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Nucleic Acids Res. 2013 Sep;41(16):e155. doi: 10.1093/nar/gkt599. Epub 2013 Jul 4.

Identification of active regulatory regions from DNA methylation data.

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1
Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, 4058 Basel, Switzerland, Swiss Institute of Bioinformatics, Maulbeerstrasse 66, 4058 Basel, Switzerland and University of Basel, Petersplatz 1, 4003 Basel, Switzerland.

Abstract

We have recently shown that transcription factor binding leads to defined reduction in DNA methylation, allowing for the identification of active regulatory regions from high-resolution methylomes. Here, we present MethylSeekR, a computational tool to accurately identify such footprints from bisulfite-sequencing data. Applying our method to a large number of published human methylomes, we demonstrate its broad applicability and generalize our previous findings from a neuronal differentiation system to many cell types and tissues. MethylSeekR is available as an R package at www.bioconductor.org.

PMID:
23828043
PMCID:
PMC3763559
DOI:
10.1093/nar/gkt599
[Indexed for MEDLINE]
Free PMC Article
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