메뉴 건너뛰기




Volumn 7, Issue 1, 2015, Pages

Widespread intron retention diversifies most cancer transcriptomes

Author keywords

[No Author keywords available]

Indexed keywords

ISOCITRATE DEHYDROGENASE 1; ISOCITRATE DEHYDROGENASE 2; TRANSCRIPTOME;

EID: 84933515376     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-015-0168-9     Document Type: Article
Times cited : (260)

References (63)
  • 2
    • 84555192302 scopus 로고    scopus 로고
    • Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes
    • Graubert TA, Shen D, Ding L, Okeyo-Owuor T, Lunn CL, Shao J, et al. Recurrent mutations in the U2AF1 splicing factor in myelodysplastic syndromes. Nat Genet. 2012;44:53-7.
    • (2012) Nat Genet , vol.44 , pp. 53-57
    • Graubert, T.A.1    Shen, D.2    Ding, L.3    Okeyo-Owuor, T.4    Lunn, C.L.5    Shao, J.6
  • 4
    • 84857994411 scopus 로고    scopus 로고
    • SF3B1, a splicing factor is frequently mutated in refractory anemia with ring sideroblasts
    • Visconte V, Makishima H, Jankowska A, Szpurka H, Traina F, Jerez A, et al. SF3B1, a splicing factor is frequently mutated in refractory anemia with ring sideroblasts. Leukemia. 2012;26:542-5.
    • (2012) Leukemia , vol.26 , pp. 542-545
    • Visconte, V.1    Makishima, H.2    Jankowska, A.3    Szpurka, H.4    Traina, F.5    Jerez, A.6
  • 5
    • 84555171449 scopus 로고    scopus 로고
    • Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia
    • Quesada VV, Conde LL, Villamor NN, Ordóñez GRG, Jares PP, Bassaganyas LL, et al. Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nat Genet. 2012;44:47-52.
    • (2012) Nat Genet , vol.44 , pp. 47-52
    • Quesada, V.V.1    Conde, L.L.2    Villamor, N.N.3    Ordóñez, G.R.G.4    Jares, P.P.5    Bassaganyas, L.L.6
  • 6
    • 84866410479 scopus 로고    scopus 로고
    • Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing
    • Imielinski M, Berger AH, Hammerman PS, Hernandez B, Pugh TJ, Hodis E, et al. Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing. Cell. 2012;150:1107-20.
    • (2012) Cell , vol.150 , pp. 1107-1120
    • Imielinski, M.1    Berger, A.H.2    Hammerman, P.S.3    Hernandez, B.4    Pugh, T.J.5    Hodis, E.6
  • 7
    • 84877028141 scopus 로고    scopus 로고
    • Comprehensive molecular portraits of human breast tumours
    • Cancer Genome Atlas Network. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490:61-70.
    • (2012) Nature , vol.490 , pp. 61-70
  • 9
    • 84881030814 scopus 로고    scopus 로고
    • Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3
    • Martin M, Maßhöfer L, Temming P, Rahmann S, Metz C, Bornfeld N, et al. Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3. Nat Genet. 2013;45:933-6.
    • (2013) Nat Genet , vol.45 , pp. 933-936
    • Martin, M.1    Maßhöfer, L.2    Temming, P.3    Rahmann, S.4    Metz, C.5    Bornfeld, N.6
  • 11
    • 84899748605 scopus 로고    scopus 로고
    • A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events
    • Brooks AN, Choi PS, de Waal L, Sharifnia T, Imielinski M, Saksena G, et al. A pan-cancer analysis of transcriptome changes associated with somatic mutations in U2AF1 reveals commonly altered splicing events. PLoS One. 2014;9:e87361-1.
    • (2014) PLoS One , vol.9 , pp. e87361-e87361
    • Brooks, A.N.1    Choi, P.S.2    Waal, L.3    Sharifnia, T.4    Imielinski, M.5    Saksena, G.6
  • 14
    • 84929162813 scopus 로고    scopus 로고
    • SRSF2 mutations contribute to myelodysplasia by mutant-specific effects on exon recognition
    • Kim E, Ilagan JO, Liang Y, Daubner MG, Lee S-W, Ramakrishnan A, et al. SRSF2 mutations contribute to myelodysplasia by mutant-specific effects on exon recognition. Cancer Cell. 2015;27:617-30.
