Using ChIP-seq technology to identify targets of zinc finger transcription factors

Henriette O'Geen, Seth Frietze, Peggy J. Farnham

Research output: Chapter in Book/Report/Conference proceedingChapter

34 Citations (Scopus)

Abstract

Half of all human transcription factors are zinc finger proteins and yet very little is known concerning the biological role of the majority of these factors. In particular, very few genome-wide studies of the in vivo binding of zinc finger factors have been performed. Based on in vitro studies and other methods that allow selection of high affinity-binding sites in artificial conditions, a zinc finger code has been developed that can be used to compose a putative recognition motif for a particular zinc finger factor (ZNF). Theoretically, a simple bioinformatics analysis could then predict the genomic locations of all the binding sites for that ZNF. However, it is unlikely that all of the sequences in the human genome having a good match to a predicted motif are in fact occupied in vivo (due to negative influences from repressive chromatin, nucleosomal positioning, overlap of binding sites with other factors, etc). A powerful method to identify in vivo binding sites for transcription factors on a genome-wide scale is the chromatin immunoprecipitation (ChIP) assay, followed by hybridization of the precipitated DNA to microarrays (ChIP-chip) or by high throughput DNA sequencing of the sample (ChIP-seq). Such comprehensive in vivo binding studies would not only identify target genes of a particular zinc finger factor, but also provide binding motif data that could be used to test the validity of the zinc finger code. This chapter describes in detail the steps needed to prepare ChIP samples and libraries for high throughput sequencing using the Illumina GA2 platform and includes descriptions of quality control steps necessary to ensure a successful ChIP-seq experiment.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
Pages437-455
Number of pages19
Volume649
DOIs
StatePublished - 2010

Publication series

NameMethods in Molecular Biology
Volume649
ISSN (Print)10643745

Fingerprint

Chromatin Immunoprecipitation
Zinc Fingers
Transcription Factors
Technology
Binding Sites
Genome
High-Throughput Nucleotide Sequencing
Human Genome
Oligonucleotide Array Sequence Analysis
Computational Biology
Quality Control
Libraries
Chromatin
Genes
Proteins

Keywords

  • ChIP-seq
  • chromatin immunoprecipitation
  • next generation sequencing
  • Zinc fingers

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Medicine(all)

Cite this

O'Geen, H., Frietze, S., & Farnham, P. J. (2010). Using ChIP-seq technology to identify targets of zinc finger transcription factors. In Methods in Molecular Biology (Vol. 649, pp. 437-455). (Methods in Molecular Biology; Vol. 649). https://doi.org/10.1007/978-1-60761-753-2_27

Using ChIP-seq technology to identify targets of zinc finger transcription factors. / O'Geen, Henriette; Frietze, Seth; Farnham, Peggy J.

Methods in Molecular Biology. Vol. 649 2010. p. 437-455 (Methods in Molecular Biology; Vol. 649).

Research output: Chapter in Book/Report/Conference proceedingChapter

O'Geen, H, Frietze, S & Farnham, PJ 2010, Using ChIP-seq technology to identify targets of zinc finger transcription factors. in Methods in Molecular Biology. vol. 649, Methods in Molecular Biology, vol. 649, pp. 437-455. https://doi.org/10.1007/978-1-60761-753-2_27
O'Geen H, Frietze S, Farnham PJ. Using ChIP-seq technology to identify targets of zinc finger transcription factors. In Methods in Molecular Biology. Vol. 649. 2010. p. 437-455. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-60761-753-2_27
O'Geen, Henriette ; Frietze, Seth ; Farnham, Peggy J. / Using ChIP-seq technology to identify targets of zinc finger transcription factors. Methods in Molecular Biology. Vol. 649 2010. pp. 437-455 (Methods in Molecular Biology).
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