{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,6]],"date-time":"2026-10-06T02:12:41Z","timestamp":1791252761129,"version":"4.1.0"},"reference-count":20,"publisher":"National Academy of Sciences","issue":"22","content-domain":{"domain":["www.pnas.org"],"crossmark-restriction":true},"short-container-title":["Proc. Natl. Acad. Sci. U.S.A."],"published-print":{"date-parts":[[2011,5,31]]},"abstract":"<jats:p>\n                    Transcription-induced chimeric RNAs, possessing sequences from different genes, are expected to increase the proteomic diversity through chimeric proteins or altered regulation. Despite their importance, few studies have focused on chimeric RNAs especially regarding their presence\/roles in human cancers. By deep sequencing the transcriptome of 20 human prostate cancer and 10 matched benign prostate tissues, we obtained 1.3 billion sequence reads, which led to the identification of 2,369 chimeric RNA candidates. Chimeric RNAs occurred in significantly higher frequency in cancer than in matched benign samples. Experimental investigation of a selected 46 set led to the confirmation of 32 chimeric RNAs, of which 27 were highly recurrent and previously undescribed in prostate cancer. Importantly, a subset of these chimeras was present in prostate cancer cell lines, but not detectable in primary human prostate epithelium cells, implying their associations with cancer. These chimeras contain discernable 5\u2032 and 3\u2032 splice sites at the RNA junction, indicating that their formation is mediated by splicing. Their presence is also largely independent of the expression of parental genes, suggesting that other factors are involved in their production and regulation. One chimera,\n                    <jats:italic>TMEM79-SMG5<\/jats:italic>\n                    , is highly differentially expressed in human cancer samples and therefore a potential biomarker. The prevalence of chimeric RNAs may allow the limited number of human genes to encode a substantially larger number of RNAs and proteins, forming an additional layer of cellular complexity. Together, our results suggest that chimeric RNAs are widespread, and increased chimeric RNA events could represent a unique class of molecular alteration in cancer.\n                  <\/jats:p>","DOI":"10.1073\/pnas.1100489108","type":"journal-article","created":{"date-parts":[[2011,5,13]],"date-time":"2011-05-13T20:35:26Z","timestamp":1305318926000},"page":"9172-9177","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":165,"title":["Recurrent chimeric RNAs enriched in human prostate cancer identified by deep sequencing"],"prefix":"10.1073","volume":"108","author":[{"given":"Kalpana","family":"Kannan","sequence":"first","affiliation":[{"name":"Department of Pathology and Immunology,"},{"name":"Department of Molecular and Cellular Biology,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liguo","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cellular Biology,"},{"name":"Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianghua","family":"Wang","sequence":"additional","affiliation":[{"name":"Department of Pathology and Immunology,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael M.","family":"Ittmann","sequence":"additional","affiliation":[{"name":"Department of Pathology and Immunology,"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wei","family":"Li","sequence":"additional","affiliation":[{"name":"Department of Molecular and Cellular Biology,"},{"name":"Division of Biostatistics, Dan L. Duncan Cancer Center, Baylor College of Medicine, Houston, TX 77030"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laising","family":"Yen","sequence":"additional","affiliation":[{"name":"Department of Pathology and Immunology,"},{"name":"Department of Molecular and Cellular Biology,"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"341","published-online":{"date-parts":[[2011,5,12]]},"reference":[{"key":"e_1_3_4_1_2","doi-asserted-by":"crossref","first-page":"206","DOI":"10.1038\/nature08452","article-title":"Implications of chimaeric non-co-linear transcripts","volume":"461","author":"Gingeras TR","year":"2009","unstructured":"TR Gingeras, Implications of chimaeric non-co-linear transcripts. 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Cancer Res 66, 8337\u20138341 (2006).","journal-title":"Cancer Res"},{"key":"e_1_3_4_10_2","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1126\/science.1117679","article-title":"Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer","volume":"310","author":"Tomlins SA","year":"2005","unstructured":"SA Tomlins, et al., Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science 310, 644\u2013648 (2005).","journal-title":"Science"},{"key":"e_1_3_4_11_2","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1146\/annurev.genom.9.081307.164359","article-title":"Next-generation DNA sequencing methods","volume":"9","author":"Mardis ER","year":"2008","unstructured":"ER Mardis, Next-generation DNA sequencing methods. 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