{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T11:07:09Z","timestamp":1776942429216,"version":"3.51.4"},"reference-count":63,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2014,11,6]],"date-time":"2014-11-06T00:00:00Z","timestamp":1415232000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"DOI":"10.1371\/journal.pgen.1004771","type":"journal-article","created":{"date-parts":[[2014,11,6]],"date-time":"2014-11-06T19:11:41Z","timestamp":1415301101000},"page":"e1004771","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":28,"title":["Regulation of mRNA Abundance by Polypyrimidine Tract-Binding Protein-Controlled Alternate 5\u2032 Splice Site Choice"],"prefix":"10.1371","volume":"10","author":[{"given":"Fursham M.","family":"Hamid","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eugene V.","family":"Makeyev","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2014,11,6]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"802","DOI":"10.1261\/rna.876308","article-title":"Splicing regulation: from a parts list of regulatory elements to an integrated splicing code","volume":"14","author":"Z Wang","year":"2008","journal-title":"RNA"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"457","DOI":"10.1038\/nature08909","article-title":"Expansion of the eukaryotic proteome by alternative splicing","volume":"463","author":"TW Nilsen","year":"2010","journal-title":"Nature"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"715","DOI":"10.1038\/nrg3052","article-title":"Functional consequences of developmentally regulated alternative splicing","volume":"12","author":"A Kalsotra","year":"2011","journal-title":"Nat Rev Genet"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1252","DOI":"10.1016\/j.cell.2013.02.034","article-title":"Dynamic integration of splicing within gene regulatory pathways","volume":"152","author":"U Braunschweig","year":"2013","journal-title":"Cell"},{"key":"ref5","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":"DL Black","year":"2003","journal-title":"Annu Rev Biochem"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"R74","DOI":"10.1186\/gb-2004-5-10-r74","article-title":"Variation in alternative splicing across human tissues","volume":"5","author":"G Yeo","year":"2004","journal-title":"Genome Biol"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"470","DOI":"10.1038\/nature07509","article-title":"Alternative isoform regulation in human tissue transcriptomes","volume":"456","author":"ET Wang","year":"2008","journal-title":"Nature"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"954","DOI":"10.1128\/MCB.06130-11","article-title":"Proteins associated with the exon junction complex also control the alternative splicing of apoptotic regulators","volume":"32","author":"L Michelle","year":"2012","journal-title":"Mol Cell Biol"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"4059","DOI":"10.1074\/jbc.M110.199927","article-title":"G Run-mediated recognition of proteolipid protein and DM20 5\u2032 splice sites by U1 small nuclear RNA is regulated by context and proximity to the splice site","volume":"286","author":"E Wang","year":"2011","journal-title":"J Biol Chem"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"129","DOI":"10.1101\/gad.209759.112","article-title":"Pick one, but be quick: 5\u2032 splice sites and the problems of too many choices","volume":"27","author":"X Roca","year":"2013","journal-title":"Genes Dev"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"61","DOI":"10.1016\/j.molcel.2006.05.018","article-title":"General and specific functions of exonic splicing silencers in splicing control","volume":"23","author":"Z Wang","year":"2006","journal-title":"Mol Cell"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"1224","DOI":"10.1016\/j.cell.2008.10.046","article-title":"Dynamic regulation of alternative splicing by silencers that modulate 5\u2032 splice site competition","volume":"135","author":"Y Yu","year":"2008","journal-title":"Cell"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"96","DOI":"10.1261\/rna.037044.112","article-title":"Position-dependent splicing activation and repression by SR and hnRNP proteins rely on common mechanisms","volume":"19","author":"S Erkelenz","year":"2013","journal-title":"RNA"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1038\/418236a","article-title":"Alternative pre-mRNA splicing and proteome expansion in metazoans","volume":"418","author":"T Maniatis","year":"2002","journal-title":"Nature"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1016\/j.mcn.2013.01.003","article-title":"Regulation