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          Institute: MPI für molekulare Genetik     Collection: Department of Vertebrate Genomics     Display Documents



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ID: 547657.0, MPI für molekulare Genetik / Department of Vertebrate Genomics
Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage
Authors:Chavez, L.; Jozefczuk, J.; Grimm, C.; Dietrich, J.; Timmermann, B.; Lehrach, H.; Herwig, R.; Adjaye, J.
Date of Publication (YYYY-MM-DD):2010-08-27
Title of Journal:Genome Research
Journal Abbrev.:Genome Res
Volume:20
Start Page:1441
End Page:1450
Copyright:© 2010 by Cold Spring Harbor Laboratory Press
Review Status:not specified
Audience:Experts Only
Abstract / Description:The generation of genome-wide data derived from methylated DNA immunoprecipitation followed by sequencing (MeDIP-seq) has become a major tool for epigenetic studies in health and disease. The computational analysis of such data, however, still falls short on accuracy, sensitivity, and speed. We propose a time-efficient statistical method that is able to cope with the inherent complexity of MeDIP-seq data with similar performance compared with existing methods. In order to demonstrate the computational approach, we have analyzed alterations in DNA methylation during the differentiation of human embryonic stem cells (hESCs) to definitive endoderm. We show improved correlation of normalized MeDIP-seq data in comparison to available whole-genome bisulfite sequencing data, and investigated the effect of differential methylation on gene expression. Furthermore, we analyzed the interplay between DNA methylation, histone modifications, and transcription factor binding and show that in contrast to de novo methylation, demethylation is mainly associated with regions of low CpG densities.
External Publication Status:published
Document Type:Article
Communicated by:Hans Lehrach
Affiliations:MPI für molekulare Genetik
External Affiliations:The Stem Cell Unit, Department of Anatomy, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia
Identifiers:ISSN:1549-5469 (Electronic) [ID No:1]
DOI:10.1101/gr.110114.110 [ID No:2]
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