TY - JOUR AU - Lim, K. H. AU - Ferraris, L. AU - Filloux, M. E. AU - Raphael, B. J. AU - Fairbrother, W. G. PY - 2011 DA - 2011// TI - Using positional distribution to identify splicing elements and predict pre-mRNA processing defects in human genes JO - Proc Natl Acad Sci U S A VL - 108 UR - https://doi.org/10.1073/pnas.1101135108 DO - 10.1073/pnas.1101135108 ID - Lim2011 ER - TY - JOUR AU - Sterne-Weiler, T. AU - Howard, J. AU - Mort, M. AU - Cooper, D. N. AU - Sanford, J. R. PY - 2011 DA - 2011// TI - Loss of exon identity is a common mechanism of human inherited disease JO - Genome Res VL - 21 UR - https://doi.org/10.1101/gr.118638.110 DO - 10.1101/gr.118638.110 ID - Sterne-Weiler2011 ER - TY - JOUR AU - Lorson, C. L. AU - Hahnen, E. AU - Androphy, E. J. AU - Wirth, B. PY - 1999 DA - 1999// TI - A single nucleotide in the SMN gene regulates splicing and is responsible for spinal muscular atrophy JO - Proc Natl Acad Sci U S A VL - 96 UR - https://doi.org/10.1073/pnas.96.11.6307 DO - 10.1073/pnas.96.11.6307 ID - Lorson1999 ER - TY - JOUR AU - Cartegni, L. AU - Hastings, M. L. AU - Calarco, J. A. AU - Stanchina, E. AU - Krainer, A. R. PY - 2006 DA - 2006// TI - Determinants of exon 7 splicing in the spinal muscular atrophy genes, SMN1 and SMN2 JO - Am J Hum Genet VL - 78 UR - https://doi.org/10.1086/498853 DO - 10.1086/498853 ID - Cartegni2006 ER - TY - JOUR AU - Kashima, T. AU - Rao, N. AU - David, C. J. AU - Manley, J. L. PY - 2007 DA - 2007// TI - hnRNP A1 functions with specificity in repression of SMN2 exon 7 splicing JO - Hum Mol Genet VL - 16 UR - https://doi.org/10.1093/hmg/ddm276 DO - 10.1093/hmg/ddm276 ID - Kashima2007 ER - TY - JOUR AU - Singh, N. N. AU - Androphy, E. J. AU - Singh, R. N. PY - 2004 DA - 2004// TI - An extended inhibitory context causes skipping of exon 7 of SMN2 in spinal muscular atrophy JO - Biochem Biophys Res Commun VL - 315 UR - https://doi.org/10.1016/j.bbrc.2004.01.067 DO - 10.1016/j.bbrc.2004.01.067 ID - Singh2004 ER - TY - JOUR AU - Kashima, T. AU - Manley, J. L. PY - 2003 DA - 2003// TI - A negative element in SMN2 exon 7 inhibits splicing in spinal muscular atrophy JO - Nat Genet VL - 34 UR - https://doi.org/10.1038/ng1207 DO - 10.1038/ng1207 ID - Kashima2003 ER - TY - JOUR AU - Nielsen, K. B. AU - Sorensen, S. AU - Cartegni, L. AU - Corydon, T. J. AU - Doktor, T. K. AU - Schroeder, L. D. PY - 2007 DA - 2007// TI - 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 JO - Am J Hum Genet VL - 80 UR - https://doi.org/10.1086/511992 DO - 10.1086/511992 ID - Nielsen2007 ER - TY - JOUR AU - Du, L. AU - Gatti, R. A. PY - 2009 DA - 2009// TI - Progress toward therapy with antisense-mediated splicing modulation JO - Curr Opin Mol Ther VL - 11 ID - Du2009 ER - TY - JOUR AU - Veltrop, M. AU - Aartsma-Rus, A. PY - 2014 DA - 2014// TI - Antisense-mediated exon skipping: taking advantage of a trick from Mother Nature to treat rare genetic diseases JO - Exp Cell Res VL - 325 UR - https://doi.org/10.1016/j.yexcr.2014.01.026 DO - 10.1016/j.yexcr.2014.01.026 ID - Veltrop2014 ER - TY - JOUR AU - Hua, Y. AU - Vickers, T. A. AU - Okunola, H. L. AU - Bennett, C. F. AU - Krainer, A. R. PY - 2008 DA - 2008// TI - Antisense masking of an hnRNP A1/A2 intronic splicing silencer corrects SMN2 splicing in transgenic mice JO - Am J Hum Genet VL - 82 UR - https://doi.org/10.1016/j.ajhg.2008.01.014 DO - 10.1016/j.ajhg.2008.01.014 ID - Hua2008 ER - TY - JOUR AU - Singh, N. K. AU - Singh, N. N. AU - Androphy, E. J. AU - Singh, R. N. PY - 2006 DA - 2006// TI - Splicing of a critical exon of human Survival Motor Neuron is regulated by a unique silencer element located in the last intron JO - Mol Cell Biol VL - 26 UR - https://doi.org/10.1128/MCB.26.4.1333-1346.2006 DO - 10.1128/MCB.26.4.1333-1346.2006 ID - Singh2006 ER - TY - JOUR AU - Singh, N. N. AU - Shishimorova, M. AU - Cao, L. C. AU - Gangwani, L. AU - Singh, R. N. PY - 2009 DA - 2009// TI - A short antisense oligonucleotide masking a unique intronic motif prevents skipping of a critical exon in spinal muscular atrophy JO - RNA Biol VL - 6 UR - https://doi.org/10.4161/rna.6.3.8723 DO - 10.4161/rna.6.3.8723 ID - Singh2009 ER - TY - JOUR AU - Rigo, F. AU - Hua, Y. AU - Krainer, A. R. AU - Bennett, C. F. PY - 2012 DA - 2012// TI - Antisense-based therapy for the treatment of spinal muscular atrophy JO - J Cell Biol VL - 199 UR - https://doi.org/10.1083/jcb.201207087 DO - 10.1083/jcb.201207087 ID - Rigo2012 ER - TY - JOUR AU - Fu, X. D. AU - Ares, M. PY - 2014 DA - 2014// TI - Context-dependent control of alternative splicing by RNA-binding proteins JO - Nature Reviews Genet ID - Fu2014 ER - TY - JOUR AU - Anko, M. L. AU - Muller-McNicoll, M. AU - Brandl, H. AU - Curk, T. AU - Gorup, C. AU - Henry, I. PY - 2012 DA - 2012// TI - The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes JO - Genome Biol VL - 13 UR - https://doi.org/10.1186/gb-2012-13-3-r17 DO - 10.1186/gb-2012-13-3-r17 ID - Anko2012 ER - TY - JOUR AU - Huelga, S. C. AU - Vu, A. Q. AU - Arnold, J. D. AU - Liang, T. Y. AU - Liu, P. P. AU - Yan, B. Y. PY - 2012 DA - 2012// TI - Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins JO - Cell Rep VL - 1 UR - https://doi.org/10.1016/j.celrep.2012.02.001 DO - 10.1016/j.celrep.2012.02.001 ID - Huelga2012 ER - TY - JOUR AU - Konig, J. AU - Zarnack, K. AU - Rot, G. AU - Curk, T. AU - Kayikci, M. AU - Zupan, B. PY - 2010 DA - 2010// TI - iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution JO - Nat Struct Mol Biol VL - 17 UR - https://doi.org/10.1038/nsmb.1838 DO - 10.1038/nsmb.1838 ID - Konig2010 ER - TY - JOUR AU - Masuda, A. AU - Andersen, H. S. AU - Doktor, T. K. AU - Okamoto, T. AU - Ito, M. AU - Andresen, B. S. PY - 2012 DA - 2012// TI - CUGBP1 and MBNL1 preferentially bind to 3′ UTRs and facilitate mRNA decay JO - Sci Rep. VL - 2 ID - Masuda2012 ER - TY - JOUR AU - Pandit, S. AU - Zhou, Y. AU - Shiue, L. AU - Coutinho-Mansfield, G. AU - Li, H. AU - Qiu, J. PY - 2013 DA - 2013// TI - Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing JO - Mol Cell VL - 50 UR - https://doi.org/10.1016/j.molcel.2013.03.001 DO - 10.1016/j.molcel.2013.03.001 ID - Pandit2013 ER - TY - JOUR AU - Rossbach, O. AU - Hung, L. H. AU - Khrameeva, E. AU - Schreiner, S. AU - Konig, J. AU - Curk, T. PY - 2014 DA - 2014// TI - Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L JO - RNA Biol VL - 11 UR - https://doi.org/10.4161/rna.27991 DO - 10.4161/rna.27991 ID - Rossbach2014 ER - TY - JOUR AU - Sanford, J. R. AU - Wang, X. AU - Mort, M. AU - Vanduyn, N. AU - Cooper, D. N. AU - Mooney, S. D. PY - 2009 DA - 2009// TI - Splicing factor SFRS1 recognizes a functionally diverse landscape of RNA transcripts JO - Genome Res VL - 19 UR - https://doi.org/10.1101/gr.082503.108 DO - 10.1101/gr.082503.108 ID - Sanford2009 ER - TY - JOUR AU - Ule, J. AU - Jensen, K. B. AU - Ruggiu, M. AU - Mele, A. AU - Ule, A. AU - Darnell, R. B. PY - 2003 DA - 2003// TI - CLIP identifies Nova-regulated RNA networks in the brain JO - Science VL - 302 UR - https://doi.org/10.1126/science.1090095 DO - 10.1126/science.1090095 ID - Ule2003 ER - TY - JOUR AU - Weyn-Vanhentenryck, S. M. AU - Mele, A. AU - Yan, Q. AU - Sun, S. AU - Farny, N. AU - Zhang, Z. PY - 2014 DA - 2014// TI - HITS-CLIP and integrative modeling define the Rbfox splicing-regulatory network linked to brain development and autism JO - Cell Rep VL - 6 UR - https://doi.org/10.1016/j.celrep.2014.02.005 DO - 10.1016/j.celrep.2014.02.005 ID - Weyn-Vanhentenryck2014 ER - TY - JOUR AU - Burd, C. G. AU - Dreyfuss, G. PY - 1994 DA - 1994// TI - RNA binding specificity of hnRNP A1: significance of hnRNP A1 high-affinity binding sites in pre-mRNA splicing JO - EMBO J VL - 13 ID - Burd1994 ER - TY - JOUR AU - Jean-Philippe, J. AU - Paz, S. AU - Caputi, M. PY - 2013 DA - 2013// TI - hnRNP A1: the Swiss army knife of