{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T17:45:59Z","timestamp":1792172759769,"version":"4.4.0"},"reference-count":51,"publisher":"Elsevier BV","issue":"2","license":[{"start":{"date-parts":[[2012,2,1]],"date-time":"2012-02-01T00:00:00Z","timestamp":1328054400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2012,2,1]],"date-time":"2012-02-01T00:00:00Z","timestamp":1328054400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2013,7,20]],"date-time":"2013-07-20T00:00:00Z","timestamp":1374278400000},"content-version":"vor","delay-in-days":535,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc-nd\/3.0\/"}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports"],"published-print":{"date-parts":[[2012,2]]},"DOI":"10.1016\/j.celrep.2012.02.001","type":"journal-article","created":{"date-parts":[[2012,2,16]],"date-time":"2012-02-16T13:13:21Z","timestamp":1329398001000},"page":"167-178","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":455,"title":["Integrative Genome-wide Analysis Reveals Cooperative Regulation of Alternative Splicing by hnRNP Proteins"],"prefix":"10.1016","volume":"1","author":[{"given":"Stephanie\u00a0C.","family":"Huelga","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony\u00a0Q.","family":"Vu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Justin\u00a0D.","family":"Arnold","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tiffany\u00a0Y.","family":"Liang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patrick\u00a0P.","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bernice\u00a0Y.","family":"Yan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John\u00a0Paul","family":"Donohue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lily","family":"Shiue","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shawn","family":"Hoon","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sydney","family":"Brenner","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"suffix":"Jr.","given":"Manuel","family":"Ares","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gene\u00a0W.","family":"Yeo","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.celrep.2012.02.001_bib1","doi-asserted-by":"crossref","first-page":"291","DOI":"10.1146\/annurev.biochem.72.121801.161720","article-title":"Mechanisms of alternative pre-messenger RNA splicing","volume":"72","author":"Black","year":"2003","journal-title":"Annu. Rev. Biochem."},{"key":"10.1016\/j.celrep.2012.02.001_bib2","doi-asserted-by":"crossref","first-page":"1939","DOI":"10.1093\/emboj\/18.7.1939","article-title":"Modulation of exon skipping by high-affinity hnRNP A1-binding sites and by intron elements that repress splice site utilization","volume":"18","author":"Blanchette","year":"1999","journal-title":"EMBO J."},{"key":"10.1016\/j.celrep.2012.02.001_bib3","doi-asserted-by":"crossref","first-page":"438","DOI":"10.1016\/j.molcel.2009.01.022","article-title":"Genome-wide analysis of alternative pre-mRNA splicing and RNA-binding specificities of the Drosophila hnRNP A\/B family members","volume":"33","author":"Blanchette","year":"2009","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2012.02.001_bib4","doi-asserted-by":"crossref","first-page":"1197","DOI":"10.1002\/j.1460-2075.1994.tb06369.x","article-title":"RNA binding specificity of hnRNP A1: significance of hnRNP A1 high-affinity binding sites in pre-mRNA splicing","volume":"13","author":"Burd","year":"1994","journal-title":"EMBO J."},{"key":"10.1016\/j.celrep.2012.02.001_bib5","doi-asserted-by":"crossref","first-page":"43850","DOI":"10.1074\/jbc.M102861200","article-title":"Determination of the RNA binding specificity of the heterogeneous nuclear ribonucleoprotein (hnRNP) H\/H'\/F\/2H9 family","volume":"276","author":"Caputi","year":"2001","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.celrep.2012.02.001_bib6","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1093\/emboj\/21.4.845","article-title":"SR proteins and hnRNP H regulate the splicing of the HIV-1 tev-specific exon 6D","volume":"21","author":"Caputi","year":"2002","journal-title":"EMBO J."},{"key":"10.1016\/j.celrep.2012.02.001_bib7","first-page":"85","article-title":"The roles of heterogeneous nuclear ribonucleoproteins in tumour development and progression","volume":"1765","author":"Carpenter","year":"2006","journal-title":"Biochim. Biophys. Acta"},{"key":"10.1016\/j.celrep.2012.02.001_bib8","doi-asserted-by":"crossref","first-page":"593","DOI":"10.1101\/gad.13.5.593","article-title":"Binding of hnRNP H to an exonic splicing silencer is involved in the regulation of alternative splicing of the rat beta-tropomyosin gene","volume":"13","author":"Chen","year":"1999","journal-title":"Genes Dev."