References
- Pajares MJ, Ezponda T, Catena R, Calvo A, Pio R, Montuenga LM. Alternative splicing: an emerging topic in molecular and clinical oncology. Lancet Oncol 2007;8:349-357. https://doi.org/10.1016/S1470-2045(07)70104-3
- Wahl MC, Will CL, Lührmann R. The spliceosome: design principles of a dynamic RNP machine. Cell 2009;136:701-718. https://doi.org/10.1016/j.cell.2009.02.009
- Matlin AJ, Clark F, Smith CW. Understanding alternative splicing: towards a cellular code. Nat Rev Mol Cell Biol 2005;6:386-398. https://doi.org/10.1038/nrm1645
- Nilsen TW, Graveley BR. Expansion of the eukaryotic proteome by alternative splicing. Nature 2010;463:457-463. https://doi.org/10.1038/nature08909
- Wang ET, Sandberg R, Luo S, Khrebtukova I, Zhang L, Mayr C, et al. Alternative isoform regulation in human tissue transcriptomes. Nature 2008;456:470-476. https://doi.org/10.1038/nature07509
- Pan Q, Shai O, Lee LJ, Frey BJ, Blencowe BJ. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing. Nat Genet 2008;40:1413-1415. https://doi.org/10.1038/ng.259
- Brinkman BM. Splice variants as cancer biomarkers. Clin Biochem 2004;37:584-594. https://doi.org/10.1016/j.clinbiochem.2004.05.015
- Skotheim RI, Nees M. Alternative splicing in cancer: noise, functional, or systematic? Int J Biochem Cell Biol 2007;39:1432-1449. https://doi.org/10.1016/j.biocel.2007.02.016
- Chang YF, Imam JS, Wilkinson MF. The nonsense-mediated decay RNA surveillance pathway. Annu Rev Biochem 2007;76:51-74. https://doi.org/10.1146/annurev.biochem.76.050106.093909
- Cáceres JF, Kornblihtt AR. Alternative splicing: multiple control mechanisms and involvement in human disease. Trends Genet 2002;18:186-193. https://doi.org/10.1016/S0168-9525(01)02626-9
- Cartegni L, Chew SL, Krainer AR. Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat Rev Genet 2002;3:285-298. https://doi.org/10.1038/nrg775
- Wang J, Zhang J, Li K, Zhao W, Cui Q. SpliceDisease database: linking RNA splicing and disease. Nucleic Acids Res 2012;40:D1055-D1059. https://doi.org/10.1093/nar/gkr1171
- Venables JP. Unbalanced alternative splicing and its significance in cancer. Bioessays 2006;28:378-386. https://doi.org/10.1002/bies.20390
- Venables JP. Aberrant and alternative splicing in cancer. Cancer Res 2004;64:7647-7654. https://doi.org/10.1158/0008-5472.CAN-04-1910
- Black DL. Mechanisms of alternative pre-messenger RNA splicing. Annu Rev Biochem 2003;72:291-336. https://doi.org/10.1146/annurev.biochem.72.121801.161720
- López-Bigas N, Ouzounis CA. Genome-wide identification of genes likely to be involved in human genetic disease. Nucleic Acids Res 2004;32:3108-3114. https://doi.org/10.1093/nar/gkh605
- López-Bigas N, Audit B, Ouzounis C, Parra G, Guigó R. Are splicing mutations the most frequent cause of hereditary disease? FEBS Lett 2005;579:1900-1903. https://doi.org/10.1016/j.febslet.2005.02.047
- Weisschuh N, Wissinger B, Gramer E. A splice site mutation in the PAX6 gene which induces exon skipping causes autosomal dominant inherited aniridia. Mol Vis 2012;18:751-757.
- Kurahashi H, Takami K, Oue T, Kusafuka T, Okada A, Tawa A, et al. Biallelic inactivation of the APC gene in hepatoblastoma. Cancer Res 1995;55:5007-5011.
- Agrawal A, Hamvas A, Cole FS, Wambach JA, Wegner D, Coghill C, et al. An intronic ABCA3 mutation that is responsible for respiratory disease. Pediatr Res 2012;71:633-637. https://doi.org/10.1038/pr.2012.21
- Jackson IJ. A reappraisal of non-consensus mRNA splice sites. Nucleic Acids Res 1991;19:3795-3798. https://doi.org/10.1093/nar/19.14.3795
- Xue J, Rask L. The unusual 5' splicing border GC is used in myrosinase genes of the Brassicaceae. Plant Mol Biol 1995;29:167-171. https://doi.org/10.1007/BF00019128
- Burset M, Seledtsov IA, Solovyev VV. Analysis of canonical and non-canonical splice sites in mammalian genomes. Nucleic Acids Res 2000;28:4364-4375. https://doi.org/10.1093/nar/28.21.4364
- Xiong F, Gao J, Li J, Liu Y, Feng G, Fang W, et al. Noncanonical and canonical splice sites: a novel mutation at the rare noncanonical splice-donor cut site (IVS4 + 1A > G) of SEDL causes variable splicing isoforms in X-linked spondyloepiphyseal dysplasia tarda. Eur J Hum Genet 2009;17:510-516. https://doi.org/10.1038/ejhg.2008.219
- Kim E, Goren A, Ast G. Insights into the connection between cancer and alternative splicing. Trends Genet 2008;24:7-10. https://doi.org/10.1016/j.tig.2007.10.001
- Dominissini D, Moshitch-Moshkovitz S, Amariglio N, Rechavi G. Adenosine-to-inosine RNA editing meets cancer. Carcinogenesis 2011;32:1569-1577. https://doi.org/10.1093/carcin/bgr124
- Maniatis T, Tasic B. Alternative pre-mRNA splicing and proteome expansion in metazoans. Nature 2002;418:236-243. https://doi.org/10.1038/418236a
- Dreyfuss G, Matunis MJ, Piñol-Roma S, Burd CG. hnRNP proteins and the biogenesis of mRNA. Annu Rev Biochem 1993; 62:289-321. https://doi.org/10.1146/annurev.bi.62.070193.001445
- Tacke R, Manley JL. Functions of SR and Tra2 proteins in pre-mRNA splicing regulation. Proc Soc Exp Biol Med 1999;220:59-63.