gene expression JO - Int J Mol Sci VL - 14 UR - https://doi.org/10.3390/ijms140918999 DO - 10.3390/ijms140918999 ID - Jean-Philippe2013 ER - TY - JOUR AU - Clery, A. AU - Sinha, R. AU - Anczukow, O. AU - Corrionero, A. AU - Moursy, A. AU - Daubner, G. M. PY - 2013 DA - 2013// TI - Isolated pseudo-RNA-recognition motifs of SR proteins can regulate splicing using a noncanonical mode of RNA recognition JO - Proc Natl Acad Sci U S A VL - 110 UR - https://doi.org/10.1073/pnas.1303445110 DO - 10.1073/pnas.1303445110 ID - Clery2013 ER - TY - JOUR AU - Eperon, I. C. AU - Makarova, O. V. AU - Mayeda, A. AU - Munroe, S. H. AU - Caceres, J. F. AU - Hayward, D. G. PY - 2000 DA - 2000// TI - Selection of alternative 5′ splice sites: role of U1 snRNP and models for the antagonistic effects of SF2/ASF and hnRNP A1 JO - Mol Cell Biol VL - 20 UR - https://doi.org/10.1128/MCB.20.22.8303-8318.2000 DO - 10.1128/MCB.20.22.8303-8318.2000 ID - Eperon2000 ER - TY - JOUR AU - Bonomi, S. AU - Matteo, A. AU - Buratti, E. AU - Cabianca, D. S. AU - Baralle, F. E. AU - Ghigna, C. PY - 2013 DA - 2013// TI - HnRNP A1 controls a splicing regulatory circuit promoting mesenchymal-to-epithelial transition JO - Nucleic Acids Res VL - 41 UR - https://doi.org/10.1093/nar/gkt579 DO - 10.1093/nar/gkt579 ID - Bonomi2013 ER - TY - JOUR AU - Tange, T. O. AU - Damgaard, C. K. AU - Guth, S. AU - Valcarcel, J. AU - Kjems, J. PY - 2001 DA - 2001// TI - The hnRNP A1 protein regulates HIV-1 tat splicing via a novel intron silencer element JO - EMBO J VL - 20 UR - https://doi.org/10.1093/emboj/20.20.5748 DO - 10.1093/emboj/20.20.5748 ID - Tange2001 ER - TY - JOUR AU - Okunola, H. L. AU - Krainer, A. R. PY - 2009 DA - 2009// TI - Cooperative-binding and splicing-repressive properties of hnRNP A1 JO - Mol Cell Biol VL - 29 UR - https://doi.org/10.1128/MCB.01678-08 DO - 10.1128/MCB.01678-08 ID - Okunola2009 ER - TY - JOUR AU - Nasim, F. U. AU - Hutchison, S. AU - Cordeau, M. AU - Chabot, B. PY - 2002 DA - 2002// TI - High-affinity hnRNP A1 binding sites and duplex-forming inverted repeats have similar effects on 5′ splice site selection in support of a common looping out and repression mechanism JO - RNA VL - 8 UR - https://doi.org/10.1017/S1355838202024056 DO - 10.1017/S1355838202024056 ID - Nasim2002 ER - TY - JOUR AU - Blanchette, M. AU - Chabot, B. PY - 1999 DA - 1999// TI - Modulation of exon skipping by high-affinity hnRNP A1-binding sites and by intron elements that repress splice site utilization JO - EMBO J VL - 18 UR - https://doi.org/10.1093/emboj/18.7.1939 DO - 10.1093/emboj/18.7.1939 ID - Blanchette1999 ER - TY - JOUR AU - Martinez-Contreras, R. AU - Fisette, J. F. AU - Nasim, F. U. AU - Madden, R. AU - Cordeau, M. AU - Chabot, B. PY - 2006 DA - 2006// TI - Intronic binding sites for hnRNP A/B and hnRNP F/H proteins stimulate pre-mRNA splicing JO - PLoS Biol VL - 4 UR - https://doi.org/10.1371/journal.pbio.0040021 DO - 10.1371/journal.pbio.0040021 ID - Martinez-Contreras2006 ER - TY - JOUR AU - Boukakis, G. AU - Patrinou-Georgoula, M. AU - Lekarakou, M. AU - Valavanis, C. AU - Guialis, A. PY - 2010 DA - 2010// TI - Deregulated expression of hnRNP A/B proteins in human non-small cell lung cancer: parallel assessment of protein and mRNA levels in paired tumour/non-tumour tissues JO - BMC Cancer. VL - 10 UR - https://doi.org/10.1186/1471-2407-10-434 DO - 10.1186/1471-2407-10-434 ID - Boukakis2010 ER - TY - JOUR AU - Ushigome, M. AU - Ubagai, T. AU - Fukuda, H. AU - Tsuchiya, N. AU - Sugimura, T. AU - Takatsuka, J. PY - 2005 DA - 2005// TI - Up-regulation of hnRNP A1 gene in sporadic human colorectal cancers JO - Int J Oncol VL - 26 ID - Ushigome2005 ER - TY - JOUR AU - Pino, I. AU - Pio, R. AU - Toledo, G. AU - Zabalegui, N. AU - Vicent, S. AU - Rey, N. PY - 2003 DA - 2003// TI - Altered patterns of expression of members of the heterogeneous nuclear ribonucleoprotein (hnRNP) family in lung