DOI: 10.1101/gad.943102. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis

Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis

10.1101/gad.943102

Crossref journal-article

Cold Spring Harbor Laboratory

Genes & Development (246)

Abstract

Previously, identification of promoters regulated by mammalian transcription factors has relied upon overexpression studies. Here we present the identification of a large set of promoters that are bound by E2F in physiological conditions. Probing a human CpG microarray with chromatin immunoprecipitated using an antibody to E2F4, we have identified 68 unique target loci; 15% are bidirectional promoters and 25% recruit E2F via a mechanism distinct from the defined consensus site. Interestingly, although E2F has been shown previously to regulate genes involved in cell cycle progression, many of the new E2F target genes encode proteins involved in DNA repair or recombination. We suggest that human CpG microarrays, in combination with chromatin immunoprecipitation, will allow rapid identification of target promoters for many mammalian transcription factors.

Bibliography

Weinmann, A. S., Yan, P. S., Oberley, M. J., Huang, T. H.-M., & Farnham, P. J. (2002). Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes & Development, 16(2), 235â244.

Authors 5

Amy S. Weinmann (first)
Pearlly S. Yan (additional)
Matthew J. Oberley (additional)
Tim Hui-Ming Huang (additional)
Peggy J. Farnham (additional)

References 27 Referenced 344

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10.1038/ng0394-236
10.1128/MCB.15.8.4215 / Mol. Cell. Biol. / Cellular targets for activation by the E2F1 transcription factor include DNA synthesis- and G1/S-regulatory genes. by DeGregori (1995)
10.1093/bioinformatics/17.suppl_1.S90 / Bioinformatics / Promoter prediction in the human genome. by Hannenhalli (2001)
10.1093/hmg/8.3.459
10.1038/79189
10.1128/MCB.21.14.4684-4699.2001
10.1038/35054095
10.1038/365349a0
{'key': '2021111507560687000_16.2.235.11', 'first-page': '2707', 'article-title': 'Thymidylate synthase expression correlates closely with E2F1 expression in colon cancer.', 'volume': '6', 'author': 'Kasahara', 'year': '2000', 'journal-title': 'Clin. Cancer Res.'} / Clin. Cancer Res. / Thymidylate synthase expression correlates closely with E2F1 expression in colon cancer. by Kasahara (2000)
10.1006/jmbi.2001.4650
10.1128/jvi.69.4.2491-2500.1995 / J. Virol. / E2F1 overexpression in quiescent fibroblasts leads to induction of cellular DNA synthesis and apoptosis. by Kowalik (1995)
10.1002/j.1460-2075.1993.tb05932.x / EMBO J. / An E2F-binding site mediates cell-cycle regulated repression of mouse B-myb transcription. by Lam (1993)
10.1038/sj.onc.1203556
10.1038/ng569
10.1128/MCB.21.17.6006-6016.2001
10.1101/gad.864201
10.1038/35087620
10.1128/MCB.16.5.1889 / Mol. Cell. Biol. / The E2F transcription ractor activates a replication-dependent Human H2A gene in early S phase of the cell cycle. by Oswald (1996)
10.1073/pnas.91.23.10918
10.1126/science.290.5500.2306
{'key': '2021111507560687000_16.2.235.23', 'first-page': '8166', 'article-title': 'Deregulated expression of E2F1 induces S-phase entry and leads to apoptosis.', 'volume': '14', 'author': 'Shan', 'year': '1994', 'journal-title': 'Mol. Cell. Biol.'} / Mol. Cell. Biol. / Deregulated expression of E2F1 induces S-phase entry and leads to apoptosis. by Shan (1994)
{'key': '2021111507560687000_16.2.235.24', 'first-page': '299', 'article-title': 'The transcription factor E2F-1 mediates the autoregulation of RB gene expression.', 'volume': '14', 'author': 'Shan', 'year': '1994', 'journal-title': 'Mol. Cell. Biol.'} / Mol. Cell. Biol. / The transcription factor E2F-1 mediates the autoregulation of RB gene expression. by Shan (1994)
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{'key': '2021111507560687000_16.2.235.27', 'first-page': '8375', 'article-title': 'Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays.', 'volume': '61', 'author': 'Yan', 'year': '2001', 'journal-title': 'Cancer Res.'} / Cancer Res. / Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays. by Yan (2001)

Dates

Type	When
Created	23 years, 1 month ago (July 26, 2002, 7:59 p.m.)
Deposited	3 years, 9 months ago (Nov. 15, 2021, 10:57 a.m.)
Indexed	2 weeks, 1 day ago (Aug. 20, 2025, 8:36 a.m.)
Issued	23 years, 7 months ago (Jan. 15, 2002)
Published	23 years, 7 months ago (Jan. 15, 2002)
Published Online	23 years, 7 months ago (Jan. 15, 2002)
Published Print	23 years, 7 months ago (Jan. 15, 2002)

Funders 0

None

BibTeX

@article{Weinmann_2002, title={Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis}, volume={16}, ISSN={1549-5477}, url={http://dx.doi.org/10.1101/gad.943102}, DOI={10.1101/gad.943102}, number={2}, journal={Genes & Development}, publisher={Cold Spring Harbor Laboratory}, author={Weinmann, Amy S. and Yan, Pearlly S. and Oberley, Matthew J. and Huang, Tim Hui-Ming and Farnham, Peggy J.}, year={2002}, month=jan, pages={235–244} }

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