Regulation of alternative splicing by local histone modifications: potential roles for RNA-guided mechanisms
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Hua-Lin Zhou | Jo Ann Wise | J. Wise | Hua-Lin Zhou | G. Luo | H. Lou | Hua Lou | Guangbin Luo
[1] J. Manley,et al. Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches , 2009, Nature Reviews Molecular Cell Biology.
[2] K. Nishikura,et al. Altered G Protein‐Coupling Functions of RNA Editing Isoform and Splicing Variant Serotonin2C Receptors , 2000, Journal of neurochemistry.
[3] Y. Osheim,et al. RNP particles at splice junction sequences on Drosophila chorion transcripts , 1985, Cell.
[4] J. Manley,et al. The RNA polymerase II CTD coordinates transcription and RNA processing. , 2012, Genes & development.
[5] A. Hoffmann,et al. A Unifying Model for the Selective Regulation of Inducible Transcription by CpG Islands and Nucleosome Remodeling , 2009, Cell.
[6] Tracy L. Johnson,et al. Acetylation by the Transcriptional Coactivator Gcn5 Plays a Novel Role in Co-Transcriptional Spliceosome Assembly , 2009, PLoS genetics.
[7] J. Ahringer,et al. Differential chromatin marking of introns and expressed exons by H3K36me3 , 2008, Nature Genetics.
[8] Ananda L Roy,et al. Regulation of primary response genes. , 2011, Molecular cell.
[9] André L. Martins,et al. Signaling pathways differentially affect RNA polymerase II initiation, pausing, and elongation rate in cells. , 2013, Molecular cell.
[10] S. Preibisch,et al. Global analysis of nascent RNA reveals transcriptional pausing in terminal exons. , 2010, Molecular cell.
[11] O. Rando,et al. Combinatorial complexity in chromatin structure and function: revisiting the histone code. , 2012, Current opinion in genetics & development.
[12] M. Grunstein,et al. Functions of site-specific histone acetylation and deacetylation. , 2007, Annual review of biochemistry.
[13] J. Whetstine,et al. Chromatin landscape , 2011, Epigenetics.
[14] C. Allis,et al. The language of covalent histone modifications , 2000, Nature.
[15] Jaroslav Icha,et al. Histone Deacetylase Activity Modulates Alternative Splicing , 2011, PloS one.
[16] J. Kjems,et al. A 5' splice site enhances the recruitment of basal transcription initiation factors in vivo. , 2008, Molecules and Cells.
[17] D. Brow,et al. Allosteric cascade of spliceosome activation. , 2002, Annual review of genetics.
[18] J. Svejstrup. Histones Face the FACT , 2003, Science.
[19] P. Herrlich,et al. CD44: From adhesion molecules to signalling regulators , 2003, Nature Reviews Molecular Cell Biology.
[20] J. Bell,et al. The identification of a new alternative exon with highly restricted tissue expression in transcripts encoding the mouse Pgp-1 (CD44) homing receptor. Comparison of all 10 variable exons between mouse, human, and rat. , 1993, The Journal of biological chemistry.
[21] Michael Thomas,et al. MALAT-1, a novel noncoding RNA, and thymosin β4 predict metastasis and survival in early-stage non-small cell lung cancer , 2003, Oncogene.
[22] H. Lou,et al. Regulation of Neuron-Specific Alternative Splicing of Neurofibromatosis Type 1 Pre-mRNA , 2007, Molecular and Cellular Biology.
[23] J. M. Izquierdo. Hu Antigen R (HuR) Functions as an Alternative Pre-mRNA Splicing Regulator of Fas Apoptosis-promoting Receptor on Exon Definition* , 2008, Journal of Biological Chemistry.
[24] Howard Y. Chang,et al. Cytotopic localization by long noncoding RNAs. , 2013, Current opinion in cell biology.
[25] T. Nilsen,et al. Expansion of the eukaryotic proteome by alternative splicing , 2010, Nature.
[26] A. G. de Herreros,et al. A natural antisense transcript regulates Zeb2/Sip1 gene expression during Snail1-induced epithelial-mesenchymal transition. , 2008, Genes & development.
[27] R. F. Luco,et al. Epigenetics in Alternative Pre-mRNA Splicing , 2011, Cell.
