Abe N, Matsumoto K, Nishihara M, et al. (2015) Rolling circle translation of circular RNA in living human cells. Scientific Reports 5: 16435.
Bachmayr‐Heyda A, Reiner AT, Auer K, et al. (2015) Correlation of circular RNA abundance with proliferation–exemplified with colorectal and ovarian cancer, idiopathic lung fibrosis, and normal human tissues. Scientific Reports 5: 8057.
Barash Y, Calarco JA, Gao W, et al. (2010) Deciphering the splicing code. Nature 465: 53–59.
Barbosa‐Morais NL, Irimia M, Pan Q, et al. (2012) The evolutionary landscape of alternative splicing in vertebrate species. Science 338: 1587–1593.
Birgens H and Ljung R (2007) The thalassaemia syndromes. Scandinavian Journal of Clinical and Laboratory Investigation 67: 11–25.
Boon KL, Grainger RJ, Ehsani P, et al. (2007) prp8 mutations that cause human retinitis pigmentosa lead to a U5 snRNP maturation defect in yeast. Nature Structural and Molecular Biology 14: 1077–1083.
Burghes AH and Beattie CE (2009) Spinal muscular atrophy: why do low levels of survival motor neuron protein make motor neurons sick? Nature Reviews. Neuroscience 10: 597–609.
Chabot B and Shkreta L (2016) Defective control of pre‐messenger RNA splicing in human disease. The Journal of Cell Biology 212: 13–27.
Chakarova CF, Hims MM, Bolz H, et al. (2002) Mutations in HPRP3, a third member of pre‐mRNA splicing factor genes, implicated in autosomal dominant retinitis pigmentosa. Human Molecular Genetics 11: 87–92.
Chasin LA (2007) Searching for splicing motifs. Advances in Experimental Medicine and Biology 623: 85–106.
Chiriboga CA, Swoboda KJ, Darras BT, et al. (2016) Results from a phase 1 study of nusinersen (ISIS‐SMN(Rx)) in children with spinal muscular atrophy. Neurology 86: 890–897.
Clayton NP, Nelson CA, Weeden T, et al. (2014) Antisense oligonucleotide‐mediated suppression of muscle glycogen synthase 1 synthesis as an approach for substrate reduction therapy of Pompe disease. Molecular Therapy. Nucleic Acids 3: e206.
Convertini P, Shen M, Potter PM, et al. (2014) Sudemycin E influences alternative splicing and changes chromatin modifications. Nucleic Acids Research 42 (8): 4947–4961.
Cooper TA and Mattox W (1997) The regulation of splice‐site selection, and its role in human disease. American Journal of Human Genetics 61: 259–266.
Cooper DN, Stenson PD and Chuzhanova NA (2006) The Human Gene Mutation Database (HGMD) and its exploitation in the study of mutational mechanisms. Current Protocols in Bioinformatics, Chapter 1, Unit 1 13.
Corrionero A, Minana B and Valcarcel J (2011) Reduced fidelity of branch point recognition and alternative splicing induced by the anti‐tumor drug spliceostatin A. Genes & Development 25: 445–459.
Daguenet E, Dujardin G and Valcarcel J (2015) The pathogenicity of splicing defects: mechanistic insights into pre‐mRNA processing inform novel therapeutic approaches. EMBO Reports 16: 1640–1655.
Desmet FO, Hamroun D, Lalande M, et al. (2009) Human Splicing Finder: an online bioinformatics tool to predict splicing signals. Nucleic Acids Research 37: e67.
Dey BK, Mueller AC and Dutta A (2014) Long non‐coding RNAs as emerging regulators of differentiation, development, and disease. Transcription 5: e944014.
Diederichs S, Bartsch L, Berkmann JC, et al. (2016) The dark matter of the cancer genome: aberrations in regulatory elements, untranslated regions, splice sites, non‐coding RNA and synonymous mutations. EMBO Molecular Medicine 8: 442–457.
Donyo M, Hollander D, Abramovitch Z, Naftelberg S and Ast G (2016) Phosphatidylserine enhances IKBKAP transcription by activating the MAPK/ERK signaling pathway. Human Molecular Genetics 25: 1307–1317.
Eskens FA, Ramos FJ, Burger H, et al. (2013) Phase I pharmacokinetic and pharmacodynamic study of the first‐in‐class spliceosome inhibitor E7107 in patients with advanced solid tumors. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research 19: 6296–6304.
Falaleeva M, Pages A, Matuszek Z, et al. (2016) Dual function of C/D box snoRNAs in rRNA modification and alternative pre‐mRNA splicing Proc Natl Acad Sci U S A 113, E1625–1634.
Fan L, Lagisetti C, Edwards CC, Webb TR and Potter PM (2011) Sudemycins, novel small molecule analogues of FR901464, induce alternative gene splicing. ACS Chemical Biology 6: 582–589.
