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Chromatin Immunoprecipitation- ChIP02:36

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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.
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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
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Histone variants are the histone proteins with structural and sequence variations. These variants may be regarded as “mutant” forms that replace their canonical histone counterparts in the nucleosomes. Specific post-translational modifications on the histone variants enable further chromatin complexity and regulate tissue-specific gene expression. The most common histone variants are from histone H2A, H2B, and linker histone H1 families. However, several variants of histone H3...
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Related Experiment Video

Updated: Oct 4, 2025

ATAC-Seq Optimization for Cancer Epigenetics Research
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CATA: a comprehensive chromatin accessibility database for cancer.

Jianyuan Zhou, Yanshang Li, Haotian Cao

    Database : the Journal of Biological Databases and Curation
    |February 8, 2022
    PubMed
    Summary

    Researchers created CATA, a comprehensive database of cancer chromatin accessibility. This resource maps accessible chromatin regions (CARs) and their regulatory roles in 23 cancer types, aiding cancer research.

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    Area of Science:

    • Genomics
    • Cancer Biology
    • Bioinformatics

    Background:

    • Accessible chromatin regions (CARs) are crucial for gene regulation and are implicated in tumorigenesis.
    • Novel sequencing techniques enable detailed analysis of CARs and transcription factor (TF) binding in cancer.

    Purpose of the Study:

    • To develop CATA, a comprehensive database resource for cancer chromatin accessibility.
    • To annotate CARs with regulatory information and facilitate cancer-specific gene regulation studies.

    Main Methods:

    • Collected and curated CAR data from 23 cancer types using Assay for Transposase-accessible Chromatin Sequencing (ATAC-seq).
    • Integrated TF binding information, SNPs, copy number variations, mutations, and epigenetic data.
    • Developed functionalities for cancer survival analysis and clinical data integration.

    Main Results:

    • CATA houses over 2.99 million CARs across 23 cancer types.
    • Includes binding data for 1398 TFs and diverse annotations like SNPs, CNVs, mutations, and methylation.
    • Provides cancer survival analysis linked to CAR-associated genes and clinical information.

    Conclusions:

    • CATA offers a valuable, integrated resource for dissecting the regulatory landscape of cancer.
    • Facilitates research into the role of chromatin accessibility in cancer development and progression.
    • Supports data-driven discovery in cancer genomics and precision medicine.