Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

Cell

Volumn 164, Issue 4, 2016, Pages 805-817

  Yang, Xinping ^a,b,c   Coulombe Huntington, Jasmin ^d,o   Kang, Shuli ^e,l   Sheynkman, Gloria M ^a,b   Hao, Tong ^a,b   Richardson, Aaron ^a,b   Sun, Song ^f,g,h   Yang, Fan ^f,g   Shen, Yun A ^a,b   Murray, Ryan R ^a,b,p   Spirohn, Kerstin ^a,b   Begg, Bridget E ^a,b,q   Duran Frigola, Miquel ⁱ   MacWilliams, Andrew ^a,b,r   Pevzner, Samuel J ^a,b,j,k   Zhong, Quan ^a,b,s   Wanamaker, Shelly A ^a,b,t   Tam, Stanley ^a,b   Ghamsari, Lila ^a,b,u   Sahni, Nidhi ^a,b   Yi, Song ^a,b   Rodriguez, Maria D ^a,b,v   Balcha, Dawit ^a,b   Tan, Guihong ^f   Costanzo, Michael ^f   Andrews, Brenda ^f   Boone, Charles ^f   Zhou, Xianghong J ^l   Salehi Ashtiani, Kourosh ^a,b,w   Charloteaux, Benoit ^a,b,x   Chen, Alyce A ^a,b   Calderwood, Michael A ^a,b   Aloy, Patrick ^i,m   Roth, Frederick P ^a,f,g,n   Hill, David E ^a,b   Iakoucheva, Lilia M ^e   Xia, Yu ^a,d   Vidal, Marc ^a,b   more..

^a DANA FARBER CANCER INSTITUTE   (United States)

^b HARVARD MEDICAL SCHOOL   (United States)

^c SOUTHERN MEDICAL UNIVERSITY   (China)

^d MCGILL UNIVERSITY   (Canada)

^e UNIVERSITY OF CALIFORNIA   (United States)

^f UNIVERSITY OF TORONTO   (Canada)

^g MOUNT SINAI HOSPITAL   (Canada)

^h UPPSALA UNIVERSITY   (Sweden)

ⁱ INSTITUTE FOR RESEARCH IN BIOMEDICINE   (Spain)

^j Boston University   (United States)

^k BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^l UNIVERSITY OF SOUTHERN CALIFORNIA   (United States)

^m INSTITUCIÓ CATALANA DE RECERCA I ESTUDIS AVANÇATS ICREA   (Spain)

ⁿ CANADIAN INSTITUTE FOR ADVANCED RESEARCH   (Canada)

^o INSTITUTE FOR RESEARCH IN IMMUNOLOGY AND CANCER   (Canada)

^p UNIVERSITY OF HELSINKI   (Finland)

^q MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^r Massachusetts Institute of Technology ^*  (United States)

^s WRIGHT STATE UNIVERSITY   (United States)

^t UNIVERSITY OF CALIFORNIA   (United States)

^u Cambridge Discovery Park   (United States)

^v CEDARS SINAI MEDICAL CENTER   (United States)

^w NEW YORK UNIVERSITY ABU DHABI   (United Arab Emirates)

^x UNIVERSITY OF LIÈGE   (Belgium)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ISOPROTEIN; PROTEOME;

ALTERNATIVE RNA SPLICING; ARTICLE; CELL DISRUPTION; CELL EXPANSION; DNA BINDING; EXPRESSION VECTOR; GENETIC CODE; GENETIC COMPLEMENTATION; HUMAN; LOSS OF FUNCTION MUTATION; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN DNA INTERACTION; PROTEIN FUNCTION; PROTEIN INTERACTION; PROTEIN PROTEIN INTERACTION; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; RNA SEQUENCE; STOP CODON; ANIMAL; METABOLISM; MOLECULAR CLONING; MOLECULAR EVOLUTION; MOLECULAR MODEL; PROTEIN ANALYSIS; PROTEIN DOMAIN;

ALTERNATIVE SPLICING; ANIMALS; CLONING, MOLECULAR; EVOLUTION, MOLECULAR; HUMANS; MODELS, MOLECULAR; OPEN READING FRAMES; PROTEIN INTERACTION DOMAINS AND MOTIFS; PROTEIN INTERACTION MAPS; PROTEIN ISOFORMS; PROTEOME;

EID: 84958182784     PISSN: 00928674     EISSN: 10974172     Source Type: Journal    
DOI: 10.1016/j.cell.2016.01.029     Document Type: Article

References (43)

