title: Epigenetics and Control of RNAs.
abstract: Histone modifications are epigenetic marks that fundamentally impact the regulation of gene expression. Integrating histone modification information in the analysis of gene expression traits (eQTL mapping) has been shown to significantly enhance the prediction of eQTLs. In this chapter, we describe (1) how to perform quantitative trait locus (QTL) analysis using histone modification levels as traits and (2) how to integrate these data with information on RNA expression for the elucidation of the epigenetic control of transcript levels. We will provide a comprehensive introduction into the topic, describe in detail how ChIP-seq data are analyzed and elaborate on how to integrate ChIP-seq and RNA-seq data from a segregating disease animal model for the identification of the epigenetic control of RNA expression.
authors.affiliation: Max-Delbrück-Center for Molecular Medicine (MDC), 13125, Berlin, Germany.
authors.forename: Henrike
authors.initials: H
authors.lastname: Maatz
authors.affiliation: Max-Delbrück-Center for Molecular Medicine (MDC), 13125, Berlin, Germany.
authors.forename: Sebastiaan
authors.initials: S
authors.lastname: van Heesch
authors.affiliation: Max-Delbrück-Center for Molecular Medicine (MDC), 13125, Berlin, Germany.
authors.forename: Franziska
authors.initials: F
authors.lastname: Kreuchwig
authors.affiliation: Max-Delbrück-Center for Molecular Medicine (MDC), 13125, Berlin, Germany.
authors.forename: Allison
authors.initials: A
authors.lastname: Faber
authors.affiliation: Max-Delbrück-Center for Molecular Medicine (MDC), 13125, Berlin, Germany.
authors.forename: Eleonora
authors.initials: E
authors.lastname: Adami
authors.affiliation: Max-Delbrück-Center for Molecular Medicine (MDC), 13125, Berlin, Germany. nhuebner@mdc-berlin.de.|DZHK (German Centre for Cardiovascular Research), Partner Site, 13347, Berlin, Germany. nhuebner@mdc-berlin.de.|Charité-Universitätsmedizin, 10117, Berlin, Germany. nhuebner@mdc-berlin.de.
authors.forename: Norbert
authors.initials: N
authors.lastname: Hubner
authors.affiliation: Helmholtz Zentrum München, Institute of Computational Biology (ICB), Neuherberg, 85764, Germany. matthias.heinig@helmholtz-muenchen.de.
authors.forename: Matthias
authors.initials: M
authors.lastname: Heinig
mesh_terms: D047369:Chromatin Immunoprecipitation; D002874:Chromosome Mapping / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods*; D015870:Gene Expression; D059014:High-Throughput Nucleotide Sequencing; D006657:Histones / Q000378:metabolism; D007178:Inbreeding; D040641:Quantitative Trait Loci; D012313:RNA / Q000235:genetics*; D011995:Recombination, Genetic; D012984:Software
chemical_list: D006657:Histones; D012313:RNA
keywords: ChIP-seq; Histone modifications; Integrative analysis; QTL mapping; RNA expression; Recombinant inbred panel