{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,18]],"date-time":"2026-02-18T23:19:00Z","timestamp":1771456740935,"version":"3.50.1"},"reference-count":59,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2014,8,18]],"date-time":"2014-08-18T00:00:00Z","timestamp":1408320000000},"content-version":"unspecified","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0104567","type":"journal-article","created":{"date-parts":[[2014,8,18]],"date-time":"2014-08-18T15:31:14Z","timestamp":1408375874000},"page":"e104567","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":37,"title":["Tandem RNA Chimeras Contribute to Transcriptome Diversity in Human Population and Are Associated with Intronic Genetic Variants"],"prefix":"10.1371","volume":"9","author":[{"given":"Liliana","family":"Greger","sequence":"first","affiliation":[]},{"given":"Jing","family":"Su","sequence":"additional","affiliation":[]},{"given":"Johan","family":"Rung","sequence":"additional","affiliation":[]},{"given":"Pedro G.","family":"Ferreira","sequence":"additional","affiliation":[]},{"name":"Geuvadis consortium","sequence":"additional","affiliation":[]},{"given":"Tuuli","family":"Lappalainen","sequence":"additional","affiliation":[]},{"given":"Emmanouil T.","family":"Dermitzakis","sequence":"additional","affiliation":[]},{"given":"Alvis","family":"Brazma","sequence":"additional","affiliation":[]}],"member":"340","published-online":{"date-parts":[[2014,8,18]]},"reference":[{"key":"ref1","doi-asserted-by":"crossref","first-page":"233","DOI":"10.1038\/nrc2091","article-title":"The impact of translocations and gene fusions on cancer causation","volume":"7","author":"F Mitelman","year":"2007","journal-title":"Nat Rev Cancer"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"16005","DOI":"10.1074\/jbc.273.26.16005","article-title":"Cotranscription and intergenic splicing of human galactose-1-phosphate uridylyltransferase and interleukin-11 receptor alpha-chain genes generate a fusion mRNA in normal cells. Implication for the production of multidomain proteins during evolution","volume":"273","author":"F Magrangeas","year":"1998","journal-title":"J Biol Chem"},{"key":"ref3","doi-asserted-by":"crossref","first-page":"987","DOI":"10.1101\/gr.3455305","article-title":"Examples of the complex architecture of the human transcriptome revealed by RACE and high-density tiling arrays","volume":"15","author":"P Kapranov","year":"2005","journal-title":"Genome Res"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"746","DOI":"10.1101\/gr.5660607","article-title":"Prominent use of distal 5\u2032 transcription start sites and discovery of a large number of additional exons in ENCODE regions","volume":"17","author":"F Denoeud","year":"2007","journal-title":"Genome Res"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1101\/gr.4145906","article-title":"Tandem chimerism as a means to increase protein complexity in the human genome","volume":"16","author":"G Parra","year":"2006","journal-title":"Genome Res"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"30","DOI":"10.1101\/gr.4137606","article-title":"Transcription-mediated gene fusion in the human genome","volume":"16","author":"P Akiva","year":"2006","journal-title":"Genome Res"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"e13284","DOI":"10.1371\/journal.pone.0013284","article-title":"Expression of conjoined genes: another mechanism for gene regulation in eukaryotes","volume":"5","author":"T Prakash","year":"2010","journal-title":"PLoS ONE"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1038\/nature08452","article-title":"Implications of chimaeric non-co-linear transcripts","volume":"461","author":"TR Gingeras","year":"2009","journal-title":"Nature"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/1755-8794-4-11","article-title":"Deep RNA sequencing analysis of readthrough gene fusions in human prostate adenocarcinoma and reference samples","volume":"4","author":"S Nacu","year":"2011","journal-title":"BMC Med Genomics"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"3455","DOI":"10.1093\/nar\/gkl436","article-title":"The regulated expression of chimeric tyrosine hydroxylase-insulin transcripts during early development","volume":"34","author":"C Hern\u00e1ndez-S\u00e1nchez","year":"2006","journal-title":"Nucleic Acids Res"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"18033","DOI":"10.1074\/jbc.M109.006999","article-title":"Functional pre- mRNA trans-splicing of coactivator CoAA and corepressor RBM4 during