},{"key":"10.1016\/j.celrep.2012.02.001_bib9","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1038\/nature08170","article-title":"Argonaute HITS-CLIP decodes microRNA-mRNA interaction maps","volume":"460","author":"Chi","year":"2009","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2012.02.001_bib10","doi-asserted-by":"crossref","first-page":"439","DOI":"10.1093\/nar\/21.3.439","article-title":"The human hnRNP M proteins: identification of a methionine\/arginine-rich repeat motif in ribonucleoproteins","volume":"21","author":"Datar","year":"1993","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2012.02.001_bib11","doi-asserted-by":"crossref","first-page":"364","DOI":"10.1038\/nature08697","article-title":"HnRNP proteins controlled by c-Myc deregulate pyruvate kinase mRNA splicing in cancer","volume":"463","author":"David","year":"2010","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2012.02.001_bib12","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1146\/annurev.bi.62.070193.001445","article-title":"hnRNP proteins and the biogenesis of mRNA","volume":"62","author":"Dreyfuss","year":"1993","journal-title":"Annu. Rev. Biochem."},{"key":"10.1016\/j.celrep.2012.02.001_bib13","doi-asserted-by":"crossref","first-page":"195","DOI":"10.1038\/nrm760","article-title":"Messenger-RNA-binding proteins and the messages they carry","volume":"3","author":"Dreyfuss","year":"2002","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.celrep.2012.02.001_bib14","doi-asserted-by":"crossref","first-page":"187","DOI":"10.1038\/nsmb.1720","article-title":"Aberrant alternative splicing and extracellular matrix gene expression in mouse models of myotonic dystrophy","volume":"17","author":"Du","year":"2010","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.celrep.2012.02.001_bib15","doi-asserted-by":"crossref","first-page":"177","DOI":"10.1038\/nrc1299","article-title":"A census of human cancer genes","volume":"4","author":"Futreal","year":"2004","journal-title":"Nat. Rev. Cancer"},{"key":"10.1016\/j.celrep.2012.02.001_bib16","doi-asserted-by":"crossref","first-page":"325","DOI":"10.1186\/1471-2164-7-325","article-title":"Alternative splicing and differential gene expression in colon cancer detected by a whole genome exon array","volume":"7","author":"Gardina","year":"2006","journal-title":"BMC Genomics"},{"key":"10.1016\/j.celrep.2012.02.001_bib17","doi-asserted-by":"crossref","first-page":"706","DOI":"10.1038\/ng.841","article-title":"The splicing regulator Rbfox1 (A2BP1) controls neuronal excitation in the mammalian brain","volume":"43","author":"Gehman","year":"2011","journal-title":"Nat. Genet."},{"key":"10.1016\/j.celrep.2012.02.001_bib18","doi-asserted-by":"crossref","first-page":"4464","DOI":"10.1158\/0008-5472.CAN-10-4410","article-title":"Splicing factor hnRNP A2\/B1 regulates tumor suppressor gene splicing and is an oncogenic driver in glioblastoma","volume":"71","author":"Golan-Gerstl","year":"2011","journal-title":"Cancer Res."},{"key":"10.1016\/j.celrep.2012.02.001_bib19","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1016\/j.cell.2010.03.009","article-title":"Transcriptome-wide identification of RNA-binding protein and microRNA target sites by PAR-CLIP","volume":"141","author":"Hafner","year":"2010","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2012.02.001_bib20","doi-asserted-by":"crossref","first-page":"379","DOI":"10.1042\/BJ20100396","article-title":"Functional diversity of the hnRNPs: past, present and perspectives","volume":"430","author":"Han","year":"2010","journal-title":"Biochem. J."},{"key":"10.1016\/j.celrep.2012.02.001_bib21","doi-asserted-by":"crossref","first-page":"576","DOI":"10.1016\/j.molcel.2010.05.004","article-title":"Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities","volume":"38","author":"Heinz","year":"2010","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2012.02.001_bib22","doi-asserted-by":"crossref","first-page":"29745","DOI":"10.1074\/jbc.M203633200","article-title":"Distinct sets of adjacent heterogeneous nuclear ribonucleoprotein (hnRNP) A1\/A2 binding sites control 5\u2032 splice site selection in the hnRNP A1 mRNA precursor","volume":"277","author":"Hutchison","year":"2002","journal-title":"J. Biol. Chem."},{"key":"10.1016\/j.celrep.2012.02.001_bib23","doi-asserted-by":"crossref","first-page":"390","DOI":"10.1101\/gr.111070.110","article-title":"Global impact of RNA polymerase II elongation inhibition on alternative splicing regulation","volume":"21","author":"Ip","year":"2011","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2012.02.001_bib24","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1038\/ng1207","article-title":"A negative element in SMN2 exon 7 inhibits splicing in spinal muscular atrophy","volume":"34","author":"Kashima","year":"2003","journal-title":"Nat. Genet."