[28] David G. Knowles,et al. Deep sequencing of subcellular RNA fractions shows splicing to be predominantly co-transcriptional in the human genome but inefficient for lncRNAs , 2012, Genome research.
[29] Paul Tempst,et al. Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. , 2007, Molecular cell.
[30] B. Blencowe,et al. Regulation of Alternative Splicing by Histone Modifications , 2010, Science.
[31] A. Helmrich,et al. Transcription-replication encounters, consequences and genomic instability , 2013, Nature Structural &Molecular Biology.
[32] Hyunmin Kim,et al. Pre-mRNA splicing is a determinant of histone H3K36 methylation , 2011, Proceedings of the National Academy of Sciences.
[33] Jan Komorowski,et al. Nucleosomes are well positioned in exons and carry characteristic histone modifications. , 2009, Genome research.
[34] J. Wise,et al. Evidence for Splice Site Pairing via Intron Definition in Schizosaccharomyces pombe , 2000, Molecular and Cellular Biology.
[35] B. Blencowe. Alternative Splicing: New Insights from Global Analyses , 2006, Cell.
[36] D. Moazed. Small RNAs in transcriptional gene silencing and genome defence , 2009, Nature.
[37] Piero Carninci,et al. Long non-coding RNA modifies chromatin , 2011, BioEssays : news and reviews in molecular, cellular and developmental biology.
[38] Michael Q. Zhang,et al. High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing , 2009 .
[39] J. Svejstrup. Transcription. Histones face the FACT. , 2003, Science.
[40] T. Gingeras,et al. Genome-wide transcription and the implications for genomic organization , 2007, Nature Reviews Genetics.
[41] J. Bähler,et al. Differential patterns of intronic and exonic DNA regions with respect to RNA polymerase II occupancy, nucleosome density and H3K36me3 marking in fission yeast , 2011, Genome Biology.
[42] X. Darzacq,et al. The In Vivo Kinetics of RNA Polymerase II Elongation during Co-Transcriptional Splicing , 2011, PLoS biology.
[43] Shaun K Olsen,et al. Receptor Specificity of the Fibroblast Growth Factor Family , 2006, Journal of Biological Chemistry.
[44] A. Kornblihtt,et al. A slow RNA polymerase II affects alternative splicing in vivo. , 2003, Molecular cell.
[45] Hua-Lin Zhou,et al. Hu proteins regulate alternative splicing by inducing localized histone hyperacetylation in an RNA-dependent manner , 2011, Proceedings of the National Academy of Sciences.
[46] M. Yaniv,et al. The human SWI/SNF subunit Brm is a regulator of alternative splicing , 2006, Nature Structural &Molecular Biology.
[47] G. C. Roberts,et al. Co-transcriptional commitment to alternative splice site selection. , 1998, Nucleic acids research.
[48] D. Black. Mechanisms of alternative pre-messenger RNA splicing. , 2003, Annual review of biochemistry.
[49] S. Forêt,et al. The Honey Bee Epigenomes: Differential Methylation of Brain DNA in Queens and Workers , 2010, PLoS biology.
[50] John L Rinn,et al. RNA traffic control of chromatin complexes. , 2010, Current opinion in genetics & development.
[51] Noah Spies,et al. Biased chromatin signatures around polyadenylation sites and exons. , 2009, Molecular cell.
[52] E. White,et al. New insights into form and function of fibronectin splice variants , 2008, The Journal of pathology.
[53] D. Black,et al. Transcript Dynamics of Proinflammatory Genes Revealed by Sequence Analysis of Subcellular RNA Fractions , 2012, Cell.
[54] G. Hong,et al. Nucleic Acids Research , 2015, Nucleic Acids Research.
[55] C. Muchardt,et al. Histone H3 lysine 9 trimethylation and HP1γ favor inclusion of alternative exons , 2011, Nature Structural &Molecular Biology.
[56] M. Rosbash,et al. Nascent-seq indicates widespread cotranscriptional pre-mRNA splicing in Drosophila. , 2011, Genes & development.
[57] Songtao Jia,et al. RNAi-Mediated Targeting of Heterochromatin by the RITS Complex , 2004, Science.
[58] H. Erdjument-Bromage,et al. Multiple Mechanisms Confining RNA Polymerase II Ubiquitylation to Polymerases Undergoing Transcriptional Arrest , 2005, Cell.
