title: Identification of active regulatory regions from DNA methylation data.
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.
authors.affiliation: 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.
authors.forename: Lukas
authors.initials: L
authors.lastname: Burger
authors.forename: Dimos
authors.initials: D
authors.lastname: Gaidatzis
authors.forename: Dirk
authors.initials: D
authors.lastname: Schübeler
authors.forename: Michael B
authors.initials: MB
authors.lastname: Stadler
mesh_terms: D000818:Animals; D018899:CpG Islands; D019175:DNA Methylation; D014644:Genetic Variation; D006801:Humans; D051379:Mice; D050436:Regulatory Elements, Transcriptional; D017422:Sequence Analysis, DNA; D012984:Software