Delineation of Methyl-DNA Binding Protein Interactions in the Prostate Cancer Genome (PC110091).

摘要

The purpose of this study is to generate a genome-wide association profile of Methyl-CpG Domain-containing (MBD) proteins, such as MeCP2, MBD1, MBD2 and MBD4, in malignant prostate cancer cells and matched normal or benign prostate cells using Chromatin Immunoprecipitation followed by Next Generation Sequencing (ChIP-Seq). ChIP-Seq experiments to examine those four proteins have been performed on two or three matched sets of prostate tissues. The results have been analyzed using a combination of software packages including Genomics Suite (Partek), RSEG and Galaxy to identify sets of common association regions or sites for each protein. The genes that overlap these common sites were identified and the genes among these with increased or decreased gene expression by microarray analysis have been listed. In parallel, RNA expression profiles from the same tissues were generated to allow comparison of differential patterns of gene expression with differential patterns of MBD protein association. Microarray analysis has been performed and has identified genes that are up-regulated and down-regulated in Stage 3 prostate cancer cells. This data has been useful in facilitating the bioinformatics analysis of the ChIP-Seq results and is also useful on its own to identify genes with altered patterns of regulation in malignant tissues.