cancer JO - Lung Cancer VL - 41 UR - https://doi.org/10.1016/S0169-5002(03)00193-4 DO - 10.1016/S0169-5002(03)00193-4 ID - Pino2003 ER - TY - JOUR AU - Patry, C. AU - Bouchard, L. AU - Labrecque, P. AU - Gendron, D. AU - Lemieux, B. AU - Toutant, J. PY - 2003 DA - 2003// TI - Small interfering RNA-mediated reduction in heterogeneous nuclear ribonucleoparticule A1/A2 proteins induces apoptosis in human cancer cells but not in normal mortal cell lines JO - Cancer Res VL - 63 ID - Patry2003 ER - TY - JOUR AU - Berson, A. AU - Barbash, S. AU - Shaltiel, G. AU - Goll, Y. AU - Hanin, G. AU - Greenberg, D. S. PY - 2012 DA - 2012// TI - Cholinergic-associated loss of hnRNP-A/B in Alzheimer’s disease impairs cortical splicing and cognitive function in mice JO - EMBO Mol Med VL - 4 UR - https://doi.org/10.1002/emmm.201100995 DO - 10.1002/emmm.201100995 ID - Berson2012 ER - TY - JOUR AU - Olsen, R. K. AU - Broner, S. AU - Sabaratnam, R. AU - Doktor, T. K. AU - Andersen, H. S. AU - Bruun, G. H. PY - 2014 DA - 2014// TI - The ETFDH c.158A > G variation disrupts the balanced interplay of ESE- and ESS-binding proteins thereby causing missplicing and multiple Acyl-CoA dehydrogenation deficiency JO - Hum Mutat VL - 35 UR - https://doi.org/10.1002/humu.22455 DO - 10.1002/humu.22455 ID - Olsen2014 ER - TY - JOUR AU - Dobrowolski, S. F. AU - Andersen, H. S. AU - Doktor, T. K. AU - Andresen, B. S. PY - 2010 DA - 2010// TI - The phenylalanine hydroxylase c.30C > G synonymous variation (p.G10G) creates a common exonic splicing silencer JO - Mol Genet Metab VL - 100 UR - https://doi.org/10.1016/j.ymgme.2010.04.002 DO - 10.1016/j.ymgme.2010.04.002 ID - Dobrowolski2010 ER - TY - JOUR AU - Yu, C. Y. AU - Theusch, E. AU - Lo, K. AU - Mangravite, L. M. AU - Naidoo, D. AU - Kutilova, M. PY - 2014 DA - 2014// TI - HNRNPA1 regulates HMGCR alternative splicing and modulates cellular cholesterol metabolism JO - Hum Mol Genet VL - 23 UR - https://doi.org/10.1093/hmg/ddt422 DO - 10.1093/hmg/ddt422 ID - Yu2014 ER - TY - JOUR AU - Bruun, G. H. AU - Doktor, T. K. AU - Andresen, B. S. PY - 2013 DA - 2013// TI - A synonymous polymorphic variation in ACADM exon 11 affects splicing efficiency and may affect fatty acid oxidation JO - Mol Genet Metab VL - 110 UR - https://doi.org/10.1016/j.ymgme.2013.06.005 DO - 10.1016/j.ymgme.2013.06.005 ID - Bruun2013 ER - TY - JOUR AU - Huppertz, I. AU - Attig, J. AU - D’Ambrogio, A. AU - Easton, L. E. AU - Sibley, C. R. AU - Sugimoto, Y. PY - 2014 DA - 2014// TI - iCLIP: protein-RNA interactions at nucleotide resolution JO - Methods VL - 65 UR - https://doi.org/10.1016/j.ymeth.2013.10.011 DO - 10.1016/j.ymeth.2013.10.011 ID - Huppertz2014 ER - TY - JOUR AU - Caceres, J. F. AU - Misteli, T. AU - Screaton, G. R. AU - Spector, D. L. AU - Krainer, A. R. PY - 1997 DA - 1997// TI - Role of the modular domains of SR proteins in subnuclear localization and alternative splicing specificity JO - J Cell Biol VL - 138 UR - https://doi.org/10.1083/jcb.138.2.225 DO - 10.1083/jcb.138.2.225 ID - Caceres1997 ER - TY - JOUR AU - Allemand, E. AU - Guil, S. AU - Myers, M. AU - Moscat, J. AU - Caceres, J. F. AU - Krainer, A. R. PY - 2005 DA - 2005// TI - Regulation of heterogenous nuclear ribonucleoprotein A1 transport by phosphorylation in cells stressed by osmotic shock JO - Proc Natl Acad Sci U S A VL - 102 UR - https://doi.org/10.1073/pnas.0409889102 DO - 10.1073/pnas.0409889102 ID - Allemand2005 ER - TY - STD TI - Konig J, Zarnack K, Rot G, Curk T, Kayikci M, Zupan B, et al. iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution. J Vis Exp. 2011;(50). Epub 2011/05/12. doi: 10.3791/2638. PubMed PMID: 21559008; PubMed Central PMCID: PMC3169244 ID - ref47 ER - TY - JOUR AU - Zhang, C. AU - Darnell, R. B. PY - 2011 DA - 2011// TI - Mapping in vivo protein-RNA interactions at single-nucleotide resolution from HITS-CLIP data JO - Nat Biotechnol VL - 29 UR - https://doi.org/10.1038/nbt.1873 