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Nucleosome positioning as a determinant of exon recognition

Abstract

Chromatin structure influences transcription, but its role in subsequent RNA processing is unclear. Here we present analyses of high-throughput data that imply a relationship between nucleosome positioning and exon definition. First, we have found stable nucleosome occupancy within human and Caenorhabditis elegans exons that is stronger in exons with weak splice sites. Conversely, we have found that pseudoexons—intronic sequences that are not included in mRNAs but are flanked by strong splice sites—show nucleosome depletion. Second, the ratio between nucleosome occupancy within and upstream from the exons correlates with exon-inclusion levels. Third, nucleosomes are positioned central to exons rather than proximal to splice sites. These exonic nucleosomal patterns are also observed in non-expressed genes, suggesting that nucleosome marking of exons exists in the absence of transcription. Our analysis provides a framework that contributes to the understanding of splicing on the basis of chromatin architecture.

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Figure 1: Observed and predicted nucleosome occupancy.
Figure 2: Nuclesome occupancy and expression of genes and exons.
Figure 3: Nucleosome occupancy in internal exons of different lengths, initial exons and terminal exons.
Figure 4: Profile of histone modifications in expressed genes in resting CD4+ T cells.

References

  1. Maniatis, T. & Reed, R. An extensive network of coupling among gene expression machines. Nature 416, 499–506 (2002).

    CAS  Article  PubMed  Google Scholar 

  2. Moore, M.J. & Proudfoot, N.J. Pre-mRNA processing reaches back to transcription and ahead to translation. Cell 136, 688–700 (2009).

    CAS  Article  PubMed  Google Scholar 

  3. Bentley, D.L. Rules of engagement: co-transcriptional recruitment of pre-mRNA processing factors. Curr. Opin. Cell Biol. 17, 251–256 (2005).

    CAS  Article  PubMed  Google Scholar 

  4. Pandit, S., Wang, D. & Fu, X.D. Functional integration of transcriptional and RNA processing machineries. Curr. Opin. Cell Biol. 20, 260–265 (2008).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  5. Kornblihtt, A.R. Coupling transcription and alternative splicing. Adv. Exp. Med. Biol. 623, 175–189 (2007).

    Article  PubMed  Google Scholar 

  6. 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).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  7. 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).

    Article  PubMed  Google Scholar 

  8. 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. Cell 28, 665–676 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  9. 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. USA 106, 4325–4330 (2009).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  10. Das, R. et al. SR proteins function in coupling RNAP II transcription to pre-mRNA splicing. Mol. Cell 26, 867–881 (2007).

    CAS  Article  PubMed  Google Scholar 

  11. Phatnani, H.P. & Greenleaf, A.L. Phosphorylation and functions of the RNA polymerase II CTD. Genes Dev. 20, 2922–2936 (2006).

    CAS  Article  PubMed  Google Scholar 

  12. 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).

    CAS  Article  PubMed  Google Scholar 

  13. Auboeuf, D., Honig, A., Berget, S.M. & O'Malley, B.W. Coordinate regulation of transcription and splicing by steroid receptor coregulators. Science 298, 416–419 (2002).

    CAS  Article  PubMed  Google Scholar 

  14. Monsalve, M. et al. Direct coupling of transcription and mRNA processing through the thermogenic coactivator PGC-1. Mol. Cell 6, 307–316 (2000).

    CAS  Article  PubMed  Google Scholar 

  15. Li, X. & Manley, J.L. Cotranscriptional processes and their influence on genome stability. Genes Dev. 20, 1838–1847 (2006).

    CAS  Article  PubMed  Google Scholar 

  16. Luna, R., Gaillard, H., Gonzalez-Aguilera, C. & Aguilera, A. Biogenesis of mRNPs: integrating different processes in the eukaryotic nucleus. Chromosoma 117, 319–331 (2008).

    CAS  Article  PubMed  Google Scholar 

  17. 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).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  18. de la Mata, M. et al. A slow RNA polymerase II affects alternative splicing in vivo. Mol. Cell 12, 525–532 (2003).

    CAS  Article  PubMed  Google Scholar 

  19. Howe, K.J., Kane, C.M. & Ares, M. Jr. Perturbation of transcription elongation influences the fidelity of internal exon inclusion in Saccharomyces cerevisiae. RNA 9, 993–1006 (2003).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  20. Muñoz, M.J. et al. DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation. Cell 137, 708–720 (2009).

    Article  PubMed  Google Scholar 

  21. Allo, M. et al. Control of alternative splicing through siRNA-mediated transcriptional gene silencing. Nat. Struct. Mol. Biol. 16, 717–724 (2009).

    CAS  Article  PubMed  Google Scholar 

  22. Fraser, P. & Bickmore, W. Nuclear organization of the genome and the potential for gene regulation. Nature 447, 413–417 (2007).

    CAS  Article  PubMed  Google Scholar 

  23. Kouzarides, T. Chromatin modifications and their function. Cell 128, 693–705 (2007).

    CAS  Article  PubMed  Google Scholar 

  24. Allemand, E., Batsche, E. & Muchardt, C. Splicing, transcription, and chromatin: a ménage à trois. Curr. Opin. Genet. Dev. 18, 145–151 (2008).

