MINE is a Method for Detecting Spatial Density of Regulatory Chromatin Interactions Based on a Multi-modal Network

Overview

Journal Cell Rep Methods

Specialty Cell Biology

Date 2023 Feb 23

PMID 36814847

Authors

Haiyan Gong

Minghong Li

Mengdie Ji

Xiaotong Zhang

Zan Yuan

Sichen Zhang

Yi Yang

Chun Li

Yang Chen

Affiliations

Soon will be listed here.

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.

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