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

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 hype...

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Main Authors:	Aaron L. Statham, Phillippa C. Taberlay, Theresa K. Kelly, Peter A. Jones, Susan J. Clark
Format:	Article
Language:	English
Published:	Elsevier 2015-03-01
Series:	Genomics Data
Subjects:	Epigenetics Methylation Nucleosome positioning NOMe-seq
Online Access:	http://www.sciencedirect.com/science/article/pii/S2213596014001251

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spelling	doaj-287f87645bde4dab872ced9c5558446b2020-11-25T02:10:02ZengElsevierGenomics Data2213-59602015-03-013C949610.1016/j.gdata.2014.11.012Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell linesAaron L. Statham0Phillippa C. Taberlay1Theresa K. Kelly2Peter A. Jones3Susan J. Clark4Epigenetics Research Program, Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, AustraliaEpigenetics Research Program, Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, AustraliaActive Motif, Inc., Carlsbad, CA 92008, USAVan Andel Research Institute, Grand Rapids, MI 49503, USAEpigenetics Research Program, Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, AustraliaDNA 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.http://www.sciencedirect.com/science/article/pii/S2213596014001251EpigeneticsMethylationNucleosome positioningNOMe-seq
collection	DOAJ
language	English
format	Article
sources	DOAJ
author	Aaron L. Statham Phillippa C. Taberlay Theresa K. Kelly Peter A. Jones Susan J. Clark
spellingShingle	Aaron L. Statham Phillippa C. Taberlay Theresa K. Kelly Peter A. Jones Susan J. Clark Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines Genomics Data Epigenetics Methylation Nucleosome positioning NOMe-seq
author_facet	Aaron L. Statham Phillippa C. Taberlay Theresa K. Kelly Peter A. Jones Susan J. Clark
author_sort	Aaron L. Statham
title	Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines
title_short	Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines
title_full	Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines
title_fullStr	Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines
title_full_unstemmed	Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines
title_sort	genome-wide nucleosome occupancy and dna methylation profiling of four human cell lines
publisher	Elsevier
series	Genomics Data
issn	2213-5960
publishDate	2015-03-01
description	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.
topic	Epigenetics Methylation Nucleosome positioning NOMe-seq
url	http://www.sciencedirect.com/science/article/pii/S2213596014001251
work_keys_str_mv	AT aaronlstatham genomewidenucleosomeoccupancyanddnamethylationprofilingoffourhumancelllines AT phillippactaberlay genomewidenucleosomeoccupancyanddnamethylationprofilingoffourhumancelllines AT theresakkelly genomewidenucleosomeoccupancyanddnamethylationprofilingoffourhumancelllines AT peterajones genomewidenucleosomeoccupancyanddnamethylationprofilingoffourhumancelllines AT susanjclark genomewidenucleosomeoccupancyanddnamethylationprofilingoffourhumancelllines
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Genome-wide nucleosome occupancy and DNA methylation profiling of four human cell lines

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