    • (2015) Cancer Cell , vol.27 , pp. 617-630
    • Kim, E.1    Ilagan, J.O.2    Liang, Y.3    Daubner, M.G.4    Lee, S.-W.5    Ramakrishnan, A.6
  • 15
    • 0030466895 scopus 로고    scopus 로고
    • New antitumor substances, FR901463, FR901464 and FR901465, II. Activities against experimental tumors in mice and mechanism of action
    • Nakajima H, Hori Y, Terano H, Okuhara M, Manda T, Matsumoto S, et al. New antitumor substances, FR901463, FR901464 and FR901465, II. Activities against experimental tumors in mice and mechanism of action. J Antibiot. 1996;49:1204-11.
    • (1996) J Antibiot , vol.49 , pp. 1204-1211
    • Nakajima, H.1    Hori, Y.2    Terano, H.3    Okuhara, M.4    Manda, T.5    Matsumoto, S.6
  • 17
    • 84877308573 scopus 로고    scopus 로고
    • Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A
    • Hubert CG, Bradley RK, Ding Y, Toledo CM, Herman J, Skutt-Kakaria K, et al. Genome-wide RNAi screens in human brain tumor isolates reveal a novel viability requirement for PHF5A. Genes Dev. 2013;27:1032-45.
    • (2013) Genes Dev , vol.27 , pp. 1032-1045
    • Hubert, C.G.1    Bradley, R.K.2    Ding, Y.3    Toledo, C.M.4    Herman, J.5    Skutt-Kakaria, K.6
  • 18
    • 80054962704 scopus 로고    scopus 로고
    • Increased levels of noisy splicing in cancers, but not for oncogene-derived transcripts
    • Chen L, Tovar-Corona JM, Urrutia AO. Increased levels of noisy splicing in cancers, but not for oncogene-derived transcripts. Hum Mol Genet. 2011;20:4422-9.
    • (2011) Hum Mol Genet , vol.20 , pp. 4422-4429
    • Chen, L.1    Tovar-Corona, J.M.2    Urrutia, A.O.3
  • 19
    • 84893664978 scopus 로고    scopus 로고
    • Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects
    • Simon JM, Hacker KE, Singh D, Brannon AR, Parker JS, Weiser M, et al. Variation in chromatin accessibility in human kidney cancer links H3K36 methyltransferase loss with widespread RNA processing defects. Genome Res. 2014;24:241-50.
    • (2014) Genome Res , vol.24 , pp. 241-250
    • Simon, J.M.1    Hacker, K.E.2    Singh, D.3    Brannon, A.R.4    Parker, J.S.5    Weiser, M.6
  • 20
    • 84921718196 scopus 로고    scopus 로고
    • Whole transcriptome sequencing reveals extensive unspliced mRNA in metastatic castration-resistant prostate cancer
    • Sowalsky AG, Xia Z, Wang L, Zhao H, Chen S, Bubley GJ, et al. Whole transcriptome sequencing reveals extensive unspliced mRNA in metastatic castration-resistant prostate cancer. Mol Cancer Res. 2015;13:98-106.
    • (2015) Mol Cancer Res , vol.13 , pp. 98-106
    • Sowalsky, A.G.1    Xia, Z.2    Wang, L.3    Zhao, H.4    Chen, S.5    Bubley, G.J.6
  • 23
    • 79952122331 scopus 로고    scopus 로고
    • Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing
    • Sun Z, Asmann YW, Kalari KR, Bot B, Eckel-Passow JE, Baker TR, et al. Integrated analysis of gene expression, CpG island methylation, and gene copy number in breast cancer cells by deep sequencing. PLoS One. 2011;6, e17490.
    • (2011) PLoS One , vol.6
    • Sun, Z.1    Asmann, Y.W.2    Kalari, K.R.3    Bot, B.4    Eckel-Passow, J.E.5    Baker, T.R.6
  • 25
    • 78649714014 scopus 로고    scopus 로고
    • Analysis and design of RNA sequencing experiments for identifying isoform regulation
    • Katz Y, Wang ET, Airoldi EM, Burge CB. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat Methods. 2010;7:1009-15.
