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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.
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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Related Experiment Video

Updated: Aug 31, 2025

Formaldehyde-assisted Isolation of Regulatory Elements to Measure Chromatin Accessibility in Mammalian Cells
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FFPE-ATAC: A Highly Sensitive Method for Profiling Chromatin Accessibility in Formalin-Fixed Paraffin-Embedded

Ram Prakash Yadav1, Vamsi Krishna Polavarapu1, Pengwei Xing1

  • 1Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.

Current Protocols
|August 22, 2022
PubMed
Summary

We developed FFPE-ATAC, a new method to profile chromatin accessibility in challenging formalin-fixed paraffin-embedded (FFPE) cancer samples. This technique overcomes DNA damage in FFPE tissues, enabling gene regulation studies in archived samples.

Keywords:
T7-Tn5-mediated transpositionchromatin accessibilityformalin-fixed paraffin-embedded (FFPE) samplein vitro transcription

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Area of Science:

  • Molecular Biology
  • Genomics
  • Cancer Research

Background:

  • Formalin-fixed paraffin-embedded (FFPE) tissues are crucial for cancer research but difficult to analyze due to DNA damage.
  • Chromatin accessibility is vital for understanding gene regulation in health and disease.
  • Accurate profiling of chromatin accessibility in FFPE samples is challenging.

Purpose of the Study:

  • To establish a sensitive method for mapping chromatin accessibility in FFPE tissues.
  • To enable the study of gene regulation using archived FFPE samples.
  • To overcome limitations of DNA damage in FFPE samples for chromatin profiling.

Main Methods:

  • Developed FFPE-ATAC, a method using T7-Tn5 transposition and in vitro transcription (IVT).
  • T7-Tn5 adaptors are inserted post-FFPE preparation to withstand DNA breakage.
  • IVT converts DNA fragment ends to RNA for library preparation and sequencing.

Main Results:

  • FFPE-ATAC generates high-quality chromatin accessibility profiles from FFPE tissues.
  • The method is sensitive, requiring only 500-50,000 nuclei.
  • It successfully decodes accessible chromatin flanking regions despite DNA breaks.

Conclusions:

  • FFPE-ATAC provides a robust approach for chromatin accessibility profiling in FFPE samples.
  • This method facilitates the study of gene regulation in specific tissue regions and disease contexts.
  • It is applicable to dissecting chromatin profiles from small tissue sections.