1. N.L. Barbosa-Morais, M. Irimia, Q. Pan, H.Y. Xiong, S. Gueroussov, L.J. Lee, V. Slobodeniuc, C. Kutter, S. Watt, R. Colak, and et al. The evolutionary landscape of alternative splicing in vertebrate species Science 338 2012 1587 1593
2. B.J. Blencowe Alternative splicing: new insights from global analyses Cell 126 2006 37 47
3. M. Buljan, G. Chalancon, S. Eustermann, G.P. Wagner, M. Fuxreiter, A. Bateman, and M.M. Babu Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks Mol. Cell 46 2012 871 883
4. R. Corominas, X. Yang, G.N. Lin, S. Kang, Y. Shen, L. Ghamsari, M. Broly, M. Rodriguez, S. Tam, S.A. Trigg, and et al. Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism Nat. Commun. 5 2014 3650
5. H. Dinkel, S. Michael, R.J. Weatheritt, N.E. Davey, K. Van Roey, B. Altenberg, G. Toedt, B. Uyar, M. Seiler, A. Budd, and et al. ELM - the database of eukaryotic linear motifs Nucleic Acids Res. 40 2012 D242 D251
6. M. Dreze, D. Monachello, C. Lurin, M.E. Cusick, D.E. Hill, M. Vidal, and P. Braun High-quality binary interactome mapping Methods Enzymol. 470 2010 281 315
7. J. Eid, A. Fehr, J. Gray, K. Luong, J. Lyle, G. Otto, P. Peluso, D. Rank, P. Baybayan, B. Bettman, and et al. Real-time DNA sequencing from single polymerase molecules Science 323 2009 133 138
8. J.D. Ellis, M. Barrios-Rodiles, R. Colak, M. Irimia, T. Kim, J.A. Calarco, X. Wang, Q. Pan, D. O'Hanlon, P.M. Kim, and et al. Tissue-specific alternative splicing remodels protein-protein interaction networks Mol. Cell 46 2012 884 892
9. R.D. Finn, M. Marshall, and A. Bateman iPfam: visualization of protein-protein interactions in PDB at domain and amino acid resolutions Bioinformatics 21 2005 410 412
10. R.D. Finn, J. Clements, and S.R. Eddy HMMER web server: interactive sequence similarity searching Nucleic Acids Res. 39 2011 W29 W37
11. R.D. Finn, A. Bateman, J. Clements, P. Coggill, R.Y. Eberhardt, S.R. Eddy, A. Heger, K. Hetherington, L. Holm, J. Mistry, and et al. Pfam: the protein families database Nucleic Acids Res. 42 2014 D222 D230
12. C. Haynes, C.J. Oldfield, F. Ji, N. Klitgord, M.E. Cusick, P. Radivojac, V.N. Uversky, M. Vidal, and L.M. Iakoucheva Intrinsic disorder is a common feature of hub proteins from four eukaryotic interactomes PLoS Comput. Biol. 2 2006 e100
13. K. Inoue PLP1-related inherited dysmyelinating disorders: Pelizaeus-Merzbacher disease and spastic paraplegia type 2 Neurogenetics 6 2005 1 16
14. S. Jones, M. Stewart, A. Michie, M.B. Swindells, C. Orengo, and J.M. Thornton Domain assignment for protein structures using a consensus approach: characterization and analysis Protein Sci. 7 1998 233 242
15. A.H. Kachroo, J.M. Laurent, C.M. Yellman, A.G. Meyer, C.O. Wilke, and E.M. Marcotte Evolution. Systematic humanization of yeast genes reveals conserved functions and genetic modularity Science 348 2015 921 925
16. O. Kelemen, P. Convertini, Z. Zhang, Y. Wen, M. Shen, M. Falaleeva, and S. Stamm Function of alternative splicing Gene 514 2013 1 30
17. P. Lamesch, N. Li, S. Milstein, C. Fan, T. Hao, G. Szabo, Z. Hu, K. Venkatesan, G. Bethel, P. Martin, and et al. hORFeome v3.1: A resource of human open reading frames representing over 10,000 human genes Genomics 89 2007 307 315
18. B. Li, and C.N. Dewey RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome BMC Bioinformatics 12 2011 323
19. J. Merkin, C. Russell, P. Chen, and C.B. Burge Evolutionary dynamics of gene and isoform regulation in Mammalian tissues Science 338 2012 1593 1599
20. R. Mosca, A. Céol, and P. Aloy Interactome3D: adding structural details to protein networks Nat. Methods 10 2013 47 53
21. R. Mosca, A. Céol, A. Stein, R. Olivella, and P. Aloy 3did: A catalog of domain-based interactions of known three-dimensional structure Nucleic Acids Res. 42 2014 D374 D379
22. V. Neduva, and R.B. Russell DILIMOT: discovery of linear motifs in proteins Nucleic Acids Res. 34 2006 W350 W355
23. Q. Pan, O. Shai, L.J. Lee, B.J. Frey, and B.J. Blencowe Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing Nat. Genet. 40 2008 1413 1415