- Colapietro P, Gervasini C, Natacci F, Rossi L, Riva P, Larizza L. NF1 exon 7 skipping and sequence alterations in exonic splice enhancers (ESEs) in a neurofibromatosis 1 patient. Hum Genet 2003;113:551-554. https://doi.org/10.1007/s00439-003-1009-2
- Ghigna C, Giordano S, Shen H, Benvenuto F, Castiglioni F, Comoglio PM, et al. Cell motility is controlled by SF2/ASF through alternative splicing of the Ron protooncogene. Mol Cell 2005;20:881-890. https://doi.org/10.1016/j.molcel.2005.10.026
- Schwartz S, Meshorer E, Ast G. Chromatin organization marks exon-intron structure. Nat Struct Mol Biol 2009;16:990-995. https://doi.org/10.1038/nsmb.1659
- Luco RF, Pan Q, Tominaga K, Blencowe BJ, Pereira-Smith OM, Misteli T. Regulation of alternative splicing by histone modifications. Science 2010;327:996-1000. https://doi.org/10.1126/science.1184208
- Zhou Y, Lu Y, Tian W. Epigenetic features are significantly associated with alternative splicing. BMC Genomics 2012;13:123. https://doi.org/10.1186/1471-2164-13-123
- Andersson R, Enroth S, Rada-Iglesias A, Wadelius C, Komorowski J. Nucleosomes are well positioned in exons and carry characteristic histone modifications. Genome Res 2009;19:1732-1741. https://doi.org/10.1101/gr.092353.109
- Kolasinska-Zwierz P, Down T, Latorre I, Liu T, Liu XS, Ahringer J. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat Genet 2009;41:376-381. https://doi.org/10.1038/ng.322
- Wilhelm BT, Marguerat S, Aligianni S, Codlin S, Watt S, Bähler J. Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast. Genome Biol 2011;12:R82. https://doi.org/10.1186/gb-2011-12-8-r82
- Gunderson FQ, Merkhofer EC, Johnson TL. Dynamic histone acetylation is critical for cotranscriptional spliceosome assembly and spliceosomal rearrangements. Proc Natl Acad Sci U S A 2011;108:2004-2009. https://doi.org/10.1073/pnas.1011982108
- Shukla S, Kavak E, Gregory M, Imashimizu M, Shutinoski B, Kashlev M, et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing. Nature 2011;479:74-79. https://doi.org/10.1038/nature10442
- David CJ, Manley JL. Alternative pre-mRNA splicing regulation in cancer: pathways and programs unhinged. Genes Dev 2010;24:2343-2364. https://doi.org/10.1101/gad.1973010
- Venables JP, Klinck R, Koh C, Gervais-Bird J, Bramard A, Inkel L, et al. Cancer-associated regulation of alternative splicing. Nat Struct Mol Biol 2009;16:670-676. https://doi.org/10.1038/nsmb.1608
- Stickeler E, Kittrell F, Medina D, Berget SM. Stage-specific changes in SR splicing factors and alternative splicing in mammary tumorigenesis. Oncogene 1999;18:3574-3582. https://doi.org/10.1038/sj.onc.1202671
- Naor D, Nedvetzki S, Golan I, Melnik L, Faitelson Y. CD44 in cancer. Crit Rev Clin Lab Sci 2002;39:527-579. https://doi.org/10.1080/10408360290795574
- Faustino NA, Cooper TA. Pre-mRNA splicing and human disease. Genes Dev 2003;17:419-437. https://doi.org/10.1101/gad.1048803
- Kalnina Z, Zayakin P, Silina K, Linē A. Alterations of premRNA splicing in cancer. Genes Chromosomes Cancer 2005;42:342-357. https://doi.org/10.1002/gcc.20156
- Okumura N, Yoshida H, Kitagishi Y, Nishimura Y, Matsuda S. Alternative splicings on p53, BRCA1 and PTEN genes involved in breast cancer. Biochem Biophys Res Commun 2011;413:395-399. https://doi.org/10.1016/j.bbrc.2011.08.098
- Wei J, Zaika E, Zaika A. p53 family: role of protein isoforms in human cancer. J Nucleic Acids 2012;2012:687359.