    CAS  Article  PubMed  Google Scholar 

  25. Beckmann, J.S. & Trifonov, E.N. Splice junctions follow a 205-base ladder. Proc. Natl. Acad. Sci. USA 88, 2380–2383 (1991).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  26. Denisov, D.A., Shpigelman, E.S. & Trifonov, E.N. Protective nucleosome centering at splice sites as suggested by sequence-directed mapping of the nucleosomes. Gene 205, 145–149 (1997).

    CAS  Article  PubMed  Google Scholar 

  27. Kogan, S. & Trifonov, E.N. Gene splice sites correlate with nucleosome positions. Gene 352, 57–62 (2005).

    CAS  Article  PubMed  Google Scholar 

  28. Schones, D.E. et al. Dynamic regulation of nucleosome positioning in the human genome. Cell 132, 887–898 (2008).

    CAS  Article  PubMed  Google Scholar 

  29. 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).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  30. 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).

  31. Kolasinska-Zwierz, P. et al. Differential chromatin marking of introns and expressed exons by H3K36me3. Nat. Genet. 41, 376–381 (2009).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  32. Sammeth, M., Foissac, S. & Guigo, R. A general definition and nomenclature for alternative splicing events. PLOS Comput. Biol. 4, e1000147 (2008).

    Article  PubMed  PubMed Central  Google Scholar 

  33. Wang, E.T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470–476 (2008).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  34. Barski, A. et al. High-resolution profiling of histone methylations in the human genome. Cell 129, 823–837 (2007).

    CAS  Article  PubMed  Google Scholar 

  35. Kharchenko, P.V., Woo, C.J., Tolstorukov, M.Y., Kingston, R.E. & Park, P.J. Nucleosome positioning in human HOX gene clusters. Genome Res. 18, 1554–1561 (2008).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  36. Peckham, H.E. et al. Nucleosome positioning signals in genomic DNA. Genome Res. 17, 1170–1177 (2007).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  37. Harrow, J. et al. GENCODE: producing a reference annotation for ENCODE. Genome Biol. 7 (Suppl 1), S4 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  38. Berget, S.M. Exon recognition in vertebrate splicing. J. Biol. Chem. 270, 2411–2414 (1995).

    CAS  Article  PubMed  Google Scholar 

  39. Das, R. et al. Functional coupling of RNAP II transcription to spliceosome assembly. Genes Dev. 20, 1100–1109 (2006).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  40. 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).

    CAS  Article  PubMed  Google Scholar 

  41. 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 Genomics 7, 67 (2006).

    Article  PubMed  PubMed Central  Google Scholar 

  42. Jabbari, K., Clay, O. & Bernardi, G. GC3 heterogeneity and body temperature in vertebrates. Gene 317, 161–163 (2003).

    CAS  Article  PubMed  Google Scholar 

  43. Katz, L. & Burge, C.B. Widespread selection for local RNA secondary structure in coding regions of bacterial genes. Genome Res. 13, 2042–2051 (2003).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  44. Duret, L. Detecting genomic features under weak selective pressure: the example of codon usage in animals and plants. Bioinformatics 18 (Suppl 2), S91 (2002).

    Article  PubMed  Google Scholar 

  45. Willie, E. & Majewski, J. Evidence for codon bias selection at the pre-mRNA level in eukaryotes. Trends Genet. 20, 534–538 (2004).

    CAS  Article  PubMed  Google Scholar 

  46. 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).

    CAS  Article  PubMed  Google Scholar 

  47. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. & Wheeler, D.L. GenBank. Nucleic Acids Res. 36, D25–D30 (2008).

    CAS  Article  PubMed  Google Scholar 

  48. Kent, W.J. et al. The human genome browser at UCSC. Genome Res. 12, 996–1006 (2002).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  49. Blanco, E., Parra, G. & Guigo, R. Using geneid to identify genes. Curr. Protoc. Bioinformatics, Chapter 4: Unit 4.3 (2007).

  50. Parra, G., Blanco, E. & Guigo, R. GeneID in Drosophila. Genome Res. 10, 511–515 (2000).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  51. Sheth, N. et al. Comprehensive splice-site analysis using comparative genomics. Nucleic Acids Res. 34, 3955–3967 (2006).

    CAS  Article  PubMed  PubMed Central  Google Scholar 

  52. Alioto, T.S. U12DB: a database of orthologous U12-type spliceosomal introns. Nucleic Acids Res. 35, D110–D115 (2007).

    CAS  Article  PubMed  Google Scholar 

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Acknowledgements

We thank D.E. Schones for help with the data and its interpretation and members of the Guigó laboratory, especially D. Gonzalez, for help with data analysis. This work was supported by the Spanish Ministry of Science with fellowships to M.S. and S.A., and with grant number BIO2006-03380 to R.G.

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Correspondence to Roderic Guigó.

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Tilgner, H., Nikolaou, C., Althammer, S. et al. Nucleosome positioning as a determinant of exon recognition. Nat Struct Mol Biol 16, 996–1001 (2009). https://doi.org/10.1038/nsmb.1658

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