24. R. Pollitt, R. McMahon, J. Nunn, R. Bamford, A. Afifi, N. Bishop, and A. Dalton Mutation analysis of COL1A1 and COL1A2 in patients diagnosed with osteogenesis imperfecta type I-IV Hum. Mutat. 27 2006 716
25. M.L. Raff, W.J. Craigen, L.T. Smith, D.R. Keene, and P.H. Byers Partial COL1A2 gene duplication produces features of osteogenesis imperfecta and Ehlers-Danlos syndrome type VII Hum. Genet. 106 2000 19 28
26. A.P. Rideau, C. Gooding, P.J. Simpson, T.P. Monie, M. Lorenz, S. Hüttelmaier, R.H. Singer, S. Matthews, S. Curry, and C.W. Smith A peptide motif in Raver1 mediates splicing repression by interaction with the PTB RRM2 domain Nat. Struct. Mol. Biol. 13 2006 839 848
27. T. Rolland, M. Taşan, B. Charloteaux, S.J. Pevzner, Q. Zhong, N. Sahni, S. Yi, I. Lemmens, C. Fontanillo, R. Mosca, and et al. A proteome-scale map of the human interactome network Cell 159 2014 1212 1226
28. P.R. Romero, S. Zaidi, Y.Y. Fang, V.N. Uversky, P. Radivojac, C.J. Oldfield, M.S. Cortese, M. Sickmeier, T. LeGall, Z. Obradovic, and A.K. Dunker Alternative splicing in concert with protein intrinsic disorder enables increased functional diversity in multicellular organisms Proc. Natl. Acad. Sci. USA 103 2006 8390 8395
29. J.-F. Rual, K. Venkatesan, T. Hao, T. Hirozane-Kishikawa, A. Dricot, N. Li, G.F. Berriz, F.D. Gibbons, M. Dreze, N. Ayivi-Guedehoussou, and et al. Towards a proteome-scale map of the human protein-protein interaction network Nature 437 2005 1173 1178
30. M. Safran, I. Dalah, J. Alexander, N. Rosen, T. Iny Stein, M. Shmoish, N. Nativ, I. Bahir, T. Doniger, H. Krug, and et al. GeneCards Version 3: the human gene integrator Database (Oxford) 2010 2010 baq020
31. K. Salehi-Ashtiani, X. Yang, A. Derti, W. Tian, T. Hao, C. Lin, K. Makowski, L. Shen, R.R. Murray, D. Szeto, and et al. Isoform discovery by targeted cloning, 'deep-well' pooling and parallel sequencing Nat. Methods 5 2008 597 600
32. C. Schwerk, and K. Schulze-Osthoff Regulation of apoptosis by alternative pre-mRNA splicing Mol. Cell 19 2005 1 13
33. D. Sharon, H. Tilgner, F. Grubert, and M. Snyder A single-molecule long-read survey of the human transcriptome Nat. Biotechnol. 31 2013 1009 1014
34. L.M. Smith, N.L. Kelleher Consortium for Top Down Proteomics Proteoform: A single term describing protein complexity Nat. Methods 10 2013 186 187
35. G. Temple, D.S. Gerhard, R. Rasooly, E.A. Feingold, P.J. Good, C. Robinson, A. Mandich, J.G. Derge, J. Lewis, D. Shoaf, et al. MGC Project Team The completion of the Mammalian Gene Collection (MGC) Genome Res. 19 2009 2324 2333
36. H. Tilgner, F. Jahanbani, T. Blauwkamp, A. Moshrefi, E. Jaeger, F. Chen, I. Harel, C.D. Bustamante, M. Rasmussen, and M.P. Snyder Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events Nat. Biotechnol. 33 2015 736 742
37. J.C. Tran, L. Zamdborg, D.R. Ahlf, J.E. Lee, A.D. Catherman, K.R. Durbin, J.D. Tipton, A. Vellaichamy, J.F. Kellie, M. Li, and et al. Mapping intact protein isoforms in discovery mode using top-down proteomics Nature 480 2011 254 258
38. K. Venkatesan, J.-F. Rual, A. Vazquez, U. Stelzl, I. Lemmens, T. Hirozane-Kishikawa, T. Hao, M. Zenkner, X. Xin, K.I. Goh, and et al. An empirical framework for binary interactome mapping Nat. Methods 6 2009 83 90
39. M. Vidal, M.E. Cusick, and A.-L. Barabási Interactome networks and human disease Cell 144 2011 986 998
40. A.J. Walhout, G.F. Temple, M.A. Brasch, J.L. Hartley, M.A. Lorson, S. van den Heuvel, and M. Vidal GATEWAY recombinational cloning: application to the cloning of large numbers of open reading frames or ORFeomes Methods Enzymol. 328 2000 575 592
41. E.T. Wang, R. Sandberg, S. Luo, I. Khrebtukova, L. Zhang, C. Mayr, S.F. Kingsmore, G.P. Schroth, and C.B. Burge Alternative isoform regulation in human tissue transcriptomes Nature 456 2008 470 476
42. W.M. Wojtowicz, W. Wu, I. Andre, B. Qian, D. Baker, and S.L. Zipursky A vast repertoire of Dscam binding specificities arises from modular interactions of variable Ig domains Cell 130 2007 1134 1145
43. S. Yellaboina, A. Tasneem, D.V. Zaykin, B. Raghavachari, and R. Jothi DOMINE: A comprehensive collection of known and predicted domain-domain interactions Nucleic Acids Res. 39 2011 D730 D735