},{"key":"10.1016\/j.celrep.2012.02.001_bib25","doi-asserted-by":"crossref","first-page":"1009","DOI":"10.1038\/nmeth.1528","article-title":"Analysis and design of RNA sequencing experiments for identifying isoform regulation","volume":"7","author":"Katz","year":"2010","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2012.02.001_bib26","doi-asserted-by":"crossref","first-page":"2655","DOI":"10.1002\/j.1460-2075.1992.tb05331.x","article-title":"Primary structure and binding activity of the hnRNP U protein: binding RNA through RGG box","volume":"11","author":"Kiledjian","year":"1992","journal-title":"EMBO J."},{"key":"10.1016\/j.celrep.2012.02.001_bib27","doi-asserted-by":"crossref","first-page":"909","DOI":"10.1038\/nsmb.1838","article-title":"iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution","volume":"17","author":"K\u00f6nig","year":"2010","journal-title":"Nat. Struct. Mol. Biol."},{"issue":"R1","key":"10.1016\/j.celrep.2012.02.001_bib28","doi-asserted-by":"crossref","first-page":"R46","DOI":"10.1093\/hmg\/ddq137","article-title":"TDP-43 and FUS\/TLS: emerging roles in RNA processing and neurodegeneration","volume":"19","author":"Lagier-Tourenne","year":"2010","journal-title":"Hum. Mol. Genet."},{"key":"10.1016\/j.celrep.2012.02.001_bib29","doi-asserted-by":"crossref","first-page":"961","DOI":"10.1158\/1541-7786.MCR-09-0528","article-title":"Exon-level microarray analyses identify alternative splicing programs in breast cancer","volume":"8","author":"Lapuk","year":"2010","journal-title":"Mol. Cancer Res."},{"key":"10.1016\/j.celrep.2012.02.001_bib30","doi-asserted-by":"crossref","first-page":"464","DOI":"10.1038\/nature07488","article-title":"HITS-CLIP yields genome-wide insights into brain alternative RNA processing","volume":"456","author":"Licatalosi","year":"2008","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2012.02.001_bib31","doi-asserted-by":"crossref","first-page":"1114","DOI":"10.1038\/nsmb.1881","article-title":"Position-dependent alternative splicing activity revealed by global profiling of alternative splicing events regulated by PTB","volume":"17","author":"Llorian","year":"2010","journal-title":"Nat. Struct. Mol. Biol."},{"key":"10.1016\/j.celrep.2012.02.001_bib32","doi-asserted-by":"crossref","first-page":"e21","DOI":"10.1371\/journal.pbio.0040021","article-title":"Intronic binding sites for hnRNP A\/B and hnRNP F\/H proteins stimulate pre-mRNA splicing","volume":"4","author":"Martinez-Contreras","year":"2006","journal-title":"PLoS Biol."},{"key":"10.1016\/j.celrep.2012.02.001_bib33","doi-asserted-by":"crossref","first-page":"123","DOI":"10.1007\/978-0-387-77374-2_8","article-title":"hnRNP proteins and splicing control","volume":"623","author":"Martinez-Contreras","year":"2007","journal-title":"Adv. Exp. Med. Biol."},{"key":"10.1016\/j.celrep.2012.02.001_bib34","doi-asserted-by":"crossref","first-page":"5483","DOI":"10.1002\/j.1460-2075.1994.tb06883.x","article-title":"Function of conserved domains of hnRNP A1 and other hnRNP A\/B proteins","volume":"13","author":"Mayeda","year":"1994","journal-title":"EMBO J."},{"key":"10.1016\/j.celrep.2012.02.001_bib35","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1186\/1471-2164-11-565","article-title":"Expression proteomics of UPF1 knockdown in HeLa cells reveals autoregulation of hnRNP A2\/B1 mediated by alternative splicing resulting in nonsense-mediated mRNA decay","volume":"11","author":"McGlincy","year":"2010","journal-title":"BMC Genomics"},{"key":"10.1016\/j.celrep.2012.02.001_bib37","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1128\/MCB.00709-10","article-title":"Global profiling and molecular characterization of alternative splicing events misregulated in lung cancer","volume":"31","author":"Misquitta-Ali","year":"2011","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.celrep.2012.02.001_bib38","doi-asserted-by":"crossref","first-page":"621","DOI":"10.1038\/nmeth.1226","article-title":"Mapping and quantifying mammalian transcriptomes by RNA-Seq","volume":"5","author":"Mortazavi","year":"2008","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2012.02.001_bib39","doi-asserted-by":"crossref","first-page":"327","DOI":"10.1016\/j.molcel.2011.06.007","article-title":"Integrative regulatory mapping indicates that the RNA-binding protein HuR couples pre-mRNA processing and mRNA stability","volume":"43","author":"Mukherjee","year":"2011","journal-title":"Mol Cell"},{"key":"10.1016\/j.celrep.2012.02.001_bib40","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1101\/gad.1525507","article-title":"Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay","volume":"21","author":"Ni","year":"2007","journal-title":"Genes Dev."