The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

被引：721

作者：

Barbosa-Morais, Nuno L. ^{[1
,2
]}

Irimia, Manuel ^{[1
]}

Pan, Qun ^{[1
]}

Xiong, Hui Y. ^{[3
]}

Gueroussov, Serge ^{[1
,4
]}

Lee, Leo J. ^{[3
]}

Slobodeniuc, Valentina ^{[1
]}

Kutter, Claudia ^{[5
]}

Watt, Stephen ^{[5
]}

Colak, Recep ^{[1
,6
]}

Kim, TaeHyung ^{[1
,7
]}

Misquitta-Ali, Christine M. ^{[1
]}

Wilson, Michael D. ^{[4
,5
,7
]}

Kim, Philip M. ^{[1
,4
,6
]}

Odom, Duncan T. ^{[5
,8
]}

Frey, Brendan J. ^{[1
,3
]}

Blencowe, Benjamin J. ^{[1
,4
]}

机构：

[1] Univ Toronto, Donnelly Ctr, Banting & Best Dept Med Res, Toronto, ON M5S 3E1, Canada

[2] Univ Lisbon, Fac Med, Inst Mol Med, P-1649028 Lisbon, Portugal

[3] Univ Toronto, Dept Elect & Comp Engn, Toronto, ON M5S 3G4, Canada

[4] Univ Toronto, Dept Mol Genet, Toronto, ON M5S 1A8, Canada

[5] Univ Cambridge, CRUK Cambridge Inst, Cambridge CB2 0RE, England

[6] Univ Toronto, Dept Comp Sci, Toronto, ON M5S 2E4, Canada

[7] Hosp Sick Children, Toronto, ON M5G 1X8, Canada

[8] Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England

来源：

SCIENCE | 2012年 / 338卷 / 6114期

基金：

加拿大自然科学与工程研究理事会; 加拿大健康研究院;

关键词：

GENE-EXPRESSION; EXON; GENOMES; EVENTS; MOUSE; BIRTH;

D O I：

10.1126/science.1230612

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

How species with similar repertoires of protein-coding genes differ so markedly at the phenotypic level is poorly understood. By comparing organ transcriptomes from vertebrate species spanning similar to 350 million years of evolution, we observed significant differences in alternative splicing complexity between vertebrate lineages, with the highest complexity in primates. Within 6 million years, the splicing profiles of physiologically equivalent organs diverged such that they are more strongly related to the identity of a species than they are to organ type. Most vertebrate species-specific splicing patterns are cis-directed. However, a subset of pronounced splicing changes are predicted to remodel protein interactions involving trans-acting regulators. These events likely further contributed to the diversification of splicing and other transcriptomic changes that underlie phenotypic differences among vertebrate species.

引用

页码：1587 / 1593

页数：7

共 34 条

[1] Deciphering the splicing code [J].

Barash, Yoseph ;

Calarco, John A. ;

Gao, Weijun ;

Pan, Qun ;

Wang, Xinchen ;

Shai, Ofer ;

Blencowe, Benjamin J. ;

Frey, Brendan J. .

NATURE, 2010, 465 (7294) :53-59

[2] An omics perspective of protein disorder [J].

Bellay, Jeremy ;

Michaut, Magali ;

Kim, TaeHyung ;

Han, Sangjo ;

Colak, Recep ;

Myers, Chad L. ;

Kim, Philip M. .

MOLECULAR BIOSYSTEMS, 2012, 8 (01) :185-193

[3] The evolution of gene expression levels in mammalian organs [J].

Brawand, David ;

Soumillon, Magali ;

Necsulea, Anamaria ;

Julien, Philippe ;

Csardi, Gabor ;

Harrigan, Patrick ;

Weier, Manuela ;

Liechti, Angelica ;

Aximu-Petri, Ayinuer ;

Kircher, Martin ;

Albert, Frank W. ;

Zeller, Ulrich ;

Khaitovich, Philipp ;

Gruetzner, Frank ;

Bergmann, Sven ;

Nielsen, Rasmus ;

Paeaebo, Svante ;

Kaessmann, Henrik .

NATURE, 2011, 478 (7369) :343-+

[4] Conservation of an RNA regulatory map between Drosophila and mammals [J].

Brooks, Angela N. ;

Yang, Li ;

Duff, Michael O. ;

Hansen, Kasper D. ;

Park, Jung W. ;

Dudoit, Sandrine ;

Brenner, Steven E. ;

Graveley, Brenton R. .

GENOME RESEARCH, 2011, 21 (02) :193-202

[5] Tissue-Specific Splicing of Disordered Segments that Embed Binding Motifs Rewires Protein Interaction Networks [J].

Buljan, Marija ;

Chalancon, Guilhem ;

Eustermann, Sebastian ;

Wagner, Gunter P. ;

Fuxreiter, Monika ;

Bateman, Alex ;

Babu, M. Madan .

MOLECULAR CELL, 2012, 46 (06) :871-883

[6] Global analysis of alternative splicing differences between humans and chimpanzees [J].

Calarco, John A. ;

Xing, Yi ;

Caceres, Mario ;

Calarco, Joseph P. ;

Xiao, Xinshu ;

Pan, Qun ;

Lee, Christopher ;

Preuss, Todd M. ;

Blencowe, Benjamin J. .

GENES & DEVELOPMENT, 2007, 21 (22) :2963-2975

[7] Expression of 24,426 human alternative splicing events and predicted cis regulation in 48 tissues and cell lines [J].

Castle, John C. ;

Zhang, Chaolin ;

Shah, Jyoti K. ;

Kulkarni, Amit V. ;

Kalsotra, Auinash ;

Cooper, Thomas A. ;

Johnson, Jason M. .

NATURE GENETICS, 2008, 40 (12) :1416-1425

[8]

Chan Esther T., 2009, Journal of Biology (London), V8, P33, DOI 10.1186/jbiol130

[9] RNA Processing: Redrawing the Map of Charted Territory [J].

Corrionero, Anna ;

Valcarcel, Juan .

MOLECULAR CELL, 2009, 36 (06) :918-919

[10] Function and structure of inherently disordered proteins [J].

Dunker, A. Keith ;

Silman, Israel ;

Uversky, Vladimir N. ;

Sussman, Joel L. .

CURRENT OPINION IN STRUCTURAL BIOLOGY, 2008, 18 (06) :756-764

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