Epigenetics and Control of RNAs

Henrike Maatz; Sebastiaan van Heesch; Franziska Kreuchwig; Allison Faber; Eleonora Adami; Norbert Hubner; Matthias Heinig

doi:10.1007/978-1-4939-6427-7_9

Epigenetics and Control of RNAs

Henrike Maatz
, Sebastiaan van Heesch
, Franziska Kreuchwig
, Allison Faber
, Eleonora Adami
, Norbert Hubner
, Matthias Heinig

Research output: Contribution to journal › Article › peer-review

3 Citations (Scopus)

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.

Original language	English
Pages (from-to)	217-237
Number of pages	21
Journal	Methods in molecular biology (Clifton, N.J.)
Volume	1488
DOIs	https://doi.org/10.1007/978-1-4939-6427-7_9
Publication status	Published - 2017
Externally published	Yes

Keywords

Chromatin Immunoprecipitation
Chromosome Mapping/methods
Computational Biology/methods
Epigenesis, Genetic
Epigenomics/methods
Gene Expression
High-Throughput Nucleotide Sequencing
Histones/metabolism
Inbreeding
Quantitative Trait Loci
RNA/genetics
Recombination, Genetic
Software

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10.1007/978-1-4939-6427-7_9

Cite this

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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.",

keywords = "Chromatin Immunoprecipitation, Chromosome Mapping/methods, Computational Biology/methods, Epigenesis, Genetic, Epigenomics/methods, Gene Expression, High-Throughput Nucleotide Sequencing, Histones/metabolism, Inbreeding, Quantitative Trait Loci, RNA/genetics, Recombination, Genetic, Software",

author = "Henrike Maatz and \{van Heesch\}, Sebastiaan and Franziska Kreuchwig and Allison Faber and Eleonora Adami and Norbert Hubner and Matthias Heinig",

year = "2017",

doi = "10.1007/978-1-4939-6427-7\_9",

language = "English",

volume = "1488",

pages = "217--237",

journal = "Methods in molecular biology (Clifton, N.J.)",

issn = "1064-3745",

publisher = "Humana Press Inc.",

}

TY - JOUR

T1 - Epigenetics and Control of RNAs

AU - Maatz, Henrike

AU - van Heesch, Sebastiaan

AU - Kreuchwig, Franziska

AU - Faber, Allison

AU - Adami, Eleonora

AU - Hubner, Norbert

AU - Heinig, Matthias

PY - 2017

Y1 - 2017

N2 - 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.

AB - 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.

KW - Chromatin Immunoprecipitation

KW - Chromosome Mapping/methods

KW - Computational Biology/methods

KW - Epigenesis, Genetic

KW - Epigenomics/methods

KW - Gene Expression

KW - High-Throughput Nucleotide Sequencing

KW - Histones/metabolism

KW - Inbreeding

KW - Quantitative Trait Loci

KW - RNA/genetics

KW - Recombination, Genetic

KW - Software

U2 - 10.1007/978-1-4939-6427-7_9

DO - 10.1007/978-1-4939-6427-7_9

M3 - Article

C2 - 27933526

SN - 1064-3745

VL - 1488

SP - 217

EP - 237

JO - Methods in molecular biology (Clifton, N.J.)

JF - Methods in molecular biology (Clifton, N.J.)

ER -

Epigenetics and Control of RNAs

Abstract

Keywords

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