DO - 10.1038/nbt.1873 ID - Zhang2011 ER - TY - JOUR AU - Granneman, S. AU - Kudla, G. AU - Petfalski, E. AU - Tollervey, D. PY - 2009 DA - 2009// TI - Identification of protein binding sites on U3 snoRNA and pre-rRNA by UV cross-linking and high-throughput analysis of cDNAs JO - Proc Natl Acad Sci U S A VL - 106 UR - https://doi.org/10.1073/pnas.0901997106 DO - 10.1073/pnas.0901997106 ID - Granneman2009 ER - TY - JOUR AU - Ule, J. AU - Jensen, K. AU - Mele, A. AU - Darnell, R. B. PY - 2005 DA - 2005// TI - CLIP: a method for identifying protein-RNA interaction sites in living cells JO - Methods VL - 37 UR - https://doi.org/10.1016/j.ymeth.2005.07.018 DO - 10.1016/j.ymeth.2005.07.018 ID - Ule2005 ER - TY - JOUR AU - Hauer, C. AU - Curk, T. AU - Anders, S. AU - Schwarzl, T. AU - Alleaume, A. M. AU - Sieber, J. PY - 2015 DA - 2015// TI - Improved binding site assignment by high-resolution mapping of RNA-protein interactions using iCLIP JO - Nat Commun. VL - 6 UR - https://doi.org/10.1038/ncomms8921 DO - 10.1038/ncomms8921 ID - Hauer2015 ER - TY - JOUR AU - Huang, M. AU - Rech, J. E. AU - Northington, S. J. AU - Flicker, P. F. AU - Mayeda, A. AU - Krainer, A. R. PY - 1994 DA - 1994// TI - The C-protein tetramer binds 230 to 240 nucleotides of pre-mRNA and nucleates the assembly of 40S heterogeneous nuclear ribonucleoprotein particles JO - Mol Cell Biol VL - 14 UR - https://doi.org/10.1128/MCB.14.1.518 DO - 10.1128/MCB.14.1.518 ID - Huang1994 ER - TY - JOUR AU - Palhais, B. AU - Praestegaard, V. S. AU - Sabaratnam, R. AU - Doktor, T. K. AU - Lutz, S. AU - Burda, P. PY - 2015 DA - 2015// TI - Splice-shifting oligonucleotide (SSO) mediated blocking of an exonic splicing enhancer (ESE) created by the prevalent c.903+469T>C MTRR mutation corrects splicing and restores enzyme activity in patient cells JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gkv275 DO - 10.1093/nar/gkv275 ID - Palhais2015 ER - TY - JOUR AU - Sorek, R. AU - Ast, G. PY - 2003 DA - 2003// TI - Intronic sequences flanking alternatively spliced exons are conserved between human and mouse JO - Genome Res VL - 13 UR - https://doi.org/10.1101/gr.1208803 DO - 10.1101/gr.1208803 ID - Sorek2003 ER - TY - JOUR AU - Yeo, G. AU - Burge, C. B. PY - 2004 DA - 2004// TI - Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals JO - J Comput Biol VL - 11 UR - https://doi.org/10.1089/1066527041410418 DO - 10.1089/1066527041410418 ID - Yeo2004 ER - TY - JOUR AU - Chen, M. AU - David, C. J. AU - Manley, J. L. PY - 2012 DA - 2012// TI - Concentration-dependent control of pyruvate kinase M mutually exclusive splicing by hnRNP proteins JO - Nat Struct Mol Biol VL - 19 UR - https://doi.org/10.1038/nsmb.2219 DO - 10.1038/nsmb.2219 ID - Chen2012 ER - TY - JOUR AU - David, C. J. AU - Chen, M. AU - Assanah, M. AU - Canoll, P. AU - Manley, J. L. PY - 2010 DA - 2010// TI - HnRNP proteins controlled by c-Myc deregulate pyruvate kinase mRNA splicing in cancer JO - Nature VL - 463 UR - https://doi.org/10.1038/nature08697 DO - 10.1038/nature08697 ID - David2010 ER - TY - JOUR AU - Clower, C. V. AU - Chatterjee, D. AU - Wang, Z. AU - Cantley, L. C. AU - Vander Heiden, M. G. AU - Krainer, A. R. PY - 2010 DA - 2010// TI - The alternative splicing repressors hnRNP A1/A2 and PTB influence pyruvate kinase isoform expression and cell metabolism JO - Proc Natl Acad Sci U S A VL - 107 UR - https://doi.org/10.1073/pnas.0914845107 DO - 10.1073/pnas.0914845107 ID - Clower2010 ER - TY - JOUR AU - Wang, Z. AU - Chatterjee, D. AU - Jeon, H. Y. AU - Akerman, M. AU - Vander Heiden, M. G. AU - Cantley, L. C. PY - 2012 DA - 2012// TI - Exon-centric regulation of pyruvate kinase M alternative splicing via mutually exclusive exons JO - J Mol Cell Biol VL - 4 UR - https://doi.org/10.1093/jmcb/mjr030 DO - 10.1093/jmcb/mjr030 ID - Wang2012 ER - TY - JOUR AU - Wang, Z. AU - Jeon, H. Y. AU - Rigo, F. AU - Bennett, C. F. AU - Krainer, A. R. PY - 2012 DA - 2012// TI - Manipulation of PK-M mutually exclusive alternative splicing by antisense oligonucleotides JO - Open Biol VL - 2 UR - https://doi.org/10.1098/rsob.120133 DO - 10.1098/rsob.120133 ID - Wang2012 ER - TY - JOUR AU - Kashima, T. AU - Rao, N. AU - Manley, J. L. PY - 2007 DA - 2007// TI - An intronic element contributes to splicing repression in spinal muscular atrophy JO - Proc Natl Acad Sci U S A VL - 104 UR - https://doi.org/10.1073/pnas.0700343104 DO - 10.1073/pnas.0700343104 ID - Kashima2007 ER - TY - JOUR AU - Cartegni, L. AU - Krainer, A. R. PY - 2002 DA - 2002// TI - Disruption of an SF2/ASF-dependent exonic splicing enhancer in SMN2 causes spinal muscular atrophy in the absence of SMN1 JO - Nat Genet VL - 30 UR - https://doi.org/10.1038/ng854 DO - 10.1038/ng854 ID - Cartegni2002 ER - TY - JOUR AU - Doktor, T. K. AU - Schroeder, L. D. AU - Vested, A. AU - Palmfeldt, J. AU - Andersen, H. S. AU - Gregersen, N. PY - 2011 DA - 2011// TI - SMN2 exon 7 splicing is inhibited by binding of hnRNP A1 to a common ESS motif that spans the 3′ splice site JO - Hum Mutat VL - 32 UR - https://doi.org/10.1002/humu.21419 DO - 10.1002/humu.21419 ID - Doktor2011 ER - TY - JOUR AU - Jeyaprakash, A. A. AU - Santamaria, A. AU - Jayachandran, U. AU - Chan, Y. W. AU - Benda, C. AU - Nigg, E. A. PY - 2012 DA - 2012// TI - Structural and functional organization of the Ska complex, a key component of the kinetochore-microtubule interface JO - Mol Cell VL - 46 UR - https://doi.org/10.1016/j.molcel.2012.03.005 DO - 10.1016/j.molcel.2012.03.005 ID - Jeyaprakash2012 ER - TY - JOUR AU - Wang, Y. AU - Zhang, Y. AU - Zhang, C. AU - Weng, H. AU - Li, Y. AU - Cai, W. PY - 2015 DA - 2015// TI - The gene pair PRR11 and SKA2 shares a NF-Y-regulated bidirectional promoter and contributes to lung cancer development JO - Biochim Biophys Acta VL - 1849 UR - https://doi.org/10.1016/j.bbagrm.2015.07.002 DO - 10.1016/j.bbagrm.2015.07.002 ID - Wang2015 ER - TY - JOUR AU - Ishii, S. AU - Nakao, S. AU - Minamikawa-Tachino, R. AU - Desnick, R. J. AU - Fan, J. Q. PY - 2002 DA - 2002// TI - Alternative splicing in the alpha-galactosidase A gene: increased exon inclusion results in the Fabry cardiac phenotype JO - Am J Hum Genet VL - 70 UR - https://doi.org/10.1086/339431 DO - 10.1086/339431 ID - Ishii2002 ER - TY - JOUR AU - Pagani, F. AU - Buratti, E. AU - Stuani, C. AU - Bendix, R. AU - Dork, T. AU - Baralle, F. E. PY - 2002 DA - 2002// TI - A new type of mutation causes a splicing defect in ATM JO - Nat Genet VL - 30 UR - https://doi.org/10.1038/ng858 DO - 10.1038/ng858 ID - Pagani2002 ER - TY - JOUR AU - King, K. AU - Flinter, F. A. AU - Nihalani, V. AU - Green, P. M. PY - 2002 DA - 2002// TI - Unusual deep intronic mutations in the COL4A5 gene cause X linked Alport syndrome JO - Hum Genet VL - 111 UR - https://doi.org/10.1007/s00439-002-0830-3 DO - 10.1007/s00439-002-0830-3 ID - King2002 ER - TY - JOUR AU - Rincon, A. AU - Aguado, C. AU - Desviat, L. R. AU - Sanchez-Alcudia, R. AU - Ugarte, M. AU - Perez, B. PY - 2007 DA - 2007// TI - Propionic and methylmalonic acidemia: antisense therapeutics for intronic variations causing aberrantly spliced messenger RNA JO - Am J Hum Genet VL - 81 UR - https://doi.org/10.1086/522376 DO - 10.1086/522376 ID - Rincon2007 ER - TY - JOUR AU - Faa, V. AU - Incani, F. AU - Meloni, A. AU - Corda, D. AU - Masala, M. AU - Baffico, A. M. PY - 2009 DA - 2009// TI - Characterization of a disease-associated mutation affecting a putative splicing regulatory element in intron 6b of the cystic fibrosis transmembrane conductance regulator (CFTR) gene JO - J Biol Chem VL - 284 UR - https://doi.org/10.1074/jbc.M109.032623 DO - 10.1074/jbc.M109.032623 ID - Faa2009 ER - TY - JOUR AU - Davis, R. L. AU - Homer, V. M. AU - George, P. M. AU - Brennan, S. O. PY - 2009 DA - 2009// TI - A deep intronic mutation in FGB creates a consensus