title: Genome-Wide Association between Transcription Factor Expression and Chromatin Accessibility Reveals Regulators of Chromatin Accessibility.
abstract: To better understand genome regulation, it is important to uncover the role of transcription factors in the process of chromatin structure establishment and maintenance. Here we present a data-driven approach to systematically characterise transcription factors that are relevant for this process. Our method uses a linear mixed modelling approach to combine datasets of transcription factor binding motif enrichments in open chromatin and gene expression across the same set of cell lines. Applying this approach to the ENCODE dataset, we confirm already known and imply numerous novel transcription factors that play a role in the establishment or maintenance of open chromatin. In particular, our approach rediscovers many factors that have been annotated as pioneer factors.
authors.affiliation: Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.|Swiss institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: David
authors.identifier: 0000-0002-9216-8825
authors.initials: D
authors.lastname: Lamparter
authors.affiliation: Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.|Swiss institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Daniel
authors.identifier: 0000-0002-6686-9249
authors.initials: D
authors.lastname: Marbach
authors.affiliation: Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.|Swiss institute of Bioinformatics, Lausanne, Switzerland.
authors.forename: Rico
authors.initials: R
authors.lastname: Rueedi
authors.affiliation: Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.|Swiss institute of Bioinformatics, Lausanne, Switzerland.|Department of Integrative Biomedical Sciences, University of Cape Town, Cape Town, South Africa.
authors.forename: Sven
authors.identifier: 0000-0002-6785-9034
authors.initials: S
authors.lastname: Bergmann
authors.affiliation: Swiss institute of Bioinformatics, Lausanne, Switzerland.|Institute of Social and Preventive Medicine (IUMSP), Lausanne University Hospital, Lausanne, Switzerland.
authors.forename: Zoltán
authors.identifier: 0000-0001-8285-7523
authors.initials: Z
authors.lastname: Kutalik
mesh_terms: D001665:Binding Sites / Q000235:genetics; D002460:Cell Line; D002843:Chromatin / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D047369:Chromatin Immunoprecipitation; D019295:Computational Biology; D055106:Genome-Wide Association Study; D006801:Humans; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism
chemical_list: D002843:Chromatin; D014157:Transcription Factors