The Analysis Of Regulatory Elements In Whole Genome

The study of transcriptional regulation networks has become a research emphasis in the post-genome era. DNA-binding transcription factors are one of the important components in this network. The reciprocity of transcription factor and regulatory element controls the transcription and expression of genes. Therefore, one major task to decipher transcriptional regulation networks is to identify and analyze all transcriptional factor binding sites (TFBS) or regulatory elements. Here we've done some work about regulatory elements based on genome.During the research of TFBS recognition , we choose search method that use mode (position weight matrix and consensus) . We fetch some regulatory elements from SCPD to test our arithmetic, it is proved to be available in transcriptional factor binding sites (TFBS) search system and further research. After we develop the method that can really predict TFBSs, we use this method to make some statistics to the distance between two chosen TFBSs, we thought that would be helpful to the research of composite element. For testifying this thought, we choose some composite elements from Compel database and sum up all the distances between the potential TFBSs of two elements, from some results we've got, we figure that this statistic method could be a reference if we want to research some unknown element pairs.We all know that regulatory elements exist in the upstream region of gene, but do they distribute in other non-coding region or even coding region, if they do exist, what's their enrichment in the different regions? The questions above consist our next job. We analyze the enrichment of TFBSs in intergenic region, upstream region of gene, exon and intron in the Saccharomyces cerevisiae genome and two chromosomes(21,22) of human genome, and we find that most (77.27%) TFBSs are observed to be over-represented in the 600bp upstream of Saccharomyces cerevisiae, but in other regions TFBSs don't show distinct enrichment. In human genome, TFBS don't show significant enrichment in upstream region as expected (50%), Many TFBSs are also distribute in other non-coding region like intergenic region and intron region, so we assumed that maybe there are more complex transcriptional mechanisms in human genome. we also find that most regulatory elements in exon are observed to be under-represented (about 22%), Almost the enrichment of TFBS in every non-coding region is higher than in coding region.Since regulatory elements in two different chromosomes have basically the same distribution in different regions, it is possible to evaluate the accuracy of experimental determined regulatory elements according to their enrichment in different regions.Finally, we develop a web-based software that combine GSFD and GRIS database in our lab, it is a helpful tool to search potential regulatory elements and it combines a statistic method about composite elements.