of gene expression in mammalian nervous system through alternative pre-mRNA splicing coupled with RNA quality control mechanisms","volume":"56","author":"K Yap","year":"2013","journal-title":"Mol Cell Neurosci"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"442","DOI":"10.1016\/j.tig.2013.04.003","article-title":"Alternative pre-mRNA splicing in neurons: growing up and extending its reach","volume":"29","author":"S Zheng","year":"2013","journal-title":"Trends Genet"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1146\/annurev-genet-111212-133424","article-title":"Organizing principles of mammalian nonsense-mediated mRNA decay","volume":"47","author":"MW Popp","year":"2013","journal-title":"Annu Rev Genet"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"612","DOI":"10.1016\/j.bbagrm.2013.02.005","article-title":"Nonsense-mediated mRNA decay - mechanisms of substrate mRNA recognition and degradation in mammalian cells","volume":"1829","author":"C Schweingruber","year":"2013","journal-title":"Biochim Biophys Acta"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"1168","DOI":"10.1042\/BST20140066","article-title":"Emerging functions of alternative splicing coupled with nonsense-mediated decay","volume":"42","author":"FM Hamid","year":"2014","journal-title":"Biochem Soc Trans"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1007\/978-0-387-77374-2_12","article-title":"The coupling of alternative splicing and nonsense-mediated mRNA decay","volume":"623","author":"LF Lareau","year":"2007","journal-title":"Adv Exp Med Biol"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"385","DOI":"10.1016\/j.tibs.2008.06.001","article-title":"Alternative splicing resulting in nonsense-mediated mRNA decay: what is the meaning of nonsense?","volume":"33","author":"NJ McGlincy","year":"2008","journal-title":"Trends Biochem Sci"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1016\/j.cell.2013.06.052","article-title":"Orchestrated intron retention regulates normal granulocyte differentiation","volume":"154","author":"JJ Wong","year":"2013","journal-title":"Cell"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"1252","DOI":"10.1016\/j.cell.2013.04.056","article-title":"Regulation of axon guidance by compartmentalized nonsense-mediated mRNA decay","volume":"153","author":"D Colak","year":"2013","journal-title":"Cell"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"e00178","DOI":"10.7554\/eLife.00178","article-title":"NOVA-dependent regulation of cryptic NMD exons controls synaptic protein levels after seizure","volume":"2","author":"T Eom","year":"2013","journal-title":"Elife"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"815","DOI":"10.1042\/BST20120044","article-title":"Defining the roles and interactions of PTB","volume":"40","author":"P Kafasla","year":"2012","journal-title":"Biochem Soc Trans"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"360","DOI":"10.3109\/10409238.2012.691456","article-title":"Neuronal regulation of pre-mRNA splicing by polypyrimidine tract binding proteins, PTBP1 and PTBP2","volume":"47","author":"N Keppetipola","year":"2012","journal-title":"Crit Rev Biochem Mol Biol"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"91","DOI":"10.1016\/S1097-2765(03)00502-1","article-title":"Autoregulation of polypyrimidine tract binding protein by alternative splicing leading to nonsense-mediated decay","volume":"13","author":"MC Wollerton","year":"2004","journal-title":"Mol Cell"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"435","DOI":"10.1016\/j.molcel.2007.07.015","article-title":"The MicroRNA miR-124 promotes neuronal differentiation by triggering brain-specific alternative pre-mRNA splicing","volume":"27","author":"EV Makeyev","year":"2007","journal-title":"Mol Cell"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"1209","DOI":"10.1101\/gad.188037.112","article-title":"Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention","volume":"26","author":"K Yap","year":"2012","journal-title":"Genes Dev"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/nn.3026","article-title":"PSD-95 is post-transcriptionally repressed during early neural development by PTBP1 and PTBP2","volume":"15","author":"S Zheng","year":"2012","journal-title":"Nat Neurosci"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"2135","DOI":"10.1016\/j.cub.2012.09.020","article-title":"BLOC-3 mutated in Hermansky-Pudlak syndrome is a Rab32\/38 guanine nucleotide exchange factor","volume":"22","author":"A Gerondopoulos","year":"2012","journal-title":"Curr Biol"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1111\/j.1600-0749.2005.00289.x","article-title":"Hermansky-Pudlak syndrome: a disease of protein trafficking and organelle function","volume":"19","author":"ML Wei","year":"2006","journal-title":"Pigment Cell Res"},{"key":"ref33","unstructured":"Cullinane AR, Huizing M, Gahl WA (2013) Molecular Genetics of Hermansky\u2013Pudlak Syndrome. eLS. Chichester: John Wiley &amp; Sons Ltd,. pp. <ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/www.els.net\" xlink:type=\"simple\">http:\/\/www.els.net<\/ext-link> [doi: 10.1002\/9780470015902.a9780470024328]."