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Related Experiment Video

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CRISPR-Mediated Reorganization of Chromatin Loop Structure
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Trac-looping measures genome structure and chromatin accessibility.

Binbin Lai1, Qingsong Tang1, Wenfei Jin2

  • 1Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA.

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|August 29, 2018
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Summary

Transposase-mediated analysis of chromatin looping (Trac-looping) identifies genome-wide interactions and accessibility. This method revealed significant enhancer-promoter reorganization in T cells upon stimulation, impacting gene expression.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Epigenetics

Background:

  • Long-range chromatin interactions are crucial for genome organization and gene transcription regulation.
  • Understanding these interactions is key to deciphering cellular processes and disease mechanisms.

Purpose of the Study:

  • To develop a novel method for simultaneously detecting multiscale genome-wide chromatin interactions and chromatin accessibility.
  • To apply this method to investigate changes in chromatin interactions during T cell activation.

Main Methods:

  • Transposase-mediated analysis of chromatin looping (Trac-looping) was developed.
  • This technique inserts a bivalent oligonucleotide linker to capture chromatin interactions without prior fragmentation or ligation.
  • Trac-looping simultaneously assesses chromatin accessibility.

Main Results:

  • Trac-looping successfully detected genome-wide chromatin interactions and accessibility.
  • Significant reorganization of enhancer-promoter interactions was observed in human CD4+ T cells after T cell receptor stimulation.
  • These interaction changes correlated with altered gene expression patterns.

Conclusions:

  • Trac-looping is an effective technique for comprehensive analysis of chromatin interactions and accessibility.
  • T cell activation involves substantial dynamic changes in regulatory element interactions.
  • This provides new insights into the epigenetic regulation of gene expression in immune cells.