Nucleosome positioning as a determinant of exon recognition (original) (raw)
Maniatis, T. & Reed, R. An extensive network of coupling among gene expression machines. Nature416, 499–506 (2002). ArticleCASPubMed Google Scholar
Moore, M.J. & Proudfoot, N.J. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell136, 688–700 (2009). ArticleCASPubMed Google Scholar
Bentley, D.L. Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors. Curr. Opin. Cell Biol.17, 251–256 (2005). ArticleCASPubMed Google Scholar
Pandit, S., Wang, D. & Fu, X.D. Functional integration of transcriptional and RNA processing machineries. Curr. Opin. Cell Biol.20, 260–265 (2008). ArticleCASPubMedPubMed Central Google Scholar
Kornblihtt, A.R. Coupling transcription and alternative splicing. Adv. Exp. Med. Biol.623, 175–189 (2007). ArticlePubMed Google Scholar
Kadener, S. et al. Antagonistic effects of T-Ag and VP16 reveal a role for RNA Pol II elongation on alternative splicing. EMBO J.20, 5759–5768 (2001). ArticleCASPubMedPubMed Central Google Scholar
Batsché, E., Yaniv, M. & Muchardt, C. The human SWI/SNF subunit Brm is a regulator of alternative splicing. Nat. Struct. Mol. Biol.13, 22–29 (2006). ArticlePubMed Google Scholar
Sims, R.J., III et al. Recognition of trimethylated histone H3 lysine 4 facilitates the recruitment of transcription postinitiation factors and pre-mRNA splicing. Mol. Cell28, 665–676 (2007). ArticleCASPubMedPubMed Central Google Scholar
Schor, I.E., Rascovan, N., Pelisch, F., Allo, M. & Kornblihtt, A.R. Neuronal cell depolarization induces intragenic chromatin modifications affecting NCAM alternative splicing. Proc. Natl. Acad. Sci. USA106, 4325–4330 (2009). ArticleCASPubMedPubMed Central Google Scholar
Das, R. et al. SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. Mol. Cell26, 867–881 (2007). ArticleCASPubMed Google Scholar
Phatnani, H.P. & Greenleaf, A.L. Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev.20, 2922–2936 (2006). ArticleCASPubMed Google Scholar
Nogues, G., Kadener, S., Cramer, P., Bentley, D. & Kornblihtt, A.R. Transcriptional activators differ in their abilities to control alternative splicing. J. Biol. Chem.277, 43110–43114 (2002). ArticleCASPubMed Google Scholar
Auboeuf, D., Honig, A., Berget, S.M. & O'Malley, B.W. Coordinate regulation of transcription and splicing by steroid receptor coregulators. Science298, 416–419 (2002). ArticleCASPubMed Google Scholar
Monsalve, M. et al. Direct coupling of transcription and mRNA processing through the thermogenic coactivator PGC-1. Mol. Cell6, 307–316 (2000). ArticleCASPubMed Google Scholar
Li, X. & Manley, J.L. Cotranscriptional processes and their influence on genome stability. Genes Dev.20, 1838–1847 (2006). ArticleCASPubMed Google Scholar
Luna, R., Gaillard, H., Gonzalez-Aguilera, C. & Aguilera, A. Biogenesis of mRNPs: integrating different processes in the eukaryotic nucleus. Chromosoma117, 319–331 (2008). ArticleCASPubMed Google Scholar
Lin, S., Coutinho-Mansfield, G., Wang, D., Pandit, S. & Fu, X.D. The splicing factor SC35 has an active role in transcriptional elongation. Nat. Struct. Mol. Biol.15, 819–826 (2008). ArticleCASPubMedPubMed Central Google Scholar
de la Mata, M. et al. A slow RNA polymerase II affects alternative splicing in vivo. Mol. Cell12, 525–532 (2003). ArticleCASPubMed Google Scholar
Howe, K.J., Kane, C.M. & Ares, M. Jr. Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. RNA9, 993–1006 (2003). ArticleCASPubMedPubMed Central Google Scholar