},{"key":"ref34","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1542\/peds.2012-4003","article-title":"Hermansky-Pudlak syndrome: health care throughout life","volume":"132","author":"SL Seward Jr","year":"2013","journal-title":"Pediatrics"},{"key":"ref35","doi-asserted-by":"crossref","unstructured":"Ribeca P, Lacroix V, Sammeth M, Guig\u00f3 R (2012) Analysis of RNA Transcripts by High-Throughput RNA Sequencing. In: Stamm S, Smith CWJ, L\u00fchrmann R, editors. Alternative pre-mRNA Splicing: Theory and Protocols: Wiley-VCH Verlag GmbH &amp; Co. KGaA.","DOI":"10.1002\/9783527636778.ch50"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"e01201","DOI":"10.7554\/eLife.01201","article-title":"The splicing regulator PTBP2 controls a program of embryonic splicing required for neuronal maturation","volume":"3","author":"Q Li","year":"2014","journal-title":"Elife"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"1626","DOI":"10.1101\/gad.191338.112","article-title":"Ptbp2 represses adult-specific splicing to regulate the generation of neuronal precursors in the embryonic brain","volume":"26","author":"DD Licatalosi","year":"2012","journal-title":"Genes Dev"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1016\/j.tcb.2010.10.001","article-title":"Metastasis: tumor cells becoming MENAcing","volume":"21","author":"F Gertler","year":"2011","journal-title":"Trends Cell Biol"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"190","DOI":"10.1016\/j.pnpbp.2014.02.006","article-title":"Pleckstrin homology domain containing 6 protein (PLEKHA6) polymorphisms are associated with psychopathology and response to treatment in schizophrenic patients","volume":"51","author":"I Spellmann","year":"2014","journal-title":"Prog Neuropsychopharmacol Biol Psychiatry"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"3733","DOI":"10.2741\/3484","article-title":"Autoantibody to NA14 is an independent marker primarily for Sjogren&apos;s syndrome","volume":"14","author":"K Nozawa","year":"2009","journal-title":"Front Biosci (Landmark Ed)"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"854","DOI":"10.1002\/gcc.20688","article-title":"Characterization and gene expression profiling in glioma cell lines with deletion of chromosome 19 before and after microcell-mediated restoration of normal human chromosome 19","volume":"48","author":"KL Drucker","year":"2009","journal-title":"Genes Chromosomes Cancer"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.canlet.2013.05.038","article-title":"Tight junction proteins: from barrier to tumorigenesis","volume":"337","author":"EA Runkle","year":"2013","journal-title":"Cancer Lett"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1002\/mc.20859","article-title":"PTBP1-dependent regulation of USP5 alternative RNA splicing plays a role in glioblastoma tumorigenesis","volume":"51","author":"DI Izaguirre","year":"2012","journal-title":"Mol Carcinog"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"616","DOI":"10.1002\/bies.20042","article-title":"Murine Hermansky-Pudlak syndrome genes: regulators of lysosome-related organelles","volume":"26","author":"W Li","year":"2004","journal-title":"Bioessays"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"1300","DOI":"10.1074\/jbc.275.2.1300","article-title":"Molecular characterization of the protein encoded by the Hermansky-Pudlak syndrome type 1 gene","volume":"275","author":"EC Dell'Angelica","year":"2000","journal-title":"J Biol Chem"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1101\/gad.1500707","article-title":"MicroRNAs regulate the expression of the alternative splicing factor nPTB during muscle development","volume":"21","author":"PL Boutz","year":"2007","journal-title":"Genes Dev"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"1636","DOI":"10.1101\/gad.1558107","article-title":"A post-transcriptional regulatory switch in polypyrimidine tract-binding proteins reprograms alternative splicing in developing