[59] James P. Orengo,et al. Alternative splicing in disease. , 2007, Advances in experimental medicine and biology.
[60] Randeep Rakwal,et al. MALAT‐1 enhances cell motility of lung adenocarcinoma cells by influencing the expression of motility‐related genes , 2010, FEBS letters.
[61] J. Davoust,et al. Differentiation state-dependent surface mobilities of two forms of the neural cell adhesion molecule , 1986, Nature.
[62] Manuel de la Mata,et al. Control of alternative splicing through siRNA-mediated transcriptional gene silencing , 2009, Nature Structural &Molecular Biology.
[63] Clifford A. Meyer,et al. Genomic mapping of RNA polymerase II reveals sites of co-transcriptional regulation in human cells , 2005, Genome Biology.
[64] Ross D. Alexander,et al. Splicing-Dependent RNA Polymerase Pausing in Yeast , 2010, Molecular cell.
[65] Zhike Lu,et al. Identification of 67 Histone Marks and Histone Lysine Crotonylation as a New Type of Histone Modification , 2011, Cell.
[66] Maria Carmo-Fonseca,et al. Splicing enhances recruitment of methyltransferase HYPB/Setd2 and methylation of histone H3 Lys36 , 2011, Nature Structural &Molecular Biology.
[67] G. Blobel,et al. Histone H3 lysine 9 methylation and HP1gamma are associated with transcription elongation through mammalian chromatin. , 2005, Molecular cell.
[68] Aaron A Hoskins,et al. The spliceosome: a flexible, reversible macromolecular machine. , 2012, Trends in biochemical sciences.
[69] Jernej Ule,et al. Psip1/Ledgf p52 Binds Methylated Histone H3K36 and Splicing Factors and Contributes to the Regulation of Alternative Splicing , 2012, PLoS genetics.
[70] D. Black,et al. Co-transcriptional splicing of constitutive and alternative exons. , 2009, RNA.
[71] Keith R. Yamamoto,et al. Reciprocal intronic and exonic histone modification regions in humans , 2010, Nature Structural &Molecular Biology.
[72] B. Frey,et al. Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing , 2008, Nature Genetics.
[73] G. Ast,et al. Chromatin organization marks exon-intron structure , 2009, Nature Structural &Molecular Biology.
[74] Bing Li,et al. Histone H3 Methylation by Set2 Directs Deacetylation of Coding Regions by Rpd3S to Suppress Spurious Intragenic Transcription , 2005, Cell.
[75] Claude C. Warzecha,et al. Dynamic fluorescent and luminescent reporters for cell-based splicing screens. , 2012, Methods in molecular biology.
[76] M. Alló,et al. Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing , 2009, Proceedings of the National Academy of Sciences.
[77] R. Padgett,et al. Rates of in situ transcription and splicing in large human genes , 2009, Nature Structural &Molecular Biology.
[78] Michael Q. Zhang,et al. A long nuclear‐retained non‐coding RNA regulates synaptogenesis by modulating gene expression , 2010, EMBO Journal.
[79] R. Sandberg,et al. CTCF-promoted RNA polymerase II pausing links DNA methylation to splicing , 2011, Nature.
[80] Kairong Cui,et al. Intragenic DNA methylation modulates alternative splicing by recruiting MeCP2 to promote exon recognition , 2013, Cell Research.
[81] J. Mattick,et al. Nucleosomes are preferentially positioned at exons in somatic and sperm cells , 2009, Cell cycle.
[82] Annick Harel-Bellan,et al. Argonaute proteins couple chromatin silencing to alternative splicing , 2012, Nature Structural &Molecular Biology.
[83] H. Stunnenberg,et al. Histone modification patterns associated with the human X chromosome , 2006, EMBO reports.
[84] B. Blencowe,et al. 5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary , 2012, Nature Structural &Molecular Biology.
[85] S. Henikoff,et al. Regulation of nucleosome dynamics by histone modifications , 2013, Nature Structural &Molecular Biology.
[86] M. Pellegrini,et al. Relationship between nucleosome positioning and DNA methylation , 2010, Nature.
[87] T. Cooper,et al. Pre-mRNA splicing in disease and therapeutics. , 2012, Trends in molecular medicine.