Fardaei M, Rogers MT, Thorpe HM, et al. (2002) Three proteins, MBNL, MBLL and MBXL, co‐localize in vivo with nuclear foci of expanded‐repeat transcripts in DM1 and DM2 cells. Human Molecular Genetics 11: 805–814.
Flanagan SE, Xie W, Caswell R, et al. (2013) Next‐generation sequencing reveals deep intronic cryptic ABCC8 and HADH splicing founder mutations causing hyperinsulinism by pseudoexon activation. American Journal of Human Genetics 92: 131–136.
Friedman KJ, Kole J, Cohn JA, et al. (1999) Correction of aberrant splicing of the cystic fibrosis transmembrane conductance regulator (CFTR) gene by antisense oligonucleotides. Journal of Biological Chemistry 274: 36193–36199.
Gaildrat P, Killian A, Martins A, et al. (2010) Use of splicing reporter minigene assay to evaluate the effect on splicing of unclassified genetic variants. Methods in Molecular Biology 653: 249–257.
Giulietti M, Piva F, D'Antonio M, et al. (2013) SpliceAid‐F: a database of human splicing factors and their RNA‐binding sites. Nucleic Acids Research 41: D125–D131.
Haque A, Buratti E and Baralle FE (2010) Functional properties and evolutionary splicing constraints on a composite exonic regulatory element of splicing in CFTR exon 12. Nucleic Acids Research 38: 647–659.
Hasegawa M, Miura T, Kuzuya K, et al. (2011) Identification of SAP155 as the target of GEX1A (Herboxidiene), an antitumor natural product. ACS Chemical Biology 6: 229–233.
Hasler J, Samuelsson T and Strub K (2007) Useful ‘junk’: Alu RNAs in the human transcriptome. Cellular and Molecular Life Sciences 64: 1793–1800.
Havens MA and Hastings ML (2016) Splice‐switching antisense oligonucleotides as therapeutic drugs. Nucleic Acids Research, pii: gkw533.
He H, Liyanarachchi S, Akagi K, et al. (2011) Mutations in U4atac snRNA, a component of the minor spliceosome, in the developmental disorder MOPD I. Science 332: 238–240.
Hirschfeld M, zur Hausen A, Bettendorf H, Jager M and Stickeler E (2009) Alternative splicing of Cyr61 is regulated by hypoxia and significantly changed in breast cancer. Cancer Research 69: 2082–2090.
Hirschfeld M, Zhang B, Jaeger M, et al. (2013) Hypoxia‐dependent mRNA expression pattern of splicing factor YT521 and its impact on oncological important target gene expression. Molecular Carcinogenesis 53 (11): 883–892.
Hong JY, Seo JY, Kim SH, et al. (2015) Mutations in the spliceosomal machinery genes SRSF2, U2AF1, and ZRSR2 and response to decitabine in myelodysplastic syndrome. Anticancer Research 35: 3081–3089.
Hua Y, Vickers TA, Baker BF, Bennett CF and Krainer AR (2007) Enhancement of SMN2 exon 7 inclusion by antisense oligonucleotides targeting the exon. PLoS Biology 5: e73.
Huang HY, Chien CH, Jen KH and Huang HD (2006) RegRNA: an integrated web server for identifying regulatory RNA motifs and elements. Nucleic Acids Research 34: W429–W434.
Ibrahim el C, Hims MM, Shomron N, et al. (2007) Weak definition of IKBKAP exon 20 leads to aberrant splicing in familial dysautonomia. Human Mutation 28: 41–53.
Jacobson RD and Feldman EL (2016) Antisense oligonucleotides for Duchenne muscular dystrophy: why no neurologist should skip this. JAMA Neurology 73: 259–260.
Jeck WR, Sorrentino JA, Wang K, et al. (2013) Circular RNAs are abundant, conserved, and associated with ALU repeats. RNA 19: 141–157.
Jiang Z, Tang H, Havlioglu N, et al. (2003) Mutations in tau gene exon 10 associated with FTDP‐17 alter the activity of an exonic splicing enhancer to interact with Tra2‐beta1. Journal of Biological Chemistry 278: 18997–19007.
Kaida D, Motoyoshi H, Tashiro E, et al. (2007) Spliceostatin A targets SF3b and inhibits both splicing and nuclear retention of pre‐mRNA. Nature Chemical Biology 3: 576–583.
Kelemen O, Convertini P, Zhang Z, et al. (2013) Function of alternative splicing. Gene 514: 1–30.
Kishore S, Khanna A and Stamm S (2008) Rapid generation of splicing reporters with pSpliceExpress. Gene 427: 104–110.
