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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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Histone Modification02:32

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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.
Acetylation
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In situ tools for chromatin structural epigenomics.

Steven Henikoff1,2, Kami Ahmad1

  • 1Fred Hutchinson Cancer Center, Seattle, Washington, USA.

Protein Science : a Publication of the Protein Society
|September 28, 2022
PubMed
Summary

Recent advances in epigenomic tools enable precise genome-wide mapping of chromatin proteins in intact cells. These methods, including in situ cleavage and tagmentation, are advancing chromatin structural epigenomics for gene regulation and disease research.

Keywords:
Micrococcal NucleaseTn5 transposasesingle-cell CUT&Tagspatial profiling

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Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Technological advancements have led to numerous genome-wide chromatin profiling tools.
  • These tools utilize low-cost short-read sequencing to map specific chromatin features.

Purpose of the Study:

  • To survey recent developments in epigenomic tools for precise chromatin protein positioning.
  • To highlight in situ cleavage and tagmentation methods and their applications.

Main Methods:

  • Tethering Micrococcal Nuclease to chromatin proteins for in situ cleavage.
  • Tethering Tn5 transposase for in situ tagmentation, eliminating library preparation.
  • Adaptations for single-cell and spatial chromatin profiling.

Main Results:

  • In situ cleavage and tagmentation tools have gained popularity due to protocol enhancements.
  • These methods provide precise genome-wide mapping of chromatin proteins in intact cells or nuclei.
  • Emerging applications in gene regulation, eukaryotic development, and human disease.

Conclusions:

  • The field of chromatin structural epigenomics is rapidly advancing.
  • New epigenomic tools are crucial for understanding complex biological processes and diseases.
  • In situ profiling methods offer powerful approaches for chromatin analysis.