- Neklason DW, Solomon CH, Dalton AL, Kuwada SK, Burt RW. Intron 4 mutation in APC gene results in splice defect and attenuated FAP phenotype. Fam Cancer 2004;3:35-40.
- Olopade OI, Adeyanju MO, Safa AR, Hagos F, Mick R, Thompson CB, et al. Overexpression of BCL-x protein in primary breast cancer is associated with high tumor grade and nodal metastases. Cancer J Sci Am 1997;3:230-237.
- Takehara T, Liu X, Fujimoto J, Friedman SL, Takahashi H. Expression and role of Bcl-xL in human hepatocellular carcinomas. Hepatology 2001;34:55-61. https://doi.org/10.1016/S0168-8278(01)81060-6
- Woolard J, Wang WY, Bevan HS, Qiu Y, Morbidelli L, Pritchard-Jones RO, et al. VEGF165b, an inhibitory vascular endothelial growth factor splice variant: mechanism of action, in vivo effect on angiogenesis and endogenous protein expression. Cancer Res 2004;64:7822-7835. https://doi.org/10.1158/0008-5472.CAN-04-0934
- Pritchard-Jones RO, Dunn DB, Qiu Y, Varey AH, Orlando A, Rigby H, et al. Expression of VEGF(xxx)b, the inhibitory isoforms of VEGF, in malignant melanoma. Br J Cancer 2007;97:223-230. https://doi.org/10.1038/sj.bjc.6603839
- Bartel F, Taubert H, Harris LC. Alternative and aberrant splicing of MDM2 mRNA in human cancer. Cancer Cell 2002;2:9-15.
- Bartel F, Harris LC, Wurl P, Taubert H. MDM2 and its splice variant messenger RNAs: expression in tumors and downregulation using antisense oligonucleotides. Mol Cancer Res 2004;2:29-35.
- Arvanitis DA, Lianos E, Soulitzis N, Delakas D, Spandidos DA. Deregulation of p73 isoform equilibrium in benign prostate hyperplasia and prostate cancer. Oncol Rep 2004;12:1131-1137.
- Line A, Slucka Z, Stengrevics A, Li G, Rees RC. Altered splicing pattern of TACC1 mRNA in gastric cancer. Cancer Genet Cytogenet 2002;139:78-83. https://doi.org/10.1016/S0165-4608(02)00607-6
- Kotoula V, Barbanis S, Nikolakaki E, Koufoyannis D, Papadimitriou CS, Karkavelas G. Relative expression of human telomerase catalytic subunit (hTERT) transcripts in astrocytic gliomas. Acta Neuropathol 2004;107:443-451. https://doi.org/10.1007/s00401-004-0832-4
- DiFeo A, Martignetti JA, Narla G. The role of KLF6 and its splice variants in cancer therapy. Drug Resist Updat 2009;12:1-7. https://doi.org/10.1016/j.drup.2008.11.001
- Li F. Role of survivin and its splice variants in tumorigenesis. Br J Cancer 2005;92:212-216. https://doi.org/10.1038/sj.bjc.6602340
- Hu Y, Fang C, Xu Y. The effect of isoforms of the cell polarity protein, human ASIP, on the cell cycle and Fas/FasL-mediated apoptosis in human hepatoma cells. Cell Mol Life Sci 2005;62:1974-1983. https://doi.org/10.1007/s00018-005-5134-z
- Barron VA, Lou H. Alternative splicing of the neurofibromatosis type I pre-mRNA. Biosci Rep 2012;32:131-138. https://doi.org/10.1042/BSR20110060
- Mohr A, Zwacka RM, Jarmy G, Büneker C, Schrezenmeier H, Döhner K, et al. Caspase-8L expression protects CD34+ hematopoietic progenitor cells and leukemic cells from CD95- mediated apoptosis. Oncogene 2005;24:2421-2429. https://doi.org/10.1038/sj.onc.1208432
- Wang XQ, Luk JM, Leung PP, Wong BW, Stanbridge EJ, Fan ST. Alternative mRNA splicing of liver intestine-cadherin in hepatocellular carcinoma. Clin Cancer Res 2005;11(2 Pt 1):483-489.
- Pettigrew CA, Brown MA. Pre-mRNA splicing aberrations and cancer. Front Biosci 2008;13:1090-1105. https://doi.org/10.2741/2747
- Cuperlovic-Culf M, Belacel N, Culf AS, Ouellette RJ. Data analysis of alternative splicing microarrays. Drug Discov Today 2006;11:983-990. https://doi.org/10.1016/j.drudis.2006.09.011
- Omenn GS, Yocum AK, Menon R. Alternative splice variants, a new class of protein cancer biomarker candidates: findings in pancreatic cancer and breast cancer with systems biology implications. Dis Markers 2010;28:241-251. https://doi.org/10.1155/2010/705847
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