Landscape and significance of human super enhancer-driven core transcription regulatory circuitry.

作者信息

Feng Chenchen, Song Chao, Jiang Yong, Zhao Jun, Zhang Jian, Wang Yuezhu, Yin Mingxue, Zhu Jiang, Ai Bo, Wang Qiuyu, Qian Fengcui, Zhang Yuexin, Shang Desi, Liu Jiaqi, Li Chunquan

机构信息

School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing 163319, China.

The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, Hunan 421001, China.

出版信息

Mol Ther Nucleic Acids. 2023 Mar 24;32:385-401. doi: 10.1016/j.omtn.2023.03.014. eCollection 2023 Jun 13.

Abstract

A core transcription regulatory circuitry (CRC) is an interconnected self-regulatory circuitry that is formed by a group of core transcription factors (TFs). These core TFs collectively regulate gene expression by binding not only to their own super enhancers (SEs) but also to the SEs of one another. For most human tissue/cell types, a global view of CRCs and core TFs has not been