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Chromatin Immunoprecipitation- ChIP

Chromatin Immunoprecipitation- ChIP

Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...

Spreading of Chromatin Modifications

Spreading of Chromatin Modifications

The histone proteins in the nucleosomes are post-translationally modified (PTM) to increase or decrease access to DNA. The commonly observed PTMs are methylation, acetylation, phosphorylation, and ubiquitination of lysine amino acids in the histone H3 tail region. These histone modifications have specific meaning for the cell. Hence, they are called "histone code". The protein complex involved in histone modification is termed as "reader-writer" complex.
Writers
The writer is an enzyme that can...

Position-effect Variegation

Position-effect Variegation

In 1928, a German botanist Emil Heitz observed the moss nuclei with a DNA binding dye. He observed that while some chromatin regions decondense and spread out in the interphase nucleus, others do not. He termed them euchromatin and heterochromatin, respectively. He proposed that the heterochromatin regions reflect a functionally inactive state of the genome. It was later confirmed that heterochromatin is transcriptionally repressed, and euchromatin is transcriptionally active chromatin.

Inheritance of Chromatin Structures

Inheritance of Chromatin Structures

Epigenetics is the study of inherited changes in a cell's phenotype without changing the DNA sequences. It provides a form of memory for the differential gene expression pattern to maintain cell lineage, position-effect variegation, dosage compensation, and maintenance of chromatin structures such as telomeres and centromeres. For example, the structure and location of the centromere on chromosomes are epigenetically inherited. Its functionality is not dictated or ensured by the underlying DNA...

Heterochromatin

Heterochromatin

The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions that take up more dye are called heterochromatin. Heterochromatin is further classified into two forms – constitutive heterochromatin and facultative heterochromatin.
Constitutive heterochromatin: It is a highly compact region of chromatin that is mostly concentrated in the centromere and telomere. Unlike euchromatin, the amino acid at 9th...

Nucleosome Remodeling

Nucleosome Remodeling

Nucleosomes are the basic units of chromatin compaction. Each nucleosome consists of the DNA bound tightly around a histone core, which makes the DNA inaccessible to DNA binding proteins such as DNA polymerase and RNA polymerase. Hence, the fundamental problem is to ensure access to DNA when appropriate, despite the compact and protective chromatin structure.
Nucleosome remodeling complex
Eukaryotic cells have specialized enzymes called ATP-dependent nucleosome remodeling enzymes. These enzymes...

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Related Experiment Video

Updated: May 23, 2026

RNA-Associated Chromatin DNA-DNA Interaction Method

RNA-Associated Chromatin DNA-DNA Interaction Method

Published on: April 30, 2026

Differential DNase I hypersensitivity reveals factor-dependent chromatin dynamics.

Housheng Hansen He¹, Clifford A Meyer, Mei Wei Chen

¹Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health, Boston, Massachusetts 02115, USA;

Genome Research

|April 18, 2012

Summary

Hormone-induced changes in DNA hypersensitivity predict androgen receptor (AR) and estrogen receptor 1 (ESR1) binding sites. This dynamic chromatin accessibility offers a general method for identifying cell-type specific transcription factor binding locations.

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Area of Science:

Molecular Biology
Genomics
Epigenetics

Background:

Transcription factor cistromes are crucial for cell-type specificity.
Chromatin accessibility, histone modifications, and nucleosome occupancy influence transcription factor binding.
Understanding these factors is key to deciphering gene regulation.

Purpose of the Study:

To investigate the predictive power of hormone-induced DNase I hypersensitivity changes (ΔDHS) for androgen receptor (AR) and estrogen receptor 1 (ESR1) binding.
To compare the chromatin interaction modes of AR and ESR1.
To establish ΔDHS as a general method for predicting cell-type specific cistromes.

Main Methods:

Analysis of hormone-induced DNase I hypersensitivity (DHS) changes.
Correlation of ΔDHS with AR and ESR1 binding sites in cancer cells.
Assessment of nucleosome occupancy dynamics in relation to receptor binding.

Main Results:

ΔDHS strongly predicts AR and ESR1 binding in prostate and breast cancer cells, respectively.
AR binding correlates with changes in local nucleosome occupancy and DNase I hypersensitivity.
Global ESR1 binding is independent of nucleosome occupancy changes, but DHS dynamics predict its cistrome.

Conclusions:

AR and ESR1 exhibit distinct chromatin interaction mechanisms.
DNase I hypersensitivity dynamics serve as a robust predictor of cell-type specific cistromes for both receptors.
This approach offers a generalized strategy for mapping transcription factor binding.