Cis- and trans-regulations of pre-mRNA splicing by RNA editing enzymes influence cancer development

[1]  S. Mirarab,et al.  Sequence Analysis , 2020, Encyclopedia of Bioinformatics and Computational Biology.

[2]  Y. Li,et al.  CSI NGS Portal: An Online Platform for Automated NGS Data Analysis and Sharing , 2019, International journal of molecular sciences.

[3]  Qinbo Yang,et al.  Targeted regulation of Rell2 by microRNA‐18a is implicated in the anti‐metastatic effect of polyphyllin VI in breast cancer cells , 2019, European journal of pharmacology.

[4]  P. Coltri,et al.  Splicing and cancer: Challenges and opportunities , 2019, Wiley interdisciplinary reviews. RNA.

[5]  Kenji Suzuki,et al.  Myelodysplastic Syndrome-Associated SRSF2 Mutations Cause Splicing Changes by Altering Binding Motif Sequences , 2019, Front. Genet..

[6]  Gene W. Yeo,et al.  Regulation of RNA editing by RNA-binding proteins in human cells , 2019, Communications Biology.

[7]  H. Jin,et al.  Epigenetic regulation of alternative splicing. , 2018, American journal of cancer research.

[8]  R. Siebert,et al.  RBFOX2 and alternative splicing in B-cell lymphoma , 2018, Blood Cancer Journal.

[9]  D. Tenen,et al.  Bidirectional regulation of adenosine-to-inosine (A-to-I) RNA editing by DEAH box helicase 9 (DHX9) in cancer , 2018, Nucleic acids research.

[10]  Hsuan Liu,et al.  Tumor-associated intronic editing of HNRPLL generates a novel splicing variant linked to cell proliferation , 2018, The Journal of Biological Chemistry.

[11]  X. Xiao,et al.  RNA editing in nascent RNA affects pre-mRNA splicing , 2018, Genome research.

[12]  Zheng Sun,et al.  PANDA: Protein function prediction using domain architecture and affinity propagation , 2018, Scientific Reports.

[13]  K. Neugebauer,et al.  Splicing and transcription touch base: co-transcriptional spliceosome assembly and function , 2017, Nature Reviews Molecular Cell Biology.

[14]  D. Tenen,et al.  An RNA editing/dsRNA binding-independent gene regulatory mechanism of ADARs and its clinical implication in cancer , 2017, Nucleic acids research.

[15]  H. Kato,et al.  Hypoxia is a Key Driver of Alternative Splicing in Human Breast Cancer Cells , 2017, Scientific Reports.

[16]  Lior Goldberg,et al.  Alternative Splicing of STAT3 Is Affected by RNA Editing. , 2017, DNA and cell biology.

[17]  H. Qin,et al.  ADAR2 functions as a tumor suppressor via editing IGFBP7 in esophageal squamous cell carcinoma. , 2017, International journal of oncology.

[18]  Sunjoo Jeong,et al.  SR Proteins: Binders, Regulators, and Connectors of RNA , 2017, Molecules and cells.

[19]  D. Tenen,et al.  ADAR-Mediated RNA Editing Predicts Progression and Prognosis of Gastric Cancer. , 2016, Gastroenterology.

[20]  Z. Li,et al.  Splicing variants of ADAR2 and ADAR2-mediated RNA editing in glioma. , 2016, Oncology letters.

[21]  A. Krainer,et al.  Global identification of hnRNP A1 binding sites for SSO-based splicing modulation , 2016, BMC Biology.

[22]  V. Timmerman,et al.  The hnRNP family: insights into their role in health and disease , 2016, Human Genetics.

[23]  Shuying Sun,et al.  SRSF1-Regulated Alternative Splicing in Breast Cancer. , 2015, Molecular cell.

[24]  Liang Han,et al.  Aberrant alternative splicing pattern of ADAR2 downregulates adenosine-to-inosine editing in glioma. , 2015, Oncology reports.

