Global Promotion of Alternative Internal Exon Usage by mRNA 3' End Formation Factors.

[1]  Paul Theodor Pyl,et al.  HTSeq—a Python framework to work with high-throughput sequencing data , 2014, bioRxiv.

[2]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[3]  M. Alló,et al.  Alternative splicing: a pivotal step between eukaryotic transcription and translation , 2013, Nature Reviews Molecular Cell Biology.

[4]  David G Hendrickson,et al.  Differential analysis of gene regulation at transcript resolution with RNA-seq , 2012, Nature Biotechnology.

[5]  Hélène Touzet,et al.  SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data , 2012, Bioinform..

[6]  Mihaela Zavolan,et al.  Genome-wide analysis of pre-mRNA 3' end processing reveals a decisive role of human cleavage factor I in the regulation of 3' UTR length. , 2012, Cell reports.

[7]  Manuel Irimia,et al.  Alternative splicing: decoding an expansive regulatory layer. , 2012, Current opinion in cell biology.

[8]  W. Huber,et al.  Detecting differential usage of exons from RNA-seq data , 2012, Genome research.

[9]  Gene W. Yeo,et al.  Integrative genome-wide analysis reveals cooperative regulation of alternative splicing by hnRNP proteins. , 2012, Cell reports.

[10]  Tomaž Curk,et al.  Analysis of alternative splicing associated with aging and neurodegeneration in the human brain. , 2011, Genome research.

[11]  Auinash Kalsotra,et al.  Functional consequences of developmentally regulated alternative splicing , 2011, Nature Reviews Genetics.

[12]  H. Martinson,et al.  An active role for splicing in 3′‐end formation , 2011, Wiley interdisciplinary reviews. RNA.

[13]  Yongsheng Shi,et al.  Pre‐mRNA 3′‐end processing complex assembly and function , 2011, Wiley Interdisciplinary Reviews - RNA.

[14]  T. Haystead,et al.  Efficient detection of RNA–protein interactions using tethered RNAs , 2011, Nucleic acids research.

[15]  J. Ule,et al.  iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution , 2010, Nature Structural &Molecular Biology.

[16]  C. Glass,et al.  Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. , 2010, Molecular cell.

[17]  Yael Mandel-Gutfreund,et al.  SFmap: a web server for motif analysis and prediction of splicing factor binding sites , 2010, Nucleic Acids Res..

[18]  David S. Lapointe,et al.  ChIPpeakAnno: a Bioconductor package to annotate ChIP-seq and ChIP-chip data , 2010, BMC Bioinformatics.

[19]  G. Ast,et al.  Alternative splicing and evolution: diversification, exon definition and function , 2010, Nature Reviews Genetics.

[20]  T. Nilsen,et al.  Expansion of the eukaryotic proteome by alternative splicing , 2010, Nature.

[21]  J. Manley,et al.  Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches , 2009, Nature Reviews Molecular Cell Biology.

[22]  Sherif Abou Elela,et al.  Cancer-associated regulation of alternative splicing , 2009, Nature Structural &Molecular Biology.

[23]  W. Marzluff,et al.  A core complex of CPSF73, CPSF100, and Symplekin may form two different cleavage factors for processing of poly(A) and histone mRNAs. , 2009, Molecular cell.

[24]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[25]  Lili Wan,et al.  RNA and Disease , 2009, Cell.

[26]  Gene W. Yeo,et al.  An RNA code for the FOX2 splicing regulator revealed by mapping RNA-protein interactions in stem cells , 2009, Nature Structural &Molecular Biology.

[27]  A. Krainer,et al.  Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2 (Genes and Development (2008) 22 (2550-2563)) , 2008 .

[28]  Eric T. Wang,et al.  Alternative Isoform Regulation in Human Tissue Transcriptomes , 2008, Nature.

[29]  Tyson A. Clark,et al.  HITS-CLIP yields genome-wide insights into brain alternative RNA processing , 2008, Nature.

[30]  Michael Q. Zhang,et al.  Defining the regulatory network of the tissue-specific splicing factors Fox-1 and Fox-2. , 2008, Genes & development.

[31]  Xiang-Dong Fu,et al.  The splicing factor SC35 has an active role in transcriptional elongation , 2008, Nature Structural &Molecular Biology.

