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Related Concept Videos

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

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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.
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...
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Heterochromatin02:38

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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...
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Spreading of Chromatin Modifications02:25

Spreading of Chromatin Modifications

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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
The writer...
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Euchromatin01:01

Euchromatin

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The extent of chromatin compaction can be studied by staining chromatin using specific DNA binding dyes. Under the microscope, the dense-compacted regions take up more dye, appearing darker, while the less-compact areas take up less dye and appear lighter. Based on the compaction level, chromatins are classified into two primary forms – euchromatin and heterochromatin.
Euchromatin is the less dense region of the chromatin and stains lighter. Euchromatin contains histone H3 extensively...
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Co-activators and Co-repressors02:04

Co-activators and Co-repressors

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Gene transcription is regulated by the synergistic action of several proteins that form a complex at a gene regulatory site. This is observed in eukaryotes, where the regulation of gene expression is a complex process. Regulatory proteins in eukaryotes can broadly be classified into two types – regulators that bind directly to specific DNA sequences and co-regulators that associate with regulatory proteins but cannot directly bind to the DNA. These co-regulators are further divided into...
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Chromatin Packaging02:21

Chromatin Packaging

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Chromatin Immunoprecipitation ChIP Protocol for Low-abundance Embryonic Samples
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CRdb: a comprehensive resource for deciphering chromatin regulators in human.

Yimeng Zhang1, Yuexin Zhang2,3,4,5,6, Chao Song2,3,4,5,6

  • 1The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou 515041, China.

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|November 1, 2022
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Summary

A new database, CRdb, integrates chromatin regulator (CR) and ChIP-seq data. This resource aids researchers in understanding CR functions and regulatory mechanisms in diseases and biological processes.

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Area of Science:

  • Genomics and Epigenetics
  • Bioinformatics and Computational Biology

Background:

  • Chromatin regulators (CRs) are crucial for gene expression by modulating epigenetic patterns.
  • The rapid increase in ChIP-seq data for CRs necessitates a centralized resource for data integration and analysis.
  • Understanding CRs' regulatory roles is vital for biological research and disease mechanism elucidation.

Purpose of the Study:

  • To establish an integrative resource, CRdb, for curating, annotating, and analyzing CR-related ChIP-seq data.
  • To provide comprehensive genetic and functional annotations for CRs and their binding regions.
  • To offer tools for exploring CR functions, regulatory mechanisms, and potential roles in diseases.

Main Methods:

  • Manual curation of 2,591 ChIP-seq samples from NCBI GEO/SRA and ENCODE databases.
  • Integration of data for 647 chromatin regulators across over 300 human tissues and cell types.
  • Development of CRdb with functionalities for gene set enrichment, binding region annotation, co-occupancy analysis, and regulatory axis analysis.

Main Results:

  • CRdb houses data for 647 CRs and 2,591 ChIP-seq samples from diverse human samples.
  • Detailed genetic annotations of CR-binding regions are provided.
  • The database supports various functional annotations and upstream regulatory analyses, including CR-TF co-occupancy.

Conclusions:

  • CRdb serves as a valuable and powerful resource for biological researchers.
  • It facilitates the exploration of CR functions and regulatory mechanisms in biological processes and diseases.
  • The integrated data and analytical tools in CRdb enhance the study of epigenetics and gene regulation.