[25]  David Gacquer,et al.  Principles Governing A-to-I RNA Editing in the Breast Cancer Transcriptome , 2015, bioRxiv.

[26]  A. Kornblihtt,et al.  [Kinetic regulation of pre-messenger RNA alternative splicing]. , 2014, Medecine sciences : M/S.

[27]  M. Ares,et al.  Context-dependent control of alternative splicing by RNA-binding proteins , 2014, Nature Reviews Genetics.

[28]  Yael Mandel-Gutfreund,et al.  RBPmap: a web server for mapping binding sites of RNA-binding proteins , 2014, Nucleic Acids Res..

[29]  D. Bentley Coupling mRNA processing with transcription in time and space , 2014, Nature Reviews Genetics.

[30]  Yan Li,et al.  Adenosine-to-inosine RNA editing mediated by ADARs in esophageal squamous cell carcinoma. , 2014, Cancer research.

[31]  Zhiqin Xie,et al.  Transcriptome analysis of alternative splicing events regulated by SRSF10 reveals position-dependent splicing modulation , 2014, Nucleic acids research.

[32]  R. Reenan,et al.  Tertiary structural elements determine the extent and specificity of messenger RNA editing , 2013, Nature Communications.

[33]  C. Ghigna,et al.  HnRNP A1 controls a splicing regulatory circuit promoting mesenchymal-to-epithelial transition , 2013, Nucleic acids research.

[34]  Kol Jia Yong,et al.  A disrupted RNA editing balance mediated by ADARs (Adenosine DeAminases that act on RNA) in human hepatocellular carcinoma , 2013, Gut.

[35]  R. Unger,et al.  Global regulation of alternative splicing by adenosine deaminase acting on RNA (ADAR). , 2013, RNA.

[36]  Gene W. Yeo,et al.  Genome-wide analysis reveals SR protein cooperation and competition in regulated splicing. , 2013, Molecular cell.

[37]  Xiang-Dong Fu,et al.  Regulation of splicing by SR proteins and SR protein-specific kinases , 2013, Chromosoma.

[38]  Julian König,et al.  Direct Competition between hnRNP C and U2AF65 Protects the Transcriptome from the Exonization of Alu Elements , 2013, Cell.

[39]  Leilei Chen,et al.  Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma , 2013, Nature Medicine.

[40]  Jessica M. Rusert,et al.  ADAR1 promotes malignant progenitor reprogramming in chronic myeloid leukemia , 2012, Proceedings of the National Academy of Sciences.

[41]  R. Reenan,et al.  The intricate relationship between RNA structure, editing, and splicing. , 2012, Seminars in cell & developmental biology.

[42]  J. Ule,et al.  The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes , 2012, Genome Biology.

[43]  Peter F. Stadler,et al.  ViennaRNA Package 2.0 , 2011, Algorithms for Molecular Biology.

[44]  Nicholas C. Flytzanis,et al.  An EMT–Driven Alternative Splicing Program Occurs in Human Breast Cancer and Modulates Cellular Phenotype , 2011, PLoS genetics.

[45]  K. Nishikura Functions and regulation of RNA editing by ADAR deaminases. , 2010, Annual review of biochemistry.

[46]  J Andrew Berglund,et al.  Role of RNA structure in regulating pre-mRNA splicing. , 2010, Trends in biochemical sciences.

[47]  C. Béroud,et al.  Human Splicing Finder: an online bioinformatics tool to predict splicing signals , 2009, Nucleic acids research.

[48]  T. Mikkelsen,et al.  Altered adenosine-to-inosine RNA editing in human cancer. , 2007, Genome research.

[49]  K. Nishikura,et al.  RNA Binding-independent Dimerization of Adenosine Deaminases Acting on RNA and Dominant Negative Effects of Nonfunctional Subunits on Dimer Functions* , 2007, Journal of Biological Chemistry.

[50]  Eli Eisenberg,et al.  RNA-editing-mediated exon evolution , 2007, Genome Biology.

