Differential Analysis of Protein-DNA Binding Using ChIP-Seq Data

doi:10.1007/978-1-0716-4071-5_5

. 2024:2846:63-89.

doi: 10.1007/978-1-0716-4071-5_5.

Differential Analysis of Protein-DNA Binding Using ChIP-Seq Data

Christiane Boeckel¹, Xavier Pastor¹, Matthias Heinig^{2

3

4}, Thomas Walzthoeni⁵

Affiliations

¹ Core Facility Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.
² Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.
³ Department of Computer Science, TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
⁴ DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.
⁵ Core Facility Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany. thomas.walzthoeni@helmholtz-munich.de.

PMID: 39141230
DOI: 10.1007/978-1-0716-4071-5_5

Differential Analysis of Protein-DNA Binding Using ChIP-Seq Data

Christiane Boeckel et al. Methods Mol Biol. 2024.

. 2024:2846:63-89.

doi: 10.1007/978-1-0716-4071-5_5.

Authors

Christiane Boeckel¹, Xavier Pastor¹, Matthias Heinig^{2

3

4}, Thomas Walzthoeni⁵

Affiliations

¹ Core Facility Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.
² Computational Health Center, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany.
³ Department of Computer Science, TUM School of Computation, Information and Technology, Technical University of Munich, Garching, Germany.
⁴ DZHK (German Centre for Cardiovascular Research), Partner Site Munich Heart Alliance, Munich, Germany.
⁵ Core Facility Genomics, Helmholtz Zentrum München Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Neuherberg, Germany. thomas.walzthoeni@helmholtz-munich.de.

PMID: 39141230
DOI: 10.1007/978-1-0716-4071-5_5

Abstract

Chromatin immunoprecipitation in combination with next-generation sequencing (ChIP-Seq) allows probing of protein-DNA binding in a rapid and genome-wide fashion. Herein we describe the required steps to preprocess ChIP-Seq data and to analyze the differential binding of proteins to DNA for perturbation experiments. In these experiments, different conditions are compared to find the underlying biological mechanisms caused by the stimulus or treatment. In addition, we provide a sample analysis using the steps outlined in the chapter.

Keywords: DiffBind; Differential ChIP-Seq analysis; ChIP-Seq.

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References

1. Allis CD, Jenuwein T (2016) The molecular hallmarks of epigenetic control. Nat Rev Genet 17(8):487–500 - DOI - PubMed
1. Buck MJ, Lieb JD (2004) ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83(3):349–360 - DOI - PubMed
1. Pellegrini M, Ferrari R (2012) Epigenetic analysis: ChIP-chip and ChIP-seq. Methods Mol Biol 802:377–387 - DOI - PubMed
1. Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10(10):669–680 - DOI - PubMed - PMC
1. Furey TS (2012) ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet 13(12):840–852 - DOI - PubMed - PMC

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[1] Allis CD, Jenuwein T (2016) The molecular hallmarks of epigenetic control. Nat Rev Genet 17(8):487–500 - DOI - PubMed

[2] Allis CD, Jenuwein T (2016) The molecular hallmarks of epigenetic control. Nat Rev Genet 17(8):487–500 - DOI - PubMed

[3] Buck MJ, Lieb JD (2004) ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83(3):349–360 - DOI - PubMed

[4] Buck MJ, Lieb JD (2004) ChIP-chip: considerations for the design, analysis, and application of genome-wide chromatin immunoprecipitation experiments. Genomics 83(3):349–360 - DOI - PubMed

[5] Pellegrini M, Ferrari R (2012) Epigenetic analysis: ChIP-chip and ChIP-seq. Methods Mol Biol 802:377–387 - DOI - PubMed

[6] Pellegrini M, Ferrari R (2012) Epigenetic analysis: ChIP-chip and ChIP-seq. Methods Mol Biol 802:377–387 - DOI - PubMed

[7] Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10(10):669–680 - DOI - PubMed - PMC

[8] Park PJ (2009) ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet 10(10):669–680 - DOI - PubMed - PMC

[9] Furey TS (2012) ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet 13(12):840–852 - DOI - PubMed - PMC

[10] Furey TS (2012) ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions. Nat Rev Genet 13(12):840–852 - DOI - PubMed - PMC

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Differential Analysis of Protein-DNA Binding Using ChIP-Seq Data

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Differential Analysis of Protein-DNA Binding Using ChIP-Seq Data

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