stem\/progenitor cell differentiation","volume":"284","author":"YS Brooks","year":"2009","journal-title":"J Biol Chem"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1186\/1471-2164-9-155","article-title":"Detailed characterization of the mouse embryonic stem cell transcriptome reveals novel genes and intergenic splicing associated with pluripotency","volume":"9","author":"G Kunarso","year":"2008","journal-title":"BMC Genomics"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"14","DOI":"10.1016\/j.ygeno.2012.05.005","article-title":"CACG: a database for comparative analysis of conjoined genes","volume":"100","author":"D-S Kim","year":"2012","journal-title":"Genomics"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1007\/s10142-011-0260-1","article-title":"Novel mechanism of conjoined gene formation in the human genome","volume":"12","author":"RN Kim","year":"2012","journal-title":"Funct Integr Genomics"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"e1003867","DOI":"10.1371\/journal.pgen.1003867","article-title":"Transcription termination and chimeric RNA formation controlled by Arabidopsis thaliana FPA","volume":"9","author":"C Duc","year":"2013","journal-title":"PLoS Genet"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"506","DOI":"10.1038\/nature12531","article-title":"Transcriptome and genome sequencing uncovers functional variation in humans","volume":"501","author":"T Lappalainen","year":"2013","journal-title":"Nature"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"1922","DOI":"10.1093\/bioinformatics\/btr310","article-title":"FusionMap: detecting fusion genes from next-generation sequencing data at base-pair resolution","volume":"27","author":"H Ge","year":"2011","journal-title":"Bioinformatics"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"589","DOI":"10.1093\/bioinformatics\/btp698","article-title":"Fast and accurate long-read alignment with Burrows-Wheeler transform","volume":"26","author":"H Li","year":"2010","journal-title":"Bioinformatics"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref20","doi-asserted-by":"crossref","first-page":"623","DOI":"10.1101\/gr.102970.109","article-title":"Genome-wide mapping and assembly of structural variant breakpoints in the mouse genome","volume":"20","author":"AR Quinlan","year":"2010","journal-title":"Genome Res"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1038\/nature08903","article-title":"Transcriptome genetics using second generation sequencing in a Caucasian population","volume":"464","author":"SB Montgomery","year":"2010","journal-title":"Nature"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"S12.1","DOI":"10.1186\/gb-2006-7-s1-s12","article-title":"AceView: a comprehensive cDNA-supported gene and transcripts annotation","volume":"7","author":"D Thierry-Mieg","year":"2006","journal-title":"Genome Biol"},{"key":"ref23","doi-asserted-by":"crossref","unstructured":"Wickham H (2009) Ggplot2: elegant graphics for data analysis. New York: Springer. 212 p.","DOI":"10.1007\/978-0-387-98141-3"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"1185","DOI":"10.1038\/nmeth.2221","article-title":"The GEM mapper: fast, accurate and versatile alignment by filtration","volume":"9","author":"S Marco-Sola","year":"2012","journal-title":"Nat Methods"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"773","DOI":"10.1038\/nature08903","article-title":"Transcriptome genetics using second generation sequencing in a Caucasian population","volume":"464","author":"SB Montgomery","year":"2010","journal-title":"Nature"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"35","DOI":"10.3389\/fgene.2012.00035","article-title":"Using Drosophila melanogaster as a Model for Genotoxic Chemical Mutational Studies with a New Program, SnpSift","volume":"3","author":"P Cingolani","year":"2012","journal-title":"Front Genet"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1007\/978-1-59745-248-9_17","article-title":"RIP-Chip analysis: RNA-Binding Protein Immunoprecipitation-Microarray (Chip) Profiling","volume":"703","author":"R Jain","year":"2011","journal-title":"Methods Mol Biol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"D56","DOI":"10.1093\/nar\/gks1172","article-title":"ENCODE data in the UCSC Genome Browser: year 5 update","volume":"41","author":"KR Rosenbloom","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"ref29","doi-asserted-by":"crossref","first-page":"841","DOI":"10.1093\/bioinformatics\/btq033","article-title":"BEDTools: a flexible suite of utilities