[51]  A. Sureau,et al.  The Polypyrimidine Tract Binding Protein (PTB) Represses Splicing of Exon 6B from the β-Tropomyosin Pre-mRNA by Directly Interfering with the Binding of the U2AF65 Subunit , 2006, Molecular and Cellular Biology.

[52]  Michael R Green,et al.  Structural basis for polypyrimidine tract recognition by the essential pre-mRNA splicing factor U2AF65. , 2006, Molecular cell.

[53]  Yukio Kawahara,et al.  A-to-I RNA Editing and Human Disease , 2006, RNA biology.

[54]  P. Sham,et al.  Evidence that RNA editing modulates splice site selection in the 5-HT2C receptor gene. , 2004, Nucleic acids research.

[55]  M. O’Connell,et al.  Adenosine deaminases acting on RNA (ADARs): RNA-editing enzymes , 2004, Genome Biology.

[56]  M Schrey,et al.  Underediting of glutamate receptor GluR-B mRNA in malignant gliomas , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[57]  P. Peterlongo,et al.  RNA hyperediting and alternative splicing of hematopoietic cell phosphatase (PTPN6) gene in acute myeloid leukemia. , 2000, Human molecular genetics.

[58]  S. Peltz,et al.  Characterization of the biochemical properties of the human Upf1 gene product that is involved in nonsense-mediated mRNA decay. , 2000, RNA.

[59]  F. He,et al.  Upf1p Control of Nonsense mRNA Translation Is Regulated by Nmd2p and Upf3p , 2000, Molecular and Cellular Biology.

[60]  R. Reenan,et al.  The mlenapts RNA Helicase Mutation in Drosophila Results in a Splicing Catastrophe of the para Na+ Channel Transcript in a Region of RNA Editing , 2000, Neuron.

[61]  T. Dawson,et al.  Regulation of alternative splicing by RNA editing , 1999, Nature.

[62]  C. Samuel,et al.  Human RNA-specific adenosine deaminase ADAR1 transcripts possess alternative exon 1 structures that initiate from different promoters, one constitutively active and the other interferon inducible. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[63]  J. Stévenin,et al.  The splicing factors 9G8 and SRp20 transactivate splicing through different and specific enhancers. , 1999, RNA.

[64]  D. Botstein,et al.  Cluster analysis and display of genome-wide expression patterns. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[65]  El Hassan El Aaoud $D_s^+ \to \phi \rho^+$ Decay , 1998, hep-ph/9801239.

[66]  C. Samuel,et al.  Expression and regulation by interferon of a double-stranded-RNA-specific adenosine deaminase from human cells: evidence for two forms of the deaminase , 1995, Molecular and cellular biology.

[67]  K. Nishikura,et al.  Mutagenic Analysis of Double-stranded RNA Adenosine Deaminase, a Candidate Enzyme for RNA Editing of Glutamate-gated Ion Channel Transcripts (*) , 1995, The Journal of Biological Chemistry.

[68]  J. Valcárcel,et al.  Distinct binding specificities and functions of higher eukaryotic polypyrimidine tract-binding proteins. , 1995, Science.

[69]  P. Seeburg,et al.  RNA editing of AMPA receptor subunit GluR-B: A base-paired intron-exon structure determines position and efficiency , 1993, Cell.

[70]  I. Schor,et al.  Coupling between transcription and alternative splicing. , 2013, Cancer treatment and research.

[71]  M. Alló,et al.  Transcriptional elongation and alternative splicing. , 2013, Biochimica et biophysica acta.

[72]  M. Alló,et al.  Connections between chromatin signatures and splicing , 2013, Wiley interdisciplinary reviews. RNA.

[73]  Ken Goldberg,et al.  RELT induces cellular death in HEK 293 epithelial cells. , 2010, Cellular immunology.

[74]  Charles Elkan,et al.  Fitting a Mixture Model By Expectation Maximization To Discover Motifs In Biopolymer , 1994, ISMB.