Links between chromatin structure and regulation of alternative pre-mRNA splicing in mammalian cells
Intron removal is a necessary step for expression of most genes in higher eukaryotes, and alternative splice selection is a highly regulated mechanism that endows a single gene with the possibility to codify for multiple transcripts. Pre-mRNA splicing occurs largely co-transcriptionally, and its out...
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| Tipo de recurso: | tesis doctoral |
| Estado: | Versión publicada |
| Fecha de publicación: | 2014 |
| País: | España |
| Institución: | CBUC, CESCA |
| Repositorio: | TDR. Tesis Doctorales en Red |
| OAI Identifier: | oai:www.tdx.cat:10803/301439 |
| Acceso en línea: | http://hdl.handle.net/10803/301439 |
| Access Level: | acceso abierto |
| Palabra clave: | Splicing pre-mRNA Chromatin Nucleosomes ENCODE Progesterone Transcription RNA pol II Alternative Splicing Exon cassette Empalme Cromatina Nucleosomas Progesterona Intrones Exones Epigenética ChIP-Seq 577 |
| Sumario: | Intron removal is a necessary step for expression of most genes in higher eukaryotes, and alternative splice selection is a highly regulated mechanism that endows a single gene with the possibility to codify for multiple transcripts. Pre-mRNA splicing occurs largely co-transcriptionally, and its outcome is influenced by transcription elongation and chromatin structure. In this thesis we have used two different approaches to study novel links between chromatin structure and alternative splicing regulation. In the first approach, we identified genome-wide progesterone-regulated cassette exons and compared them with nucleosome density profiles, with the aim of finding correlations between changes in nucleosome positioning and changes in alternative splicing. We find that, even if all exons harbor a well-positioned exonic nucleosome, four different classes of nucleosome density profiles can be identified around alternative exons, which strongly correlate with the DNA sequence GC content. Transitions between these profiles occur upon hormone stimulation and can be correlated with alternative splicing changes, although changes in nucleosome profiles are also observed in non-regulated exons. In particular hormone-induced exon inclusion is more frequently linked to changes in nucleosome density than hormone-induced skipped exons, which tend to have low nucleosome density profiles even before hormone treatment. Peaks of nucleosome density before alternative exons tend to correlate with exon inclusion. In the second approach, we took advantage of ENCODE data of chromatin epigenetic signatures and RNA-Seq in multiple cell lines to evaluate functional enrichment of histone modifications over alternative exons. We find that three histone modifications (H3K4me3, H3K27ac and H3K9ac) co-occur in a subset of exons when they are highly included. These features are sufficient to predict differential inclusion levels in other cell lines. Moreover, they are enriched in exons characterized by the presence of DNase hypersensitive sites, promoter signatures and RNA Pol II accumulation. These observations suggest a functional role for 3-dimensional genome structure in the regulation of alternative splicing. |
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