Kuyumcu‐Martinez NM, Wang GS and Cooper TA (2007) Increased steady‐state levels of CUGBP1 in myotonic dystrophy 1 are due to PKC‐mediated hyperphosphorylation. Molecular Cell 28: 68–78.
Lacerra G, Sierakowska H, Carestia C, et al. (2000) Restoration of hemoglobin A synthesis in erythroid cells from peripheral blood of thalassemic patients. Proceedings of the National Academy of Sciences of the United States of America 97: 9591–9596.
Lagisetti C, Palacios G, Goronga T, et al. (2013) Optimization of antitumor modulators of pre‐mRNA splicing. Journal of Medicinal Chemistry 56: 10033–10044.
Lasda E and Parker R (2014) Circular RNAs: diversity of form and function. RNA 20: 1829–1842.
Lee Y and Rio DC (2015) Mechanisms and regulation of alternative pre‐mRNA splicing. Annual Review of Biochemistry 84: 291–323.
Lentz JJ, Jodelka FM, Hinrich AJ, et al. (2013) Rescue of hearing and vestibular function by antisense oligonucleotides in a mouse model of human deafness. Nature Medicine 19: 345–350.
Liu T, Jin X, Zhang X, et al. (2012) A novel missense SNRNP200 mutation associated with autosomal dominant retinitis pigmentosa in a Chinese family. PLoS One 7: e45464.
Liu X, Biswas S, Berg MG, et al. (2013) Genomics‐guided discovery of thailanstatins A, B, and C As pre‐mRNA splicing inhibitors and antiproliferative agents from Burkholderia thailandensis MSMB43. Journal of Natural Products 76: 685–693.
Lopez‐Mejia IC, Vautrot V, De Toledo M, et al. (2011) A conserved splicing mechanism of the LMNA gene controls premature aging. Human Molecular Genetics 20: 4540–4555.
Lunn MR and Wang CH (2008) Spinal muscular atrophy. Lancet 371: 2120–2133.
Martin M, Masshofer L, Temming P, et al. (2013) Exome sequencing identifies recurrent somatic mutations in EIF1AX and SF3B1 in uveal melanoma with disomy 3. Nature Genetics 45: 933–936.
Merkin J, Russell C, Chen P and Burge CB (2012) Evolutionary dynamics of gene and isoform regulation in Mammalian tissues. Science 338: 1593–1599.
Nielsen KB, Sorensen S, Cartegni L, et al. (2007) Seemingly neutral polymorphic variants may confer immunity to splicing‐inactivating mutations: a synonymous SNP in exon 5 of MCAD protects from deleterious mutations in a flanking exonic splicing enhancer. American Journal of Human Genetics 80: 416–432.
Nigro JM, Cho KR, Fearon ER, et al. (1991) Scrambled exons. Cell 64: 607–613.
Ohe K and Hagiwara M (2015) Modulation of alternative splicing with chemical compounds in new therapeutics for human diseases. ACS Chemical Biology 10: 914–924.
Pecina‐Slaus N, Nikuseva Martic T, Tomas D, et al. (2008) Meningiomas exhibit loss of heterozygosity of the APC gene. Journal of Neuro‐Oncology 87: 63–70.
Pecina‐Slaus N, Majic Z, Musani V, Zeljko M and Cupic H (2010) Report on mutation in exon 15 of the APC gene in a case of brain metastasis. Journal of Neuro‐Oncology 97: 143–148.
Quesada V, Conde L, Villamor N, et al. (2012) Exome sequencing identifies recurrent mutations of the splicing factor SF3B1 gene in chronic lymphocytic leukemia. Nature Genetics 44: 47–52.
Ranum LP and Cooper TA (2006) RNA‐mediated neuromuscular disorders. Annual Review of Neuroscience 29: 259–277.
Raponi M, Upadhyaya M and Baralle D (2006) Functional splicing assay shows a pathogenic intronic mutation in neurofibromatosis type 1 (NF1) due to intronic sequence exonization. Human Mutation 27: 294–295.
Raponi M, Kralovicova J, Copson E, et al. (2011) Prediction of single‐nucleotide substitutions that result in exon skipping: identification of a splicing silencer in BRCA1 exon 6. Human Mutation 32: 436–444.
Rigo F, Chun SJ, Norris DA, et al. (2014) Pharmacology of a central nervous system delivered 2'‐O‐methoxyethyl‐modified survival of motor neuron splicing oligonucleotide in mice and non‐human primates. The Journal of Pharmacology and Experimental Therapeutics 350 (1): 46–55.
Salzman J, Chen RE, Olsen MN, Wang PL and Brown PO (2013) Cell‐type specific features of circular RNA expression. PLoS Genetics 9: e1003777.
Scaffidi P and Misteli T (2005) Reversal of the cellular phenotype in the premature aging disease Hutchinson‐Gilford progeria syndrome. Nature Medicine 11: 440–445.
