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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
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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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Histone Modification02:32

Histone Modification

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The histone proteins have a flexible N-terminal tail extending out from the nucleosome. These histone tails are often subjected to post-translational modifications such as acetylation, methylation, phosphorylation, and ubiquitination. Particular combinations of these modifications form “histone codes” that influence the chromatin folding and tissue-specific gene expression.
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BIND&MODIFY: a long-range method for single-molecule mapping of chromatin modifications in eukaryotes.

Zhe Weng1, Fengying Ruan1, Weitian Chen1,2

  • 1BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China.

Genome Biology
|March 29, 2023
PubMed
Summary

BIND&MODIFY profiles histone modifications and transcription factors on single DNA molecules using long-read sequencing. This method reveals long-range interactions and correlations, overcoming limitations of bulk assays for disease research.

Keywords:
CTCFCpG methylationEpigeneticsH3K27me3Histone modificationMethyltransferasem6A

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Area of Science:

  • Molecular Biology
  • Genomics
  • Epigenetics

Background:

  • Epigenetic histone modifications are crucial in development and disease.
  • Current methods average chromatin states and miss long-range interactions.

Purpose of the Study:

  • To introduce BIND&MODIFY, a novel method for single-molecule profiling of epigenetic marks.
  • To enable simultaneous measurement of histone modifications, transcription factor binding, and DNA methylation.

Main Methods:

  • Utilizes long-read sequencing combined with a custom-engineered protein (A-M.EcoGII) for targeted DNA labeling.
  • Employs methyltransferase M.EcoGII tethered to protein binding sites to mark neighboring DNA regions.
  • Enables single-molecule resolution analysis of chromatin architecture.

Main Results:

  • BIND&MODIFY accurately reflects bulk measurements like ChIP-seq and CUT&TAG when aggregated.
  • The method successfully measures histone modification status, transcription factor binding, and CpG 5mC methylation simultaneously.
  • Quantifies correlations between local and distal genomic elements at single-molecule resolution.

Conclusions:

  • BIND&MODIFY provides unprecedented single-molecule resolution for epigenetic profiling.
  • This technique overcomes limitations of bulk methods, offering insights into chromatin interactions and disease mechanisms.
  • Enables comprehensive analysis of epigenetic landscapes and their functional correlations.