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

Trac-looping measures genome structure and chromatin accessibility.

Author information

1
Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA.
2
Department of Biology, South University of Science and Technology of China, Shenzhen, China.
3
Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, USA.
4
Department of Animal and Avian Sciences, University of Maryland, College Park, MD, USA.
5
Protein Chemistry Core, Research Technologies Branch, NIAID, NIH, Rockville, MD, USA.
6
Laboratory of Epigenome Biology, Systems Biology Center, National Heart, Lung and Blood Institute, NIH, Bethesda, MD, USA. zhaok@nhlbi.nih.gov.

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.

PMID:
30150754
DOI:
10.1038/s41592-018-0107-y

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