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MINE 是一种基于多模态网络的检测调控染色质相互作用空间密度的方法。

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

机构信息

Beijing Advanced Innovation Center for Materials Genome Engineering, School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing 100083, China.

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.

出版信息

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

DOI:10.1016/j.crmeth.2022.100386
PMID:36814847
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9939382/
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.

摘要

染色质相互作用在染色质构象和基因表达中发挥着重要作用。然而，目前用于分析调控染色质相互作用空间密度（SD-RCI）的工具较少。在这里，我们介绍了多模态网络（MINE）工具包，包括 MINE-Loop、MINE-Density 和 MINE-Viewer。MINE-Loop 网络旨在增强 RCIs 的检测，MINE-Density 量化 SD--RCI，而 MINE-Viewer 则方便了染色质相互作用和参与调控因子（如转录因子）密度的 3D 可视化。我们应用 MINE 来研究 HeLa 细胞液-液相分离前后 SD-RCI 与染色质体积变化之间的关系。用 1,6-己二醇处理 HeLa 细胞前后的 SD-RCI 变化表明，染色质组织的变化与基因的激活或抑制程度有关。总之，MINE 工具包能够对染色质构象和调控活性的不同方面进行定量研究。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82c9/9939382/d3308c949ef1/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82c9/9939382/8362b2935c6a/fx1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82c9/9939382/d5e9364b1021/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82c9/9939382/3f95d8111589/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82c9/9939382/50c5c96450d0/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82c9/9939382/a0186b608a39/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82c9/9939382/6f4da9e41852/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82c9/9939382/d3308c949ef1/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82c9/9939382/8362b2935c6a/fx1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82c9/9939382/d5e9364b1021/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82c9/9939382/3f95d8111589/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82c9/9939382/50c5c96450d0/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82c9/9939382/a0186b608a39/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82c9/9939382/6f4da9e41852/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/82c9/9939382/d3308c949ef1/gr6.jpg

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