exonic splicing enhancer motif that results in afibrinogenemia caused by aberrant mRNA splicing, which can be corrected in vitro with antisense oligonucleotide treatment JO - Hum Mutat VL - 30 UR - https://doi.org/10.1002/humu.20839 DO - 10.1002/humu.20839 ID - Davis2009 ER - TY - JOUR AU - Homolova, K. AU - Zavadakova, P. AU - Doktor, T. K. AU - Schroeder, L. D. AU - Kozich, V. AU - Andresen, B. S. PY - 2010 DA - 2010// TI - The deep intronic c.903 + 469 T > C mutation in the MTRR gene creates an SF2/ASF binding exonic splicing enhancer, which leads to pseudoexon activation and causes the cblE type of homocystinuria JO - Hum Mutat VL - 31 UR - https://doi.org/10.1002/humu.21206 DO - 10.1002/humu.21206 ID - Homolova2010 ER - TY - JOUR AU - Sterne-Weiler, T. AU - Sanford, J. R. PY - 2014 DA - 2014// TI - Exon identity crisis: disease-causing mutations that disrupt the splicing code JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/gb4150 DO - 10.1186/gb4150 ID - Sterne-Weiler2014 ER - TY - JOUR AU - Guo, R. AU - Li, Y. AU - Ning, J. AU - Sun, D. AU - Lin, L. AU - Liu, X. PY - 2013 DA - 2013// TI - HnRNP A1/A2 and SF2/ASF regulate alternative splicing of interferon regulatory factor-3 and affect immunomodulatory functions in human non-small cell lung cancer cells JO - PLoS One VL - 8 UR - https://doi.org/10.1371/journal.pone.0062729 DO - 10.1371/journal.pone.0062729 ID - Guo2013 ER - TY - JOUR AU - Staffa, A. AU - Cochrane, A. PY - 1995 DA - 1995// TI - Identification of positive and negative splicing regulatory elements within the terminal tat-rev exon of human immunodeficiency virus type 1 JO - Mol Cell Biol VL - 15 UR - https://doi.org/10.1128/MCB.15.8.4597 DO - 10.1128/MCB.15.8.4597 ID - Staffa1995 ER - TY - JOUR AU - Zhu, J. AU - Mayeda, A. AU - Krainer, A. R. PY - 2001 DA - 2001// TI - Exon identity established through differential antagonism between exonic splicing silencer-bound hnRNP A1 and enhancer-bound SR proteins JO - Mol Cell VL - 8 UR - https://doi.org/10.1016/S1097-2765(01)00409-9 DO - 10.1016/S1097-2765(01)00409-9 ID - Zhu2001 ER - TY - JOUR AU - Mayeda, A. AU - Krainer, A. R. PY - 1992 DA - 1992// TI - Regulation of alternative pre-mRNA splicing by hnRNP A1 and splicing factor SF2 JO - Cell VL - 68 UR - https://doi.org/10.1016/0092-8674(92)90477-T DO - 10.1016/0092-8674(92)90477-T ID - Mayeda1992 ER - TY - JOUR AU - Sun, H. AU - Chasin, L. A. PY - 2000 DA - 2000// TI - Multiple splicing defects in an intronic false exon JO - Mol Cell Biol VL - 20 UR - https://doi.org/10.1128/MCB.20.17.6414-6425.2000 DO - 10.1128/MCB.20.17.6414-6425.2000 ID - Sun2000 ER - TY - JOUR AU - Mayeda, A. AU - Munroe, S. H. AU - Caceres, J. F. AU - Krainer, A. R. PY - 1994 DA - 1994// TI - Function of conserved domains of hnRNP A1 and other hnRNP A/B proteins JO - EMBO J VL - 13 ID - Mayeda1994 ER - TY - JOUR AU - Chabot, B. AU - Blanchette, M. AU - Lapierre, I. AU - Branche, H. PY - 1997 DA - 1997// TI - An intron element modulating 5′ splice site selection in the hnRNP A1 pre-mRNA interacts with hnRNP A1 JO - Mol Cell Biol VL - 17 UR - https://doi.org/10.1128/MCB.17.4.1776 DO - 10.1128/MCB.17.4.1776 ID - Chabot1997 ER - TY - JOUR AU - Hutchison, S. AU - LeBel, C. AU - Blanchette, M. AU - Chabot, B. PY - 2002 DA - 2002// TI - Distinct sets of adjacent heterogeneous nuclear ribonucleoprotein (hnRNP) A1/A2 binding sites control 5′ splice site selection in the hnRNP A1 mRNA precursor JO - J Biol Chem VL - 277 UR - https://doi.org/10.1074/jbc.M203633200 DO - 10.1074/jbc.M203633200 ID - Hutchison2002 ER - TY - JOUR AU - Luan, W. AU - Wang, Y. AU - Chen, X. AU - Shi, Y. AU - Wang, J. AU - Zhang, J. PY - 2015 DA - 2015// TI - PKM2 promotes glucose metabolism and cell growth in gliomas through a mechanism involving a let-7a/c-Myc/hnRNPA1 feedback loop JO - Oncotarget VL - 6 UR - https://doi.org/10.18632/oncotarget.3514 DO - 10.18632/oncotarget.3514 ID - Luan2015 