Epigenomic data integration for characterization of promoter regions

Abstract

Understanding the regulatory machinery is one of the current challenges for research in cancer epigenomics. Regulation of gene expression is a complex process with many components involved in it such as histone modifications, DNA methylation and chromatin accessibility, among others. In this project we are going to explore the Blueprint database of human hematopoietic cells in order to characterize regulatory regions on samples from this dataset. For this purpose we are going to carry out a number of steps to analyse the DNA methylation, epigenomic features and RNA-seq. The characterization of methylation across 92 samples of 12 different cell types have determined that methylation state at promoters and CpG islands are cell type-specific. Exploration and integration of epigenomics in one sample of cell type monocyte was carried out. We have seen the implications of two marks studied (histone modification H3K4me3 and open chromatin state) in gene expression. This characterization of promoters functionality enabled us to create a pipeline for the identification of novel regulatory regions based in the integration of epigenomic features and RNA-seq data, which we later reproduced in four samples. This project could be a start point of a bigger project for the cell type-specific promoters discovery within the Blueprint projects.