    • (2010) Nat Methods , vol.7 , pp. 1009-1015
    • Katz, Y.1    Wang, E.T.2    Airoldi, E.M.3    Burge, C.B.4
  • 28
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
    • (2009) Genome Biol , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 29
    • 79961123152 scopus 로고    scopus 로고
    • RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
    • Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinform. 2011;12:323.
    • (2011) BMC Bioinform , vol.12 , pp. 323
    • Li, B.1    Dewey, C.N.2
  • 30
    • 84876996918 scopus 로고    scopus 로고
    • TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
    • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 2013;14:R36.
    • (2013) Genome Biol , vol.14 , pp. R36
    • Kim, D.1    Pertea, G.2    Trapnell, C.3    Pimentel, H.4    Kelley, R.5    Salzberg, S.L.6
  • 32
    • 77953176036 scopus 로고    scopus 로고
    • A scaling normalization method for differential expression analysis of RNA-seq data
    • Robinson MD, Oshlack A. A scaling normalization method for differential expression analysis of RNA-seq data. Genome Biol. 2010;11:R25.
    • (2010) Genome Biol , vol.11 , pp. R25
    • Robinson, M.D.1    Oshlack, A.2
  • 33
    • 77649192250 scopus 로고    scopus 로고
    • Bayesian hypothesis testing for psychologists: a tutorial on the Savage-Dickey method
    • Wagenmakers E-J, Lodewyckx T, Kuriyal H, Grasman R. Bayesian hypothesis testing for psychologists: a tutorial on the Savage-Dickey method. Cogn Psychol. 2010;60:158-89.
    • (2010) Cogn Psychol , vol.60 , pp. 158-189
    • Wagenmakers, E.-J.1    Lodewyckx, T.2    Kuriyal, H.3    Grasman, R.4
  • 34
    • 77953212372 scopus 로고    scopus 로고
    • Gene ontology analysis for RNA-seq: accounting for selection bias
    • Young MD, Wakefield MJ, Smyth GK, Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010;11:R14.
    • (2010) Genome Biol , vol.11 , pp. R14
    • Young, M.D.1    Wakefield, M.J.2    Smyth, G.K.3    Oshlack, A.4
  • 35
    • 2442441507 scopus 로고    scopus 로고
    • Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals
    • Yeo G, Burge CB. Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals. J Comput Biol. 2004;11:377-94.
    • (2004) J Comput Biol , vol.11 , pp. 377-394
    • Yeo, G.1    Burge, C.B.2
  • 36
    • 78650862532 scopus 로고    scopus 로고
    • Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models
    • Wood SN. Fast stable restricted maximum likelihood and marginal likelihood estimation of semiparametric generalized linear models. J R Stat Soc. 2010;73:3-36.
    • (2010) J R Stat Soc , vol.73 , pp. 3-36
    • Wood, S.N.1
  • 37
    • 0036841485 scopus 로고    scopus 로고
    • Changes in differential gene expression because of warm ischemia time of radical prostatectomy specimens
    • Dash A, Maine IP, Varambally S, Shen R, Chinnaiyan AM, Rubin MA. Changes in differential gene expression because of warm ischemia time of radical prostatectomy specimens. Am J Pathol. 2002;161:1743-8.
    • (2002) Am J Pathol , vol.161 , pp. 1743-1748
    • Dash, A.1    Maine, I.P.2    Varambally, S.3    Shen, R.4    Chinnaiyan, A.M.5    Rubin, M.A.6
  • 39
    • 46249092601 scopus 로고    scopus 로고
    • Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites
    • Sandberg R, Neilson JR, Sarma A, Sharp PA, Burge CB. Proliferating cells express mRNAs with shortened 3' untranslated regions and fewer microRNA target sites. Science. 2008;320:1643-7.
    • (2008) Science , vol.320 , pp. 1643-1647
    • Sandberg, R.1    Neilson, J.R.2    Sarma, A.3    Sharp, P.A.4    Burge, C.B.5
  • 41
    • 33947653234 scopus 로고    scopus 로고
    • Sequence features responsible for intron retention in human
    • Sakabe NJ, de Souza SJ. Sequence features responsible for intron retention in human. BMC Genomics. 2007;8:59.
