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Related Experiment Video

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FACT-seq: profiling histone modifications in formalin-fixed paraffin-embedded samples with low cell numbers.

Linxuan Zhao1, Pengwei Xing1, Vamsi Krishna Polavarapu1

  • 1Department of Immunology, Genetics and Pathology, Uppsala University, 75108 Uppsala, Sweden.

Nucleic Acids Research
|September 17, 2021
PubMed
Summary

Archived FFPE tissues can now be profiled for histone modifications using FACT-seq, a new sensitive method. This technique requires minimal tissue, enabling detailed epigenetic analysis in cancer research.

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Area of Science:

  • Epigenetics
  • Molecular Biology
  • Cancer Research

Background:

  • Archived formalin-fixed paraffin-embedded (FFPE) tissues are crucial for cancer research and understanding gene regulation.
  • Current methods for profiling histone modifications in FFPE tissues require substantial amounts of tissue, limiting detailed analysis.
  • There is a need for sensitive methods that utilize minimal FFPE tissue for epigenetic profiling.

Purpose of the Study:

  • To develop a highly sensitive method for profiling histone modifications in archived FFPE tissues.
  • To enable genome-wide histone modification profiling using a minimal amount of FFPE tissue.
  • To investigate disease-specific epigenetic alterations in cancer using FFPE samples.

Main Methods:

  • Development of FFPE tissue with antibody-guided chromatin tagmentation with sequencing (FACT-seq).
  • FACT-seq combines a novel fusion protein (T7-pA-Tn5) for transposition and T7 in vitro transcription.
  • High-quality chromatin profiles generated from a low number of FFPE nuclei.

Main Results:

  • FACT-seq successfully profiled histone modifications from a small FFPE tissue section (∼4000 nuclei).
  • H3K27ac modifications were accurately decoded using FACT-seq in FFPE samples.
  • Disease-specific super enhancers were identified in human colorectal and glioblastoma cancer FFPE tissues.

Conclusions:

  • FACT-seq is the first highly sensitive method for efficient histone modification profiling in FFPE tissues.
  • This method allows for detailed epigenetic analysis using limited clinical FFPE samples.
  • FACT-seq aids in understanding epigenetic regulation in cancer and other human diseases.