Design And Implementation Of The Model Between DNA Methylation And Transcription Link By TFBS Information

DNA methylation phenomenon is the first discovered epigenetic phenomena.And it is one of the most important epigenetic phenomena, too. It is alwaysobserved association with gene expression. And the organism growth anddevelopment are closely related with it. DNA Methylation also has close ties with avariety of diseases. Many diseases which are still incurable often accompanyabnormal methylation, including various types of cancer and some of theautoimmune diseases. With the development of methylation measurement andbioinformatics technology, It’s becoming possible to explore the study of how DNAmethylation affects gene expression.Our works begin with the establishing of the model linking DNA methylationand gene expression by transcription factor information. We first designed andimplemented the algorithm to location the TFBS and clustering TF to elimination ofredundancy based on the transcription factor motif information. We also exploredthe relationship between DNA methylation and transcription factor binding. Wediscovered that DNA methylation has different effects on transcription factorbinding. There is only a portion of the transcription factor sensitive to the degree ofthe methylation of the sites around the binding sites, and the region of the sitesaround the TFBS that can affect the binding of transcription factors is rather large. Itwas also found that the transcription factors which are sensitive to DNAmethylation can predict its binding sites better within the guide of DNA methylation.It can greatly improve the accuracy without reducing the recall. In the final, we builta transcription factor centric model connecting the DNA methylation and geneexpression (the TDMEM). Based on the model, we designed a series of relatedexperiments, demonstrated the presence of methylation in gene expressionregulation. And the effects of the regulation change with the difference of the genes,and are closely related to the type and quantity of the transcription factor bindingsites within the gene’s promoter region.