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An Optimized Chromatin Immunoprecipitation Protocol for Quantification of Protein-DNA Interactions.

ABSTRACT: Transcription factors are important regulators of cell fate and function. Knowledge about where transcription factors are bound in the genome is crucial for understanding their function. A common method to study protein-DNA interactions is chromatin immunoprecipitation (ChIP). Here, we present a revised ChIP protocol to determine protein-DNA interactions for the yeast Saccharomyces cerevisiae. We optimized several aspects of the procedure, including cross-linking and quenching, cell lysis, and immunoprecipitation steps. This protocol facilitates sensitive and reproducible quantitation of protein-DNA interactions. For complete details on the use and execution of this protocol, please refer to (de Jonge et al., 2019).

SUBMITTER: de Jonge WJ

PROVIDER: S-EPMC7357673 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature

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An Optimized Chromatin Immunoprecipitation Protocol for Quantification of Protein-DNA Interactions.

de Jonge Wim J WJ Brok Mariël M Kemmeren Patrick P Holstege Frank C P FCP

STAR protocols 20200619 1

Transcription factors are important regulators of cell fate and function. Knowledge about where transcription factors are bound in the genome is crucial for understanding their function. A common method to study protein-DNA interactions is chromatin immunoprecipitation (ChIP). Here, we present a revised ChIP protocol to determine protein-DNA interactions for the yeast <i>Saccharomyces cerevisiae</i>. We optimized several aspects of the procedure, including cross-linking and quenching, cell lysis ...[more]

PMID: 32685929

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Project description:BackgroundThe processes that compose expression of a given gene are far more complex than previously thought presenting unprecedented conceptual and mechanistic challenges that require development of new tools. Chromatin structure, which is regulated by DNA methylation and histone modification, is at the center of gene regulation. Immunoprecipitations of chromatin (ChIP) and methylated DNA (MeDIP) represent a major achievement in this area that allow researchers to probe chromatin modifications as well as specific protein-DNA interactions in vivo and to estimate the density of proteins at specific sites genome-wide. Although a critical component of chromatin structure, DNA methylation has often been studied independently of other chromatin events and transcription.ResultsTo allow simultaneous measurements of DNA methylation with other genomic processes, we developed and validated a simple and easy-to-use high throughput microplate-based platform for analysis of DNA methylation. Compared to the traditional beads-based MeDIP the microplate MeDIP was more sensitive and had lower non-specific binding. We integrated the MeDIP method with a microplate ChIP assay which allows measurements of both DNA methylation and histone marks at the same time, Matrix ChIP-MeDIP platform. We illustrated several applications of this platform to relate DNA methylation, with chromatin and transcription events at selected genes in cultured cells, human cancer and in a model of diabetic kidney disease.ConclusionThe high throughput capacity of Matrix ChIP-MeDIP to profile tens and potentially hundreds of different genomic events at the same time as DNA methylation represents a powerful platform to explore complex genomic mechanism at selected genes in cultured cells and in whole tissues. In this regard, Matrix ChIP-MeDIP should be useful to complement genome-wide studies where the rich chromatin and transcription database resources provide fruitful foundation to pursue mechanistic, functional and diagnostic information at genes of interest in health and disease.

Dataset Information

An Optimized Chromatin Immunoprecipitation Protocol for Quantification of Protein-DNA Interactions.

Publications

An Optimized Chromatin Immunoprecipitation Protocol for Quantification of Protein-DNA Interactions.

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