxford)       Date:  2012-03-20       Impact factor: 3.451

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  39 in total

1.  The intracerebral hemorrhage blood transcriptome in humans differs from the ischemic stroke and vascular risk factor control blood transcriptomes.

Authors:  Boryana Stamova; Bradley P Ander; Glen Jickling; Farah Hamade; Marc Durocher; Xinhua Zhan; Da Zhi Liu; Xiyuan Cheng; Heather Hull; Alan Yee; Kwan Ng; Natasha Shroff; Frank R Sharp
Journal:  J Cereb Blood Flow Metab       Date:  2018-04-13       Impact factor: 6.200

Review 2.  Alternative splicing as a biomarker and potential target for drug discovery.

Authors:  Kai-qin Le; Bellur S Prabhakar; Wan-jin Hong; Liang-cheng Li
Journal:  Acta Pharmacol Sin       Date:  2015-06-15       Impact factor: 6.150

3.  Ambiguous splice sites distinguish circRNA and linear splicing in the human genome.

Authors:  Roozbeh Dehghannasiri; Linda Szabo; Julia Salzman
Journal:  Bioinformatics       Date:  2019-04-15       Impact factor: 6.937

Review 4.  K-Cl cotransporter KCC2--a moonlighting protein in excitatory and inhibitory synapse development and function.

Authors:  Peter Blaesse; Tobias Schmidt
Journal:  Pflugers Arch       Date:  2014-06-10       Impact factor: 3.657

5.  Genome-Wide Analysis of Alternative Splicing Provides Insights into Stress Adaptation of the Pacific Oyster.

Authors:  Baoyu Huang; Linlin Zhang; Xueying Tang; Guofan Zhang; Li Li
Journal:  Mar Biotechnol (NY)       Date:  2016-10-22       Impact factor: 3.619

6.  A large-scale analysis of alternative splicing reveals a key role of QKI in lung cancer.

Authors:  Fernando J de Miguel; María J Pajares; Elena Martínez-Terroba; Daniel Ajona; Xabier Morales; Ravi D Sharma; Francisco J Pardo; Ana Rouzaut; Angel Rubio; Luis M Montuenga; Ruben Pio
Journal:  Mol Oncol       Date:  2016-08-09       Impact factor: 6.603

Review 7.  Genetic variants of mucins: unexplored conundrum.

Authors:  Sushil Kumar; Eric Cruz; Suhasini Joshi; Asish Patel; Rahat Jahan; Surinder K Batra; Maneesh Jain
Journal:  Carcinogenesis       Date:  2017-07-01       Impact factor: 4.944

8.  High Incidence of Somatic BAP1 alterations in sporadic malignant mesothelioma.

Authors:  Masaki Nasu; Mitsuru Emi; Sandra Pastorino; Mika Tanji; Amy Powers; Hugh Luk; Francine Baumann; Yu-An Zhang; Adi Gazdar; Shreya Kanodia; Maarit Tiirikainen; Erin Flores; Giovanni Gaudino; Michael J Becich; Harvey I Pass; Haining Yang; Michele Carbone
Journal:  J Thorac Oncol       Date:  2015-04       Impact factor: 15.609

9.  Genetics of alternative splicing evolution during sunflower domestication.

Authors:  Chris C R Smith; Silas Tittes; J Paul Mendieta; Erin Collier-Zans; Heather C Rowe; Loren H Rieseberg; Nolan C Kane
Journal:  Proc Natl Acad Sci U S A       Date:  2018-06-11       Impact factor: 11.205

10.  Improved methods for RNAseq-based alternative splicing analysis.

Authors:  Patrick Pirrotte; Nicholas J Schork; Rebecca F Halperin; Apurva Hegde; Jessica D Lang; Elizabeth A Raupach; Christophe Legendre; Winnie S Liang; Patricia M LoRusso; Aleksandar Sekulic; Jeffrey A Sosman; Jeffrey M Trent; Sampathkumar Rangasamy
Journal:  Sci Rep       Date:  2021-05-24       Impact factor: 4.996

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