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An Optimized ChIP-Seq Protocol to Determine Chromatin Binding of Estrogen Receptor Beta

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Estrogen Receptors

Part of the book series: Methods in Molecular Biology ((MIMB,volume 2418))

Abstract

Estrogen regulates transcription through two nuclear receptors, ERα and ERβ, in a tissue and cellular-dependent manner. Both the receptors bind estrogen and activate transcription through direct or indirect interactions with DNA. Revealing their interactions with the chromatin is key to understanding their transcriptional activities and their biological functions. Chromatin-immunoprecipitation followed by sequencing (ChIP-Seq) is a powerful technique to map protein–DNA interactions at precise genomic locations. The genome-wide binding of ERα has been extensively studied. Similar studies of ERβ, however, have been more difficult, in part due to a lack of endogenous expression in cell lines and lack of specific antibodies. In this chapter, we provide an optimized stepwise ChIP protocol for a well-validated ERβ antibody, which is applicable for ChIP-Seq analysis of cell lines with exogenous expression of ERβ.

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Acknowledgments

We would like to thank Dr. Jun Wang and Dr. Fahmi Mesmar (previously at University of Houston) for assistance with experiments. This work was supported by the Swedish Cancer Society (CAN 2018/596) and the Swedish Research Council (2017-01658).

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Authors and Affiliations

  1. SciLifeLab, Department of Protein Science, KTH—Royal Institute of Technology, Solna, Sweden

    Rajitha Indukuri & Cecilia Williams

  2. Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden

    Rajitha Indukuri & Cecilia Williams

  3. Bioinformatics and Expression Core, Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden

    Anastasios Damdimopoulos

Authors
  1. Rajitha Indukuri
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  2. Anastasios Damdimopoulos
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  3. Cecilia Williams
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Correspondence to Cecilia Williams .

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Editors and Affiliations

  1. Sanford School of Medicine, University of South Dakota, Vermillion, SD, USA

    Kathleen M. Eyster

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Indukuri, R., Damdimopoulos, A., Williams, C. (2022). An Optimized ChIP-Seq Protocol to Determine Chromatin Binding of Estrogen Receptor Beta. In: Eyster, K.M. (eds) Estrogen Receptors. Methods in Molecular Biology, vol 2418. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1920-9_13

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  • DOI: https://doi.org/10.1007/978-1-0716-1920-9_13

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