ER - TY - JOUR AU - Li, H. AU - Durbin, R. PY - 2009 DA - 2009// TI - Fast and accurate short read alignment with Burrows-Wheeler transform JO - Bioinformatics VL - 25 UR - https://doi.org/10.1093/bioinformatics/btp324 DO - 10.1093/bioinformatics/btp324 ID - Li2009 ER - TY - JOUR AU - Lovci, M. T. AU - Ghanem, D. AU - Marr, H. AU - Arnold, J. AU - Gee, S. AU - Parra, M. PY - 2013 DA - 2013// TI - Rbfox proteins regulate alternative mRNA splicing through evolutionarily conserved RNA bridges JO - Nat Struct Mol Biol VL - 20 UR - https://doi.org/10.1038/nsmb.2699 DO - 10.1038/nsmb.2699 ID - Lovci2013 ER - TY - JOUR AU - Heinz, S. AU - Benner, C. AU - Spann, N. AU - Bertolino, E. AU - Lin, Y. C. AU - Laslo, P. PY - 2010 DA - 2010// TI - Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities JO - Mol Cell VL - 38 UR - https://doi.org/10.1016/j.molcel.2010.05.004 DO - 10.1016/j.molcel.2010.05.004 ID - Heinz2010 ER - TY - JOUR AU - Wang, L. AU - Wang, S. AU - Li, W. PY - 2012 DA - 2012// TI - RSeQC: quality control of RNA-seq experiments JO - Bioinformatics VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts356 DO - 10.1093/bioinformatics/bts356 ID - Wang2012 ER - TY - JOUR AU - Shen, L. AU - Shao, N. AU - Liu, X. AU - Nestler, E. PY - 2014 DA - 2014// TI - ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases JO - BMC Genomics. VL - 15 UR - https://doi.org/10.1186/1471-2164-15-284 DO - 10.1186/1471-2164-15-284 ID - Shen2014 ER - TY - JOUR AU - Robinson, J. T. AU - Thorvaldsdottir, H. AU - Winckler, W. AU - Guttman, M. AU - Lander, E. S. AU - Getz, G. PY - 2011 DA - 2011// TI - Integrative genomics viewer JO - Nat Biotechnol VL - 29 UR - https://doi.org/10.1038/nbt.1754 DO - 10.1038/nbt.1754 ID - Robinson2011 ER - TY - JOUR AU - Thorvaldsdottir, H. AU - Robinson, J. T. AU - Mesirov, J. P. PY - 2013 DA - 2013// TI - Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration JO - Brief Bioinform VL - 14 UR - https://doi.org/10.1093/bib/bbs017 DO - 10.1093/bib/bbs017 ID - Thorvaldsdottir2013 ER - TY - JOUR AU - Loh, Y. H. AU - Shen, L. PY - 2016 DA - 2016// TI - Analysis and visualization of ChIP-Seq and RNA-Seq sequence alignments using ngs.plot JO - Methods Mol Biol VL - 1415 UR - https://doi.org/10.1007/978-1-4939-3572-7_18 DO - 10.1007/978-1-4939-3572-7_18 ID - Loh2016 ER - TY - STD TI - Rasband WS. ImageJ U.S. National Institutes of Health, Bethesda, Maryland, USA 1997–2015. http://imagej.nih.gov/ij/. Accessed 2 Jul 2016. UR - http://imagej.nih.gov/ij/ ID - ref91 ER - TY - JOUR AU - Dobin, A. AU - Davis, C. A. AU - Schlesinger, F. AU - Drenkow, J. AU - Zaleski, C. AU - Jha, S. PY - 2013 DA - 2013// TI - STAR: ultrafast universal RNA-seq aligner JO - Bioinformatics VL - 29 UR - https://doi.org/10.1093/bioinformatics/bts635 DO - 10.1093/bioinformatics/bts635 ID - Dobin2013 ER - TY - JOUR AU - Anders, S. AU - Pyl, P. T. AU - Huber, W. PY - 2015 DA - 2015// TI - HTSeq—a Python framework to work with high-throughput sequencing data JO - Bioinformatics VL - 31 UR - https://doi.org/10.1093/bioinformatics/btu638 DO - 10.1093/bioinformatics/btu638 ID - Anders2015 ER - TY - JOUR AU - Love, M. I. AU - Huber, W. AU - Anders, S. PY - 2014 DA - 2014// TI - Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0550-8 DO - 10.1186/s13059-014-0550-8 ID - Love2014 ER - TY - JOUR AU - Hansen, K. D. AU - Irizarry, R. A. AU - Wu, Z. PY - 2012 DA - 2012// TI - Removing technical variability in RNA-seq data using conditional quantile normalization JO - Biostatistics VL - 13 UR - https://doi.org/10.1093/biostatistics/kxr054 DO - 10.1093/biostatistics/kxr054 ID - Hansen2012 ER - TY - JOUR AU - Mazin, P. AU - Xiong, J. AU - Liu, X. AU - Yan, Z. AU - Zhang, X. AU - Li, M. PY - 2013 DA - 2013// TI - Widespread splicing changes in human brain development and aging JO - Mol Syst Biol VL - 9 UR - https://doi.org/10.1038/msb.2012.67 DO - 10.1038/msb.2012.67 ID - Mazin2013 ER -