[32]  Hua-Lin Zhou,et al.  Repression of Prespliceosome Complex Formation at Two Distinct Steps by Fox-1/Fox-2 Proteins , 2008, Molecular and Cellular Biology.

[33]  L. Tong,et al.  Protein factors in pre-mRNA 3′-end processing , 2008, Cellular and Molecular Life Sciences.

[34]  Michael R. Green,et al.  An elaborate pathway required for Ras-mediated epigenetic silencing , 2007, Nature.

[35]  L. Tong,et al.  Polyadenylation factor CPSF-73 is the pre-mRNA 3'-end-processing endonuclease , 2006, Nature.

[36]  B. Blencowe,et al.  An RNA map predicting Nova-dependent splicing regulation , 2006, Nature.

[37]  Hanno Langen,et al.  Direct interactions between subunits of CPSF and the U2 snRNP contribute to the coupling of pre-mRNA 3' end processing and splicing. , 2006, Molecular cell.

[38]  D. Black,et al.  Splicing bioinformatics to biology , 2006, Genome Biology.

[39]  Peter Stoilov,et al.  Homologues of the Caenorhabditis elegans Fox-1 Protein Are Neuronal Splicing Regulators in Mammals , 2005, Molecular and Cellular Biology.

[40]  Robert Castelo,et al.  Regulation of Fas alternative splicing by antagonistic effects of TIA-1 and PTB on exon definition. , 2005, Molecular cell.

[41]  F. Clark,et al.  Understanding alternative splicing: towards a cellular code , 2005, Nature Reviews Molecular Cell Biology.

[42]  Gene W. Yeo,et al.  Systematic Identification and Analysis of Exonic Splicing Silencers , 2004, Cell.

[43]  Steven E Brenner,et al.  Genome-wide analysis reveals an unexpected function for the Drosophila splicing factor U2AF50 in the nuclear export of intronless mRNAs. , 2004, Molecular cell.

[44]  D. Black Mechanisms of alternative pre-messenger RNA splicing. , 2003, Annual review of biochemistry.

[45]  Christopher B. Burge,et al.  Maximum entropy modeling of short sequence motifs with applications to RNA splicing signals , 2003, RECOMB '03.

[46]  A. Krainer,et al.  Exon identity established through differential antagonism between exonic splicing silencer-bound hnRNP A1 and enhancer-bound SR proteins. , 2001, Molecular cell.

[47]  M. Olive,et al.  hnRNP A1 Recruited to an Exon In Vivo Can Function as an Exon Splicing Silencer , 1999, Molecular and Cellular Biology.

[48]  P. Sharp,et al.  Alternative Splicing of the Fibronectin EIIIB Exon Depends on Specific TGCATG Repeats , 1998, Molecular and Cellular Biology.

[49]  J. Manley,et al.  Mechanism and regulation of mRNA polyadenylation. , 1997, Genes & development.

[50]  L. Minvielle-Sebastia,et al.  The 30-kD subunit of mammalian cleavage and polyadenylation specificity factor and its yeast homolog are RNA-binding zinc finger proteins. , 1997, Genes & development.

[51]  K. Murthy,et al.  The 160-kD subunit of human cleavage-polyadenylation specificity factor coordinates pre-mRNA 3'-end formation. , 1995, Genes & development.

[52]  R. Hynes,et al.  Regulation of alternative pre-mRNA splicing by a novel repeated hexanucleotide element. , 1994, Genes & development.

[53]  G. Christofori,et al.  Cleavage and polyadenylation factor CPF specifically interacts with the pre‐mRNA 3′ processing signal AAUAAA. , 1991, The EMBO journal.

[54]  C. Guthrie,et al.  5' splice site selection in yeast: genetic alterations in base-pairing with U1 reveal additional requirements. , 1988, Genes & development.

[55]  B. Séraphin,et al.  A U1 snRNA:pre‐mRNA base pairing interaction is required early in yeast spliceosome assembly but does not uniquely define the 5′ cleavage site. , 1988, The EMBO journal.

[56]  Robert B Darnell,et al.  CLIP: crosslinking and immunoprecipitation of in vivo RNA targets of RNA-binding proteins. , 2008, Methods in molecular biology.