Trac-looping measures genome structure and chromatin accessibility

Nat Methods. 2018 Sep;15(9):741-747. doi: 10.1038/s41592-018-0107-y. Epub 2018 Aug 27.

Abstract

Long-range chromatin interactions play critical roles in genome organization and regulation of transcription. We now report transposase-mediated analysis of chromatin looping (Trac-looping) for simultaneous detection of multiscale genome-wide chromatin interactions among regulatory elements and chromatin accessibility. With this technique, a bivalent oligonucleotide linker is inserted between two interacting regions such that the chromatin interactions are captured without prior chromatin fragmentation and proximity-based ligation. Application of Trac-looping to human CD4+ T cells revealed substantial reorganization of enhancer-promoter interactions associated with changes in gene expression after T cell receptor stimulation.

Publication types

  • Research Support, N.I.H., Intramural

MeSH terms

  • Chromatin / chemistry
  • Chromatin / metabolism*
  • Computational Biology
  • Enhancer Elements, Genetic
  • Genome, Human*
  • Humans
  • Promoter Regions, Genetic
  • Transcription, Genetic

Substances

  • Chromatin