Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies

Ghia M. Euskirchen, Joel S. Rozowsky, Chia Lin Wei, Heng Lee Wah, Zhengdong Zhang, Stephen Hartman, Olof Emanuelsson, Viktor Stolc, Sherman Weissman, Mark B. Gerstein, Yijun Ruan, Michael Snyder

Research output: Contribution to journalArticle

154 Citations (Scopus)

Abstract

Recent progress in mapping transcription factor (TF) binding regions can largely be credited to chromatin immunoprecipitation (ChIP) technologies. We compared strategies for mapping TF binding regions in mammalian cells using two different ChIP schemes: ChIP with DNA microarray analysis (ChIP-chip) and ChIP with DNA sequencing (ChIP-PET). We first investigated parameters central to obtaining robust ChIP-chip data sets by analyzing STAT1 targets in the ENCODE regions of the human genome, and then compared ChIP-chip to ChIP-PET. We devised methods for scoring and comparing results among various tiling arrays and examined parameters such as DNA microarray format, oligonucleotide length, hybridization conditions, and the use of competitor Cot-1 DNA. The best performance was achieved with high-density oligonucleotide arrays, oligonucleotides ≥50 bases (b), the presence of competitor Cot-1 DNA and hybridizations conducted in microfluidics stations. When target identification was evaluated as a function of array number, 80%-86% of targets were identified with three or more arrays. Comparison of ChIP-chip with ChIP-PET revealed strong agreement for the highest ranked targets with less overlap for the low ranked targets. With advantages and disadvantages unique to each approach, we found that ChIP-chip and ChIP-PET are frequently complementary in their relative abilities to detect STAT1 targets for the lower ranked targets; each method detected validated targets that were missed by the other method. The most comprehensive list of STAT1 binding regions is obtained by merging results from ChIP-chip and ChIP-sequencing. Overall, this study provides information for robust identification, scoring, and validation of TF targets using ChIP-based technologies.

Original languageEnglish (US)
Pages (from-to)898-909
Number of pages12
JournalGenome Research
Volume17
Issue number6
DOIs
StatePublished - Jun 2007
Externally publishedYes

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Chromatin Immunoprecipitation
Transcription Factors
Technology
Oligonucleotide Array Sequence Analysis
Oligonucleotides
Microfluidics
DNA
Human Genome
Microarray Analysis
DNA Sequence Analysis

ASJC Scopus subject areas

  • Genetics

Cite this

Mapping of transcription factor binding regions in mammalian cells by ChIP : Comparison of array- and sequencing-based technologies. / Euskirchen, Ghia M.; Rozowsky, Joel S.; Wei, Chia Lin; Wah, Heng Lee; Zhang, Zhengdong; Hartman, Stephen; Emanuelsson, Olof; Stolc, Viktor; Weissman, Sherman; Gerstein, Mark B.; Ruan, Yijun; Snyder, Michael.

In: Genome Research, Vol. 17, No. 6, 06.2007, p. 898-909.

Research output: Contribution to journalArticle

Euskirchen, GM, Rozowsky, JS, Wei, CL, Wah, HL, Zhang, Z, Hartman, S, Emanuelsson, O, Stolc, V, Weissman, S, Gerstein, MB, Ruan, Y & Snyder, M 2007, 'Mapping of transcription factor binding regions in mammalian cells by ChIP: Comparison of array- and sequencing-based technologies', Genome Research, vol. 17, no. 6, pp. 898-909. https://doi.org/10.1101/gr.5583007
Euskirchen, Ghia M. ; Rozowsky, Joel S. ; Wei, Chia Lin ; Wah, Heng Lee ; Zhang, Zhengdong ; Hartman, Stephen ; Emanuelsson, Olof ; Stolc, Viktor ; Weissman, Sherman ; Gerstein, Mark B. ; Ruan, Yijun ; Snyder, Michael. / Mapping of transcription factor binding regions in mammalian cells by ChIP : Comparison of array- and sequencing-based technologies. In: Genome Research. 2007 ; Vol. 17, No. 6. pp. 898-909.
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