for comparing genomic features","volume":"26","author":"AR Quinlan","year":"2010","journal-title":"Bioinformatics"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1760","DOI":"10.1101\/gr.135350.111","article-title":"GENCODE: the reference human genome annotation for The ENCODE Project","volume":"22","author":"J Harrow","year":"2012","journal-title":"Genome Res"},{"key":"ref31","article-title":"Small changes in the big picture: genetic fine-tuning in transcriptome. variation across human populations","author":"PG Ferreira","year":"1914","journal-title":"PLoS Genet"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"2336","DOI":"10.1093\/bioinformatics\/btq419","article-title":"LocusZoom: regional visualization of genome-wide association scan results","volume":"26","author":"RJ Pruim","year":"2010","journal-title":"Bioinformatics"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"S2","DOI":"10.1186\/1471-2105-14-S7-S2","article-title":"State of art fusion-finder algorithms are suitable to detect transcription-induced chimeras in normal tissues?","volume":"14","author":"M Carrara","year":"2013","journal-title":"BMC Bioinformatics"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"369","DOI":"10.1101\/gr.490303","article-title":"Segmental duplications in euchromatic regions of human chromosome 5: a source of evolutionary instability and transcriptional innovation","volume":"13","author":"A Courseaux","year":"2003","journal-title":"Genome Res"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"17885","DOI":"10.1073\/pnas.0608344103","article-title":"Evolution and expression of chimeric POTE-actin genes in the human genome","volume":"103","author":"Y Lee","year":"2006","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"7316","DOI":"10.1073\/pnas.95.13.7316","article-title":"Interaction of SP100 with HP1 proteins: a link between the promyelocytic leukemia-associated nuclear bodies and the chromatin compartment","volume":"95","author":"JS Seeler","year":"1998","journal-title":"Proc Natl Acad Sci USA"},{"key":"ref37","doi-asserted-by":"crossref","first-page":"e1001156","DOI":"10.1371\/journal.pbio.1001156","article-title":"ESRRA-C11orf20 is a recurrent gene fusion in serous ovarian carcinoma","volume":"9","author":"J Salzman","year":"2011","journal-title":"PLoS Biol"},{"key":"ref38","doi-asserted-by":"crossref","first-page":"56","DOI":"10.1038\/nature11632","article-title":"An integrated map of genetic variation from 1,092 human genomes","volume":"491","author":"GR Abecasis","year":"2012","journal-title":"Nature"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1101\/gr.130062.111","article-title":"Chimeras taking shape: potential functions of proteins encoded by chimeric RNA transcripts","volume":"22","author":"M Frenkel-Morgenstern","year":"2012","journal-title":"Genome Res"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"1055","DOI":"10.1182\/blood-2007-02-075911","article-title":"Alternative splicing due to an intronic SNP in HMSD generates a novel minor histocompatibility antigen","volume":"110","author":"T Kawase","year":"2007","journal-title":"Blood"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"1921","DOI":"10.1158\/0008-5472.CAN-11-3142","article-title":"Detection of redundant fusion transcripts as biomarkers or disease-specific therapeutic targets in breast cancer","volume":"72","author":"YW Asmann","year":"2012","journal-title":"Cancer Res"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"1552","DOI":"10.1101\/gad.4.9.1552","article-title":"In vitro polyadenylation is stimulated by the presence of an upstream intron","volume":"4","author":"M Niwa","year":"1990","journal-title":"Genes Dev"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"2086","DOI":"10.1101\/gad.5.11.2086","article-title":"Mutation of the AAUAAA polyadenylation signal depresses in vitro splicing of proximal but not distal introns","volume":"5","author":"M Niwa","year":"1991","journal-title":"Genes Dev"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"849","DOI":"10.1128\/MCB.01410-07","article-title":"Functional coupling of last-intron splicing and 3\u2032-end processing to transcription in vitro: the poly(A) signal couples to splicing before committing to cleavage","volume":"28","author":"F Rigo","year":"2008","journal-title":"Mol Cell Biol"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1186\/1471-2156-10-67","article-title":"Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3","volume":"10","author":"NP Kandul","year":"2009","journal-title":"BMC