MINE is a method for detecting spatial density of regulatory chromatin interactions based on a multi-modal network

Haiyan Gong; Minghong Li; Mengdie Ji; Xiaotong Zhang; Zan Yuan; Sichen Zhang; Yi Yang; Chun Li; Yang Chen

doi:10.1016/j.crmeth.2022.100386

MINE is a method for detecting spatial density of regulatory chromatin interactions based on a multi-modal network

Cell Rep Methods. 2023 Jan 12;3(1):100386. doi: 10.1016/j.crmeth.2022.100386. eCollection 2023 Jan 23.

Authors

Haiyan Gong¹, Minghong Li¹, Mengdie Ji², Xiaotong Zhang^{1

3}, Zan Yuan², Sichen Zhang¹, Yi Yang¹, Chun Li⁴, Yang Chen²

Affiliations

¹ Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China.
² State Key Laboratory of Medical Molecular Biology, Department of Biochemistry and Molecular Biology, Institute of Basic Medical Sciences, School of Basic Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100005, China.
³ Shunde Innovation School, University of Science and Technology Beijing, Foshan 528399, China.
⁴ School of Mechanical Engineering, University of Science and Technology Beijing, Beijing 100083, China.

Abstract

Chromatin interactions play essential roles in chromatin conformation and gene expression. However, few tools exist to analyze the spatial density of regulatory chromatin interactions (SD-RCI). Here, we present the multi-modal network (MINE) toolkit, including MINE-Loop, MINE-Density, and MINE-Viewer. The MINE-Loop network aims to enhance the detection of RCIs, MINE-Density quantifies the SD--RCI, and MINE-Viewer facilitates 3D visualization of the density of chromatin interactions and participating regulatory factors (e.g., transcription factors). We applied MINE to investigate the relationship between the SD-RCI and chromatin volume change in HeLa cells before and after liquid-liquid phase separation. Changes in SD-RCI before and after treating the HeLa cells with 1,6-hexanediol suggest that changes in chromatin organization was related to the degree of activation or repression of genes. Together, the MINE toolkit enables quantitative studies on different aspects of chromatin conformation and regulatory activity.

Keywords: 3D visualization; Hi-C; multi-modal network; regulatory chromatin interactions; spatial density.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Chromatin* / genetics
Chromosomes*
HeLa Cells
Humans
Transcription Factors / genetics

Substances

Chromatin
Transcription Factors