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  Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage

Chavez, L., Jozefczuk, J., Grimm, C., Dietrich, J., Timmermann, B., Lehrach, H., et al. (2010). Computational analysis of genome-wide DNA methylation during the differentiation of human embryonic stem cells along the endodermal lineage. Genome Research, 20, 1441-1450. doi:10.1101/gr.110114.110.

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Datensatz-Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7A79-1 Versions-Permalink: http://hdl.handle.net/11858/00-001M-0000-0010-7A7A-0
Genre: Zeitschriftenartikel
Alternativer Titel : Genome Res

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 Urheber:
Chavez, L.1, Autor              
Jozefczuk, J.2, Autor              
Grimm, C.3, Autor              
Dietrich, J.4, Autor
Timmermann, B.5, Autor              
Lehrach, H.1, Autor              
Herwig, R.4, Autor
Adjaye, J.2, Autor              
Affiliations:
1Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433550              
2Molecular Embryology and Aging (James Adjaye), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479654              
3In vitro Ligand Screening (Zoltán Konthur), Dept. of Vertebrate Genomics (Head: Hans Lehrach), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479653              
4Max Planck Society, ou_persistent13              
5Sequencing, Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1433559              

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 Zusammenfassung: 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.

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 Datum: 2010-08-27
 Publikationsstatus: Im Druck publiziert
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 Identifikatoren: eDoc: 547657
DOI: 10.1101/gr.110114.110
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Titel: Genome Research
  Alternativer Titel : Genome Res
Genre der Quelle: Zeitschrift
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Ort, Verlag, Ausgabe: -
Seiten: - Band / Heft: 20 Artikelnummer: - Start- / Endseite: 1441 - 1450 Identifikator: ISSN: 1549-5469 (Electronic)