[88] M. Ares,et al. Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. , 2003, RNA.
[89] B. Blencowe,et al. The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. , 2010, Molecular cell.
[90] Kevin Struhl,et al. Eaf3 chromodomain interaction with methylated H3-K36 links histone deacetylation to Pol II elongation. , 2005, Molecular cell.
[91] William Stafford Noble,et al. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project , 2007, Nature.
[92] A. Weiss,et al. Alternative splicing of CD45: the tip of the iceberg. , 2008, Immunity.
[93] P. Herrlich,et al. Coupling of signal transduction to alternative pre‐mRNA splicing by a composite splice regulator , 1998, The EMBO journal.
[94] J. Cavaille,et al. The SNORD115 (H/MBII-52) and SNORD116 (H/MBII-85) gene clusters at the imprinted Prader–Willi locus generate canonical box C/D snoRNAs , 2012, Nucleic acids research.
[95] S. Berget. Exon Recognition in Vertebrate Splicing (*) , 1995, The Journal of Biological Chemistry.
[96] Howard Y. Chang,et al. RNA templating the epigenome , 2011, Epigenetics.
[97] S. Freier,et al. Control of RNA processing by a large non‐coding RNA over‐expressed in carcinomas , 2011, FEBS letters.
[98] R. Xi,et al. Polycomb group genes in stem cell self-renewal: A double-edged sword , 2011, Epigenetics.
[99] T. Cooper,et al. Pre-mRNA splicing and human disease. , 2003, Genes & development.
[100] E. Wagner,et al. Understanding the language of Lys36 methylation at histone H3 , 2012, Nature Reviews Molecular Cell Biology.
[101] Richard G. Jenner,et al. Noncoding RNA localisation mechanisms in chromatin regulation , 2012, Silence.
[102] Dustin E. Schones,et al. Dynamic Regulation of Nucleosome Positioning in the Human Genome , 2008, Cell.
[103] A role for phosphorylated Pol II CTD in modulating transcription coupled histone dynamics , 2011, Transcription.
[104] A. Kornblihtt,et al. Alternative splicing at the right time , 2011, RNA biology.
[105] Lili Wan,et al. RNA and Disease , 2009, Cell.
[106] M. Lazar,et al. Inhibition of c-erbA mRNA splicing by a naturally occurring antisense RNA. , 1991, The Journal of biological chemistry.
[107] Meena Kishore Sakharkar,et al. An analysis on gene architecture in human and mouse genomes , 2005, Silico Biol..
[108] Eric T. Wang,et al. Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.
[109] D. Givol,et al. Developmental localization of the splicing alternatives of fibroblast growth factor receptor-2 (FGFR2). , 1993, Developmental biology.
[110] R. Medzhitov,et al. Control of Inducible Gene Expression by Signal-Dependent Transcriptional Elongation , 2009, Cell.
[111] Christoforos Nikolaou,et al. Nucleosome positioning as a determinant of exon recognition , 2009, Nature Structural &Molecular Biology.
[112] Jane Qiu,et al. Epigenetics: Unfinished symphony , 2006, Nature.
[113] R. Wollman,et al. A genome-wide siRNA screen reveals diverse cellular processes and pathways that mediate genome stability. , 2009, Molecular cell.
[114] Bing Ren,et al. Discovery and Annotation of Functional Chromatin Signatures in the Human Genome , 2009, PLoS Comput. Biol..
[115] I. Schor,et al. Intragenic epigenetic changes modulate NCAM alternative splicing in neuronal differentiation , 2013, The EMBO journal.
[116] Kyucheol Cho,et al. Transcription Factor Interactions and Chromatin Modifications Associated with p53-Mediated, Developmental Repression of the Alpha-Fetoprotein Gene , 2005, Molecular and Cellular Biology.
[117] K. Lynch,et al. Regulation of Alternative Splicing: More than Just the ABCs* , 2008, Journal of Biological Chemistry.
[118] S. Stamm,et al. The snoRNA HBII-52 Regulates Alternative Splicing of the Serotonin Receptor 2C , 2006, Science.
[119] Bing Li,et al. The Role of Chromatin during Transcription , 2007, Cell.
[120] T. Mikkelsen,et al. Genome-wide maps of chromatin state in pluripotent and lineage-committed cells , 2007, Nature.