Dissecting splicing decisions and cell-to-cell variability with designed sequence libraries

Keywords

RNA splicing, Alternative splicing, Proteome, Computational biology, Biology

References

• Functional roles of alternative splicing factors in human diseaseBenjamin Cieply, Russ P. Carstens — 2015
• Deciphering the splicing codeYoseph Barash, John A. Calarco, Weijun Gao — 2010
• Regulation of noise in the expression of a single geneErtuğrul M. Özbudak, Mukund Thattai, Iren Kurtser — 2002
• Regulation of gene expression programmes by serine-arginine rich splicing factors.Minna‐Liisa Änkö — 2014
• Dynamic integration of splicing within gene regulatory pathwaysUlrich Braunschweig, Serge Gueroussov, Alex Plocik — 2013
• RNA structure and the mechanisms of alternative splicingC. Joel McManus, Brenton R. Graveley — 2011
• Stochastic gene expression: from single molecules to the proteome.Benjamin Kaufmann-Malaga, Alexander van Oudenaarden — 2007
• The human splicing code reveals new insights into the genetic determinants of diseaseHui Xiong, Babak Alipanahi, Leo J. Lee — 2014
• Quantitative evaluation of all hexamers as exonic splicing elements.Shengdong Ke, Shulian Shang, Sergey Kalachikov — 2011
• Learning the sequence determinants of alternative splicing from millions of random sequences.Alexander Rosenberg, Rupali P Patwardhan, Jay Shendure — 2015
• Differential GC content between exons and introns establishes distinct strategies of splice-site recognition.Maayan Amit, Maya Donyo, Dror Hollander — 2012
• Single-cell transcriptomics reveals bimodality in expression and splicing in immune cellsAlex K. Shalek, Rahul Satija, Xian Adiconis — 2013
• The alternative role of DNA methylation in splicing regulation.Galit Lev Maor, Ahuvi Yearim, Gil Ast — 2015
• From single-cell to cell-pool transcriptomes: Stochasticity in gene expression and RNA splicingGeorgi K. Marinov, Brian A. Williams, Ken McCue — 2014
• Competing Upstream 5′ Splice Sites Enhance the Rate of Proximal SplicingMartin J. Hicks, William F. Mueller, Peter J. Shepard — 2010
• BUILDING ROBUST TRANSCRIPTOMES WITH MASTER SPLICING FACTORSMohini Jangi, Phillip A. Sharp — 2014
• Cell-to-cell variability of alternative RNA splicingZeev Waks, Allon M. Klein, Pamela A. Silver — 2011
• Stochastic Gene Expression in a Single CellMichael B. Elowitz, Arnold J. Levine, Eric D. Siggia — 2002
• ATtRACT—a database of RNA-binding proteins and associated motifsGirolamo Giudice, Fátima Sánchez‐Cabo, Carlos Torroja — 2016
• Intron retention is regulated by altered MeCP2-mediated splicing factor recruitmentJustin Wong, Dadi Gao, Trung Viet Nguyen — 2017

Cited by

• High-throughput identification of RNA localization elements reveals a regulatory role for A/G rich sequencesAnkita Arora, Roberto Castro Gutierrez, Davide Eletto — 2021

Related papers

• An exonic splicing enhancer in human IGF-I pre-mRNA mediates recognition of alternative exon 5 by the serine-arginine protein splicing factor-2/alternative splicing factor.Philip J Smith, Emma Spurrell, J. H. Coakley — 2002
• Splicing of the alternative exons of the chicken, rat, and Xenopus beta tropomyosin transcripts requires class-specific elements.L. Balvay, Anne‐Marie Pret, Domenico Libri — 1994
• An erythroid differentiation-specific splicing switch in protein 4.1R mediated by the interaction of SF2/ASF with an exonic splicing enhancer.Guang Yang, Shu‐Ching Huang, Jane Y. Wu — 2005
• Splicing factor SRSF1 negatively regulates alternative splicing of MDM2 under damageDaniel F. Comiskey, Aishwarya G. Jacob, Ravi K. Singh — 2015
• Serine Arginine Splicing Factor 3 Is Involved in Enhanced Splicing of Glucose-6-phosphate Dehydrogenase RNA in Response to Nutrients and Hormones in Liver*Callee M. Walsh, Amanda L. Suchanek, Travis J. Cyphert — 2012
• Pre-mRNA splicing of IgM exons M1 and M2 is directed by a juxtaposed splicing enhancer and inhibitor.Julie L.C. Kan, M. R. Green — 1999
• Establishment of a Novel In Vivo Sex-Specific Splicing Assay System To Identify a trans-Acting Factor That Negatively Regulates Splicing of Bombyx mori dsx Female ExonsMasataka G. Suzuki, Shigeo Imanishi, Naoshi Dohmae — 2007
• Control of Pre-mRNA Splicing by the General Splicing Factors PUF60 and U2AF65Michelle L. Hastings, Eric Allemand, Dominik M. Duelli — 2007
• Coupled transcription-splicing regulation of mutually exclusive splicing events at the 5' exons of protein 4.1R gene.Shu-Ching Huang, Aeri Cho, Stephanie Norton — 2009
• Tissue-specific splicing factor gene expression signaturesAna Rita Grosso, Anita Quintal Gomes, Nuno L. Barbosa‐Morais — 2008