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Use of chromatin immunoprecipitation (chip) to detect transcription factor binding to highly homologous promoters in chromatin isolated from unstimulated and activated primary human B cells

Abstract

The Chromatin Immunoprecipiation (ChIP) provides a powerful technique for identifying the in vivo association of transcription factors with regulatory elements. However, obtaining meaningful information for promoter interactions is extremely challenging when the promoter is a member of a class of highly homologous elements. Use of PCR primers with small numbers of mutations can limit cross-hybridization with non-targeted sequences and distinguish a pattern of binding for factors with the regulatory element of interest. In this report, we demonstrate the selective in vivo association of NF-κB, p300 and CREB with the human Iγ1 promoter located in the intronic region upstream of the Cγ1 exons in the immunoglobulin heavy chain locus. These methods have the ability to extend ChIP analysis to promoters with a high degree of homology.

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Correspondence to Lori R. Covey.

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Open Access This article is published under license to BioMed Central Ltd. This is an Open Access article is distributed under the terms of the Creative Commons Attribution License ( https://creativecommons.org/licenses/by/2.0 ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Dryer, R.L., Covey, L.R. Use of chromatin immunoprecipitation (chip) to detect transcription factor binding to highly homologous promoters in chromatin isolated from unstimulated and activated primary human B cells. Biol. Proced. Online 8, 44–54 (2006). https://doi.org/10.1251/bpo117

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  • DOI: https://doi.org/10.1251/bpo117

Indexing terms

  • Gene Expression Regulation
  • Transcription Factors
  • Chromatin Immunoprecipitation
  • B cells