Scotter EL, Chen HJ and Shaw CE (2015) TDP‐43 proteinopathy and ALS: insights into disease mechanisms and therapeutic targets. Neurotherapeutics 12: 352–363.
Shen H, Zheng X, Luecke S and Green MR (2010) The U2AF35‐related protein Urp contacts the 3' splice site to promote U12‐type intron splicing and the second step of U2‐type intron splicing. Genes & Development 24: 2389–2394.
Singh NN, Androphy EJ and Singh RN (2004) An extended inhibitory context causes skipping of exon 7 of SMN2 in spinal muscular atrophy. Biochemical and Biophysical Research Communications 315: 381–388.
Singh RN (2007) Evolving concepts on human SMN pre‐mRNA splicing. RNA Biology 4: 7–10.
Singh RK and Cooper TA (2012) Pre‐mRNA splicing in disease and therapeutics. Trends in Molecular Medicine 18: 472–482.
Smith PJ, Zhang C, Wang J, et al. (2006) An increased specificity score matrix for the prediction of SF2/ASF‐specific exonic splicing enhancers. Human Molecular Genetics 15: 2490–2508.
Stoilov P, Lin CH, Damoiseaux R, Nikolic J and Black DL (2008) A high‐throughput screening strategy identifies cardiotonic steroids as alternative splicing modulators. Proceedings of the National Academy of Sciences of the United States of America 105: 11218–11223.
Stoss O, Stoilov P, Hartmann AM, Nayler O and Stamm S (1999) The in vivo minigene approach to analyze tissue‐specific splicing. Brain Research Protocols 4: 383–394.
Sumanasekera C, Watt DS and Stamm S (2008) Substances that can change alternative splice‐site selection. Biochemical Society Transactions 36: 483–490.
Supek F, Minana B, Valcarcel J, Gabaldon T and Lehner B (2014) Synonymous mutations frequently act as driver mutations in human cancers. Cell 156: 1324–1335.
Tiscornia G and Mahadevan MS (2000) Myotonic dystrophy: the role of the CUG triplet repeats in splicing of a novel DMPK exon and altered cytoplasmic DMPK mRNA isoform ratios. Molecular Cell 5: 959–967.
Turunen JJ, Niemela EH, Verma B and Frilander MJ (2013) The significant other: splicing by the minor spliceosome. Wiley Interdisciplinary Reviews: RNA 4: 61–76.
Vithana EN, Abu‐Safieh L, Allen MJ, et al. (2001) A human homolog of yeast pre‐mRNA splicing gene, PRP31, underlies autosomal dominant retinitis pigmentosa on chromosome 19q13.4 (RP11). Molecular Cell 8: 375–381.
Wang J, Takagaki Y and Manley JL (1996) Targeted disruption of an essential vertebrate gene: ASF/SF2 is required for cell viability. Genes & Development 15: 2588–2599.
Wang J, Zhang J, Li K, Zhao W and Cui Q (2012) SpliceDisease database: linking RNA splicing and disease. Nucleic Acids Research 40: D1055–D1059.
Yang YC, Di C, Hu B, et al. (2015) CLIPdb: a CLIP‐seq database for protein‐RNA interactions. BMC Genomics 16: 51.
Yang X, Coulombe‐Huntington J, Kang S, et al. (2016) Widespread expansion of protein interaction capabilities by alternative splicing. Cell 164: 805–817.
Yoshida M, Kataoka N, Miyauchi K, et al. (2015) Rectifier of aberrant mRNA splicing recovers tRNA modification in familial dysautonomia. Proceedings of the National Academy of Sciences of the United States of America 112: 2764–2769.
Zhang Z, Shen M, Gresch P, et al. (2016) Oligonucleotide‐induced alternative splicing of serotonin 2C receptor reduces food intake. EMBO Molecular Medicine 8 (8): 878–894.
Zhou Z and Fu XD (2013) Regulation of splicing by SR proteins and SR protein‐specific kinases. Chromosoma 122: 191–207.
Chabot B and Shkreta L (2016) Defective control of pre‐messenger RNA splicing in human disease. The Journal of Cell Biology 212 (1): 13–27. PMID: 26728853.
Daguenet E, Dujardin G and Valcarcel J (2015) The pathogenicity of splicing defects: mechanistic insights into pre‐mRNA processing inform novel therapeutic approaches. EMBO Reports 16 (12): 1640–1655. PMID: 26566663.
Singh RK and Cooper TA (2012) Pre‐mRNA splicing in disease and therapeutics. Trends in Molecular Medicine 18 (8): 472–482. PMID: 22819011.
Stamm S, Smith C and Lührmann R (2012) Alternative Pre‐mRNA Splicing: Theory and Applications. Weinheim: Wiley‐Blackwell.