In silico analysis of regulatory motifs in gene promoters
Regulation of gene transcription is a complex process involving many different proteins, some of which bind in a sequence-specific manner to DNA motifs in the gene promoter. The need to maintain specific interactions between transcription factors and proteins involved in the RNA polymerase II comple...
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| Tipo de recurso: | tesis doctoral |
| Estado: | Versión publicada |
| Fecha de publicación: | 2010 |
| País: | España |
| Institución: | CBUC, CESCA |
| Repositorio: | TDR. Tesis Doctorales en Red |
| OAI Identifier: | oai:www.tdx.cat:10803/7202 |
| Acceso en línea: | http://www.tdx.cat/TDX-0422110-095017 http://hdl.handle.net/10803/7202 |
| Access Level: | acceso abierto |
| Palabra clave: | Housekeeping genes Microarray RNA polymerase Transcription factor DNA Bioinformatics Ribosome Genome Transcription Promoter Consensus sequence Motif Genomics TFBS TF PWM PEAKS 575 |
| Sumario: | Regulation of gene transcription is a complex process involving many different proteins, some of which bind in a sequence-specific manner to DNA motifs in the gene promoter. The need to maintain specific interactions between transcription factors and proteins involved in the RNA polymerase II complex is expected to impose constrains on the relative position and spacing of the interacting DNA motifs. The present work includes the development of a novel approach to identify motifs that show a preferential location in DNA sequences and the implementation of a public web application called PEAKS. We investigated if the arrangement and nature of the most common motifs depended on the breath of expression of the gene. We found differences that serve to illustrate that many key specific regulatory signals may be present in the proximal promoter region in mammalian genes. We also apply other methods for the identification of specific transcription factors (TFs) involved in the co-regulation of a set of genes. Data from experimentally-verified transcription factors binding sites (TFBSs) support the biological relevance of our findings. |
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