Genome-wide absolute quantification of chromatin looping

PubMed Central 2026 Open access

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Authors: James M. Jusuf, Jin H. Yang, Jack Toppen, Simon Grosse‐Holz, Michele Gabriele, Pia Mach, Ilya M. Flyamer, Christoph Zechner, Luca Giorgetti, Leonid A. Mirny, Anders S. Hansen
DOI: 10.1038/s41594-026-01819-2
Cited by: 5
References: 98

Abstract

3D genomics methods such as Hi-C and Micro-C have uncovered chromatin loops across the genome and linked these loops to gene regulation. However, these methods only measure 3D interaction probabilities on a relative scale. Here, we overcome this limitation by using live imaging data to calibrate Micro-C in mouse embryonic stem cells, thus obtaining absolute looping probabilities for 65,929 Micro-C identified chromatin loops. We find that the looped state is generally rare, with a mean pairwise looping probability of 1.2% and a maximum of 25% across the quantified loops. On average, CTCF-CTCF loops are stronger than cis-regulatory loops (2.2% vs.

Fields of Study & Subjects

Genomics and Chromatin Dynamics Developmental Biology and Gene Regulation Genomic variations and chromosomal abnormalities

Publication details

Journal / source
PubMed Central
Publisher
Springer Science and Business Media LLC
Volume
33
Issue
7
Pages
1105-1114
Publication date
30 June 2026
Language
EN