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Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines

Abstract

DNA methylation and nucleosome positioning are two key mechanisms that contribute to the epigenetic control of gene expression. During carcinogenesis, the expression of many genes is altered alongside extensive changes in the epigenome, with repressed genes often being associated with local DNA hypermethylation and gain of nucleosomes at their promoters. However the spectrum of alterations that occur at distal regulatory regions has not been extensively studied. To address this we used Nucleosome Occupancy and Methylation sequencing (NOMe-seq) to compare the genome-wide DNA methylation and nucleosome occupancy profiles between normal and cancer cell line models of the breast and prostate. Here we describe the bioinformatic pipeline and methods that we developed for the processing and analysis of the NOMe-seq data published by (Taberlay et al., 2014 [1]) and deposited in the Gene Expression Omnibus with accession GSE57498.

Type Journal
ISBN 2213-5960 (Electronic) 2213-5960 (Linking)
Authors Statham, A. L.; Taberlay, P. C.; Kelly, T. K.; Jones, P. A.; Clark, S. J.;
Garvan Authors Aaron Statham , Dr Phillippa Taberlay , Prof Susan Clark
Publisher Name Genom Data
Published Date 2015-01-01 00:00:00
Published Volume 3
Published Pages 94-6
URL http://www.ncbi.nlm.nih.gov/pubmed/26484155
Status Published In-print
OpenAccess Link https://publications.gimr.garvan.org.au/download.php?13314_13364/main.pdf