Muñoz, M.J. et al. DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation. Cell137, 708–720 (2009). ArticlePubMed Google Scholar
Allo, M. et al. Control of alternative splicing through siRNA-mediated transcriptional gene silencing. Nat. Struct. Mol. Biol.16, 717–724 (2009). ArticleCASPubMed Google Scholar
Fraser, P. & Bickmore, W. Nuclear organization of the genome and the potential for gene regulation. Nature447, 413–417 (2007). ArticleCASPubMed Google Scholar
Allemand, E., Batsche, E. & Muchardt, C. Splicing, transcription, and chromatin: a ménage à trois. Curr. Opin. Genet. Dev.18, 145–151 (2008). ArticleCASPubMed Google Scholar
Denisov, D.A., Shpigelman, E.S. & Trifonov, E.N. Protective nucleosome centering at splice sites as suggested by sequence-directed mapping of the nucleosomes. Gene205, 145–149 (1997). ArticleCASPubMed Google Scholar
Kogan, S. & Trifonov, E.N. Gene splice sites correlate with nucleosome positions. Gene352, 57–62 (2005). ArticleCASPubMed Google Scholar
Schones, D.E. et al. Dynamic regulation of nucleosome positioning in the human genome. Cell132, 887–898 (2008). ArticleCASPubMed Google Scholar
Valouev, A. et al. A high-resolution, nucleosome position map of C. elegans reveals a lack of universal sequence-dictated positioning. Genome Res.18, 1051–1063 (2008). ArticleCASPubMedPubMed Central Google Scholar
Schwartz, S., Meshorer, E. & Ast, G. Chromatin organization marks exon-intron architecture. Nat. Struct. Mol. Biol. advance online publication, doi:10.1038/nsmb.1659 (16 August 2009).
Kolasinska-Zwierz, P. et al. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat. Genet.41, 376–381 (2009). ArticleCASPubMedPubMed Central Google Scholar
Sammeth, M., Foissac, S. & Guigo, R. A general definition and nomenclature for alternative splicing events. PLOS Comput. Biol.4, e1000147 (2008). ArticlePubMedPubMed Central Google Scholar
Ikemura, T. Correlation between the abundance of yeast transfer RNAs and the occurrence of the respective codons in protein genes. Differences in synonymous codon choice patterns of yeast and Escherichia coli with reference to the abundance of isoaccepting transfer RNAs. J. Mol. Biol.158, 573–597 (1982). ArticleCASPubMed Google Scholar
Kotlar, D. & Lavner, Y. The action of selection on codon bias in the human genome is related to frequency, complexity, and chronology of amino acids. BMC Genomics7, 67 (2006). ArticlePubMedPubMed Central Google Scholar
Jabbari, K., Clay, O. & Bernardi, G. GC3 heterogeneity and body temperature in vertebrates. Gene317, 161–163 (2003). ArticleCASPubMed Google Scholar
Katz, L. & Burge, C.B. Widespread selection for local RNA secondary structure in coding regions of bacterial genes. Genome Res.13, 2042–2051 (2003). ArticleCASPubMedPubMed Central Google Scholar
Duret, L. Detecting genomic features under weak selective pressure: the example of codon usage in animals and plants. Bioinformatics18 (Suppl 2), S91 (2002). ArticlePubMed Google Scholar
Willie, E. & Majewski, J. Evidence for codon bias selection at the pre-mRNA level in eukaryotes. Trends Genet.20, 534–538 (2004). ArticleCASPubMed Google Scholar
Pruitt, K.D., Tatusova, T. & Maglott, D.R. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res.35, D61–D65 (2007). ArticleCASPubMed Google Scholar
Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. & Wheeler, D.L. GenBank. Nucleic Acids Res.36, D25–D30 (2008). ArticleCASPubMed Google Scholar