    • (2007) BMC Genomics , vol.8 , pp. 59
    • Sakabe, N.J.1    Souza, S.J.2
  • 42
    • 84878372012 scopus 로고    scopus 로고
    • Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia
    • Cancer Genome Atlas Research Network. Genomic and epigenomic landscapes of adult de novo acute myeloid leukemia. New Eng J Med. 2013;368:2059-74.
    • (2013) New Eng J Med , vol.368 , pp. 2059-2074
  • 43
    • 84860747223 scopus 로고    scopus 로고
    • Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia
    • Smith CC, Wang Q, Chin C-S, Salerno S, Damon LE, Levis MJ, et al. Validation of ITD mutations in FLT3 as a therapeutic target in human acute myeloid leukaemia. Nature. 2012;485:260-3.
    • (2012) Nature , vol.485 , pp. 260-263
    • Smith, C.C.1    Wang, Q.2    Chin, C.-S.3    Salerno, S.4    Damon, L.E.5    Levis, M.J.6
  • 44
    • 84893735484 scopus 로고    scopus 로고
    • Recurrent mutations, including NPM1c, activate a BRD4-dependent core transcriptional program in acute myeloid leukemia
    • Dawson MA, Gudgin EJ, Horton SJ, Giotopoulos G, Meduri E, Robson S, et al. Recurrent mutations, including NPM1c, activate a BRD4-dependent core transcriptional program in acute myeloid leukemia. Leukemia. 2014;28:311-20.
    • (2014) Leukemia , vol.28 , pp. 311-320
    • Dawson, M.A.1    Gudgin, E.J.2    Horton, S.J.3    Giotopoulos, G.4    Meduri, E.5    Robson, S.6
  • 46
    • 80052322960 scopus 로고    scopus 로고
    • An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype
    • Shapiro IM, Cheng AW, Flytzanis NC, Balsamo M, Condeelis JS, Oktay MH, et al. An EMT-driven alternative splicing program occurs in human breast cancer and modulates cellular phenotype. PLoS Genet. 2011;7, e1002218.
    • (2011) PLoS Genet , vol.7
    • Shapiro, I.M.1    Cheng, A.W.2    Flytzanis, N.C.3    Balsamo, M.4    Condeelis, J.S.5    Oktay, M.H.6
  • 48
    • 80054931284 scopus 로고    scopus 로고
    • Alternatively spliced androgen receptor variants
    • Dehm SM, Tindall DJ. Alternatively spliced androgen receptor variants. Endocr Relat Cancer. 2011;18:R183-96.
    • (2011) Endocr Relat Cancer , vol.18 , pp. R183-R196
    • Dehm, S.M.1    Tindall, D.J.2
  • 49
    • 85027941046 scopus 로고    scopus 로고
    • Hallmarks of alternative splicing in cancer
    • Oltean S, Bates DO. Hallmarks of alternative splicing in cancer. Oncogene. 2014;33:5311-8.
    • (2014) Oncogene , vol.33 , pp. 5311-5318
    • Oltean, S.1    Bates, D.O.2
  • 50
    • 84868355027 scopus 로고    scopus 로고
    • The spliceosome as a target of novel antitumour drugs
    • Bonnal S, Vigevani L, Valcárcel J. The spliceosome as a target of novel antitumour drugs. Nat Rev Drug Discov. 2012;11:847-59.
    • (2012) Nat Rev Drug Discov , vol.11 , pp. 847-859
    • Bonnal, S.1    Vigevani, L.2    Valcárcel, J.3
  • 51
    • 57749093482 scopus 로고    scopus 로고
    • The biflavonoid isoginkgetin is a general inhibitor of Pre-mRNA splicing
    • O'Brien K, Matlin AJ, Lowell AM, Moore MJ. The biflavonoid isoginkgetin is a general inhibitor of Pre-mRNA splicing. J Biol Chem. 2008;283:33147-54.
    • (2008) J Biol Chem , vol.283 , pp. 33147-33154
    • O'Brien, K.1    Matlin, A.J.2    Lowell, A.M.3    Moore, M.J.4
  • 52
    • 34548095157 scopus 로고    scopus 로고
    • Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA
    • Kaida D, Motoyoshi H, Tashiro E, Nojima T, Hagiwara M, Ishigami K, et al. Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre-mRNA. Nat Chem Biol. 2007;3:576-83.