Genet"},{"key":"ref46","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1016\/j.molcel.2005.03.018","article-title":"Delay in synthesis of the 3\u2032 splice site promotes trans-splicing of the preceding 5\u2032 splice site","volume":"18","author":"T Takahara","year":"2005","journal-title":"Mol Cell"},{"key":"ref47","article-title":"Systematical identification of splicing regulatory cis-elements and cognate trans-factors","author":"Y Wang","year":"2013","journal-title":"Methods"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"270","DOI":"10.2337\/db06-0865","article-title":"Genetic control of alternative splicing in the TAP2 gene: possible implication in the genetics of type 1 diabetes","volume":"56","author":"H-Q Qu","year":"2007","journal-title":"Diabetes"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"1591","DOI":"10.1038\/sj.emboj.7601588","article-title":"A conserved role for cytoplasmic poly(A)-binding protein 1 (PABPC1) in nonsense-mediated mRNA decay","volume":"26","author":"I Behm-Ansmant","year":"2007","journal-title":"EMBO J"},{"key":"ref50","doi-asserted-by":"crossref","first-page":"223","DOI":"10.1186\/gb-2003-4-7-223","article-title":"Poly(A)-binding proteins: multifunctional scaffolds for the post-transcriptional control of gene expression","volume":"4","author":"DA Mangus","year":"2003","journal-title":"Genome Biol"},{"key":"ref51","doi-asserted-by":"crossref","first-page":"5","DOI":"10.4161\/rna.7.1.10256","article-title":"Multiple levels of post-transcriptional control of expression of the poly (A)-binding protein","volume":"7","author":"J Bag","year":"2010","journal-title":"RNA Biol"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"e39987","DOI":"10.1371\/journal.pone.0039987","article-title":"FusionFinder: a software tool to identify expressed gene fusion candidates from RNA-Seq data","volume":"7","author":"RW Francis","year":"2012","journal-title":"PLoS ONE"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"1087","DOI":"10.1593\/neo.121342","article-title":"Long-range transcriptome sequencing reveals cancer cell growth regulatory chimeric mRNA","volume":"14","author":"R Plebani","year":"2012","journal-title":"Neoplasia"},{"key":"ref54","doi-asserted-by":"crossref","first-page":"1068","DOI":"10.1093\/bioinformatics\/btr085","article-title":"Sensitive gene fusion detection using ambiguously mapping RNA-Seq read pairs","volume":"27","author":"M Kinsella","year":"2011","journal-title":"Bioinformatics"},{"key":"ref55","doi-asserted-by":"crossref","first-page":"43","DOI":"10.1038\/nature12222","article-title":"Comprehensive molecular characterization of clear cell renal cell carcinoma","volume":"499","year":"2013","journal-title":"Nature"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"20","DOI":"10.3324\/haematol.2009.011536","article-title":"TFG, a target of chromosome translocations in lymphoma and soft tissue tumors, fuses to GPR128 in healthy individuals","volume":"95","author":"A Chase","year":"2010","journal-title":"Haematologica"},{"key":"ref57","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1038\/ejhg.2012.73","article-title":"CNVs leading to fusion transcripts in individuals with autism spectrum disorder","volume":"20","author":"R Holt","year":"2012","journal-title":"Eur J Hum Genet"},{"key":"ref58","doi-asserted-by":"crossref","first-page":"348","DOI":"10.1186\/1471-2164-8-348","article-title":"RBM6-RBM5 transcription-induced chimeras are differentially expressed in tumours","volume":"8","author":"K Wang","year":"2007","journal-title":"BMC Genomics"},{"key":"ref59","doi-asserted-by":"crossref","first-page":"598","DOI":"10.1158\/2159-8290.CD-12-0042","article-title":"Chimeric transcript generated by cis-splicing of adjacent genes regulates prostate cancer cell proliferation","volume":"2","author":"Y Zhang","year":"2012","journal-title":"Cancer Discov"}],"container-title":["PLoS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0104567","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,5,8]],"date-time":"2020-05-08T18:54:06Z","timestamp":1588964046000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0104567"}},"subtitle":[],"editor":[{"given":"Thomas","family":"Preiss","sequence":"first","affiliation":[]}],"short-title":[],"issued":{"date-parts":[[2014,8,18]]},"references-count":59,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2014,8,18]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0104567","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2014,8,18]]}}}