},{"key":"10.1016\/j.celrep.2012.02.001_bib41","doi-asserted-by":"crossref","first-page":"e123","DOI":"10.1093\/nar\/gkp596","article-title":"Transcriptome analysis by strand-specific sequencing of complementary DNA","volume":"37","author":"Parkhomchuk","year":"2009","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2012.02.001_bib42","doi-asserted-by":"crossref","first-page":"459","DOI":"10.1038\/nn.2779","article-title":"Long pre-mRNA depletion and RNA missplicing contribute to neuronal vulnerability from loss of TDP-43","volume":"14","author":"Polymenidou","year":"2011","journal-title":"Nat. Neurosci."},{"key":"10.1016\/j.celrep.2012.02.001_bib43","doi-asserted-by":"crossref","first-page":"1442","DOI":"10.1128\/MCB.01689-08","article-title":"Auto- and cross-regulation of the hnRNP L proteins by alternative splicing","volume":"29","author":"Rossbach","year":"2009","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.celrep.2012.02.001_bib44","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1101\/gr.082503.108","article-title":"Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts","volume":"19","author":"Sanford","year":"2009","journal-title":"Genome Res."},{"key":"10.1016\/j.celrep.2012.02.001_bib45","doi-asserted-by":"crossref","first-page":"e4","DOI":"10.1371\/journal.pcbi.0020004","article-title":"Unusual intron conservation near tissue-regulated exons found by splicing microarrays","volume":"2","author":"Sugnet","year":"2006","journal-title":"PLoS Comput. Biol."},{"key":"10.1016\/j.celrep.2012.02.001_bib46","first-page":"2237","article-title":"Classification and purification of proteins of heterogeneous nuclear ribonucleoprotein particles by RNA-binding specificities","volume":"8","author":"Swanson","year":"1988","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.celrep.2012.02.001_bib47","doi-asserted-by":"crossref","first-page":"6033","DOI":"10.1128\/MCB.00726-08","article-title":"Multiple and specific mRNA processing targets for the major human hnRNP proteins","volume":"28","author":"Venables","year":"2008","journal-title":"Mol. Cell. Biol."},{"key":"10.1016\/j.celrep.2012.02.001_bib36","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1016\/0092-8674(91)90397-H","article-title":"Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndrome","volume":"65","author":"Verkerk","year":"1991","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2012.02.001_bib48","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/nature07509","article-title":"Alternative isoform regulation in human tissue transcriptomes","volume":"456","author":"Wang","year":"2008","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2012.02.001_bib49","doi-asserted-by":"crossref","first-page":"873","DOI":"10.1093\/bioinformatics\/btq057","article-title":"Fast and SNP-tolerant detection of complex variants and splicing in short reads","volume":"26","author":"Wu","year":"2010","journal-title":"Bioinformatics"},{"key":"10.1016\/j.celrep.2012.02.001_bib50","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1016\/j.molcel.2009.12.003","article-title":"Genome-wide analysis of PTB-RNA interactions reveals a strategy used by the general splicing repressor to modulate exon inclusion or skipping","volume":"36","author":"Xue","year":"2009","journal-title":"Mol. Cell"},{"key":"10.1016\/j.celrep.2012.02.001_bib51","doi-asserted-by":"crossref","first-page":"130","DOI":"10.1038\/nsmb.1545","article-title":"An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells","volume":"16","author":"Yeo","year":"2009","journal-title":"Nat. Struct. Mol. Biol."}],"container-title":["Cell Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124712000435?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124712000435?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2025,10,31]],"date-time":"2025-10-31T09:19:19Z","timestamp":1761902359000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2211124712000435"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2012,2]]},"references-count":51,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2012,2]]}},"alternative-id":["S2211124712000435"],"URL":"https:\/\/doi.org\/10.1016\/j.celrep.2012.02.001","relation":{},"ISSN":["2211-1247"],"issn-type":[{"value":"2211-1247","type":"print"}],"subject":[],"published":{"date-parts":[[2012,2]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Integrative Genome-wide Analysis Reveals Cooperative Regulation of Alternative Splicing by hnRNP Proteins","name":"articletitle","label":"Article Title"},{"value":"Cell Reports","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.celrep.2012.02.001","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"Copyright \u00a9 2012 The Authors. Published by Elsevier Inc.","name":"copyright","label":"Copyright"}]}}