Trac-looping measures genome structure and chromatin accessibility

Nature Methods
Binbin LaiKeji Zhao

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.

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Citations

Jan 5, 2020·Cold Spring Harbor Symposia on Quantitative Biology·Jia-Yu ChenXiang-Dong Fu
Sep 11, 2019·Bioinformatics·Yaqiang CaoJing-Dong J Han
Jul 11, 2020·Nature Communications·Tarik J SalamehFeng Yue
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Jan 29, 2020·Proceedings of the National Academy of Sciences of the United States of America·Lin DiJianbin Wang
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Oct 8, 2020·Journal of Genetics and Genomics = Yi Chuan Xue Bao·Weizhi OuyangXingwang Li
Feb 10, 2021·The New Phytologist·Liuling PeiMaojun Wang
May 18, 2021·Frontiers in Immunology·Shuai Liu, Keji Zhao
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Dec 21, 2021·Nucleic Acids Research·Yaqiang CaoKeji Zhao

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Datasets Mentioned

BETA
GM12878
cells
GSE87254

Methods Mentioned

BETA
Hi-C
Capture-C
ChIP-seq
PCR
transfection
RNA-seq

Software Mentioned

TopDom
EdgeR
DAVID
MACS
Pro Plus
SPRITE
Genome Browser
R
Trac
Homer

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