    • (2007) Nat Chem Biol , vol.3 , pp. 576-583
    • Kaida, D.1    Motoyoshi, H.2    Tashiro, E.3    Nojima, T.4    Hagiwara, M.5    Ishigami, K.6
  • 53
    • 84877108379 scopus 로고    scopus 로고
    • DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure
    • Gelfman S, Cohen N, Yearim A, Ast G. DNA-methylation effect on cotranscriptional splicing is dependent on GC architecture of the exon-intron structure. Genome Res. 2013;23:789-99.
    • (2013) Genome Res , vol.23 , pp. 789-799
    • Gelfman, S.1    Cohen, N.2    Yearim, A.3    Ast, G.4
  • 54
    • 69749092741 scopus 로고    scopus 로고
    • High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
    • Hodges E, Smith AD, Kendall J, Xuan Z, Ravi K, Rooks M, et al. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing. Genome Res. 2009;19:1593-605.
    • (2009) Genome Res , vol.19 , pp. 1593-1605
    • Hodges, E.1    Smith, A.D.2    Kendall, J.3    Xuan, Z.4    Ravi, K.5    Rooks, M.6
  • 56
    • 78649955848 scopus 로고    scopus 로고
    • The honey bee epigenomes: differential methylation of brain DNA in queens and workers
    • Lyko F, Foret S, Kucharski R, Wolf S, Falckenhayn C, Maleszka R. The honey bee epigenomes: differential methylation of brain DNA in queens and workers. PLoS Biol. 2010;8, e1000506.
    • (2010) PLoS Biol , vol.8
    • Lyko, F.1    Foret, S.2    Kucharski, R.3    Wolf, S.4    Falckenhayn, C.5    Maleszka, R.6
  • 58
    • 0034699472 scopus 로고    scopus 로고
    • The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans
    • Zhou Z, Luo MJ, Straesser K, Katahira J, Hurt E, Reed R. The protein Aly links pre-messenger-RNA splicing to nuclear export in metazoans. Nature. 2000;407:401-5.
    • (2000) Nature , vol.407 , pp. 401-405
    • Zhou, Z.1    Luo, M.J.2    Straesser, K.3    Katahira, J.4    Hurt, E.5    Reed, R.6
  • 59
    • 0035025061 scopus 로고    scopus 로고
    • Splicing factors SRp20 and 9G8 promote the nucleocytoplasmic export of mRNA
    • Huang Y, Steitz JA. Splicing factors SRp20 and 9G8 promote the nucleocytoplasmic export of mRNA. Mol Cell. 2001;7:899-905.
    • (2001) Mol Cell , vol.7 , pp. 899-905
    • Huang, Y.1    Steitz, J.A.2
  • 61
    • 0034672093 scopus 로고    scopus 로고
    • The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions
    • Le Hir H, Izaurralde E, Maquat LE, Moore MJ. The spliceosome deposits multiple proteins 20-24 nucleotides upstream of mRNA exon-exon junctions. EMBO J. 2000;19:6860-9.
    • (2000) EMBO J , vol.19 , pp. 6860-6869
    • Hir, H.1    Izaurralde, E.2    Maquat, L.E.3    Moore, M.J.4
  • 62
    • 0033634824 scopus 로고    scopus 로고
    • Pre-mRNA splicing imprints mRNA in the nucleus with a novel RNA-binding protein that persists in the cytoplasm
    • Kataoka N, Yong J, Kim VN, Velazquez F, Perkinson RA, Wang F, et al. Pre-mRNA splicing imprints mRNA in the nucleus with a novel RNA-binding protein that persists in the cytoplasm. Mol Cell. 2000;6:673-82.
    • (2000) Mol Cell , vol.6 , pp. 673-682
    • Kataoka, N.1    Yong, J.2    Kim, V.N.3    Velazquez, F.4    Perkinson, R.A.5    Wang, F.6
  • 63
    • 0033592896 scopus 로고    scopus 로고
    • Splicing is required for rapid and efficient mRNA export in metazoans
    • Luo MJ, Reed R. Splicing is required for rapid and efficient mRNA export in metazoans. Proc Natl Acad Sci U S A. 1999;96:14937-42.
    • (1999) Proc Natl Acad Sci U S A , vol.96 , pp. 14937-14942
    • Luo, M.J.1    Reed, R.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.