neurons","volume":"21","author":"PL Boutz","year":"2007","journal-title":"Genes Dev"},{"key":"ref48","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":"M Llorian","year":"2010","journal-title":"Nat Struct Mol Biol"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"420","DOI":"10.1016\/j.molcel.2007.06.016","article-title":"Crossregulation and functional redundancy between the splicing regulator PTB and its paralogs nPTB and ROD1","volume":"27","author":"R Spellman","year":"2007","journal-title":"Mol Cell"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"2054","DOI":"10.1126\/science.1114066","article-title":"Structure of PTB bound to RNA: specific binding and implications for splicing regulation","volume":"309","author":"FC Oberstrass","year":"2005","journal-title":"Science"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1261\/rna.5196404","article-title":"Comparative analysis detects dependencies among the 5\u2032 splice-site positions","volume":"10","author":"I Carmel","year":"2004","journal-title":"RNA"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"e95","DOI":"10.1371\/journal.pcbi.0030095","article-title":"The emergence of alternative 3\u2032 and 5\u2032 splice site exons from constitutive exons","volume":"3","author":"E Koren","year":"2007","journal-title":"PLoS Comput Biol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"6882","DOI":"10.1093\/emboj\/cdf668","article-title":"The splicing regulator TIA-1 interacts with U1-C to promote U1 snRNP recruitment to 5\u2032 splice sites","volume":"21","author":"P Forch","year":"2002","journal-title":"EMBO J"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"4127","DOI":"10.1016\/j.febslet.2007.08.012","article-title":"Downstream intronic splicing enhancers","volume":"581","author":"JP Venables","year":"2007","journal-title":"FEBS Lett"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1016\/j.molcel.2011.02.012","article-title":"U1 snRNA directly interacts with polypyrimidine tract-binding protein during splicing repression","volume":"41","author":"S Sharma","year":"2011","journal-title":"Mol Cell"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"580","DOI":"10.1038\/nature05304","article-title":"An RNA map predicting Nova-dependent splicing regulation","volume":"444","author":"J Ule","year":"2006","journal-title":"Nature"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"2550","DOI":"10.1101\/gad.1703108","article-title":"Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2","volume":"22","author":"C Zhang","year":"2008","journal-title":"Genes Dev"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1016\/j.celrep.2012.02.001","article-title":"Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins","volume":"1","author":"SC Huelga","year":"2012","journal-title":"Cell Rep"},{"key":"ref59","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":"Y Xue","year":"2009","journal-title":"Mol Cell"},{"key":"ref60","doi-asserted-by":"crossref","first-page":"102","DOI":"10.1152\/physiol.00041.2009","article-title":"Lysosomal storage disease: revealing lysosomal function and physiology","volume":"25","author":"EJ Parkinson-Lawrence","year":"2010","journal-title":"Physiology (Bethesda)"},{"key":"ref61","doi-asserted-by":"crossref","first-page":"12203","DOI":"10.1073\/pnas.182427099","article-title":"Purification and electron microscopic visualization of functional human spliceosomes","volume":"99","author":"Z Zhou","year":"2002","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref62","doi-asserted-by":"crossref","first-page":"1217","DOI":"10.1523\/JNEUROSCI.17-04-01217.1997","article-title":"Characterization of a CNS cell line, CAD, in which morphological differentiation is initiated by serum deprivation","volume":"17","author":"Y Qi","year":"1997","journal-title":"J Neurosci"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq","volume":"25","author":"C Trapnell","year":"2009","journal-title":"Bioinformatics"}],"container-title":["PLoS Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pgen.1004771","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,9]],"date-time":"2020-05-09T00:44:38Z","timestamp":1588985078000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1004771"}},"subtitle":[],"editor":[{"given":"Emanuele","family":"Buratti","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2014,11,6]]},"references-count":63,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2014,11,6]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1004771","relation":{},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,11,6]]}}}