Review Question 2
What is the primary purpose of chromatin sonication when performing a ChIP
experiment?
Review Question 3
Which of these is important for preparing templates for Next Generation Sequencing?
A. Isolating DNA from tissue.
B. Breaking DNA up into smaller fragments.
C. Checking the quality and quantity of the fragment library.
D. All of the above.
Answers to Review Questions
Answers to Question 1:
A transcription factor recognizes and binds to specific sites in the genome, to recruit
cofactors, and thus to regulate transcription. Thus ChIP allows identification of TF
binding motifs and the direct downstream targets of a specific TF. Consequently,
clustering of transcription-regulatory proteins at specific DNA sites can be assessed.
Answers to Question 2:
Sonication of the chromatin is performed to reduce the size of the DNA fragments.
Without this step, high molecular weight DNA would be immunoprecipitated, forming a
large complex with the antibody. This would create loss of resolution and false positive
results.
Answers to Question 3:
D
Acknowledgements We thank Prof. Dr. Anja Bosserhoff (Institute of Biochemistry (Emil-Fischer
Center), Friedrich-Alexander University Erlangen-Nürnberg) for reviewing this chapter and
suggesting extremely relevant enhancements to the original manuscript.
References
1. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple combinations of lineagedetermining transcription factors prime cis-regulatory elements required for macrophage and B
cell identities. Mol Cell. 2010;38(4):576–89.
2. Deliard S, Zhao J, Xia Q, Grant SF. Generation of high quality chromatin immunoprecipitation
DNA template for high-throughput sequencing (ChIP-seq). J Vis Exp. 2013;(74):e50286.
3. Tian B, Yang J, Brasier AR. Two-step cross-linking for analysis of protein-chromatin
interactions. Methods Mol Biol. 2012;809:105–20.
4. Jiang S, Mortazavi A. Integrating ChIP-seq with other functional genomics data. Brief Funct
Genomics. 2018;17(2):104–15.
12 Design and Analysis of Epigenetics and ChIP-Sequencing Data
191
What is the primary purpose of chromatin sonication when performing a ChIP
experiment?
Review Question 3
Which of these is important for preparing templates for Next Generation Sequencing?
A. Isolating DNA from tissue.
B. Breaking DNA up into smaller fragments.
C. Checking the quality and quantity of the fragment library.
D. All of the above.
Answers to Review Questions
Answers to Question 1:
A transcription factor recognizes and binds to specific sites in the genome, to recruit
cofactors, and thus to regulate transcription. Thus ChIP allows identification of TF
binding motifs and the direct downstream targets of a specific TF. Consequently,
clustering of transcription-regulatory proteins at specific DNA sites can be assessed.
Answers to Question 2:
Sonication of the chromatin is performed to reduce the size of the DNA fragments.
Without this step, high molecular weight DNA would be immunoprecipitated, forming a
large complex with the antibody. This would create loss of resolution and false positive
results.
Answers to Question 3:
D
Acknowledgements We thank Prof. Dr. Anja Bosserhoff (Institute of Biochemistry (Emil-Fischer
Center), Friedrich-Alexander University Erlangen-Nürnberg) for reviewing this chapter and
suggesting extremely relevant enhancements to the original manuscript.
References
1. Heinz S, Benner C, Spann N, Bertolino E, Lin YC, Laslo P, et al. Simple combinations of lineagedetermining transcription factors prime cis-regulatory elements required for macrophage and B
cell identities. Mol Cell. 2010;38(4):576–89.
2. Deliard S, Zhao J, Xia Q, Grant SF. Generation of high quality chromatin immunoprecipitation
DNA template for high-throughput sequencing (ChIP-seq). J Vis Exp. 2013;(74):e50286.
3. Tian B, Yang J, Brasier AR. Two-step cross-linking for analysis of protein-chromatin
interactions. Methods Mol Biol. 2012;809:105–20.
4. Jiang S, Mortazavi A. Integrating ChIP-seq with other functional genomics data. Brief Funct
Genomics. 2018;17(2):104–15.
12 Design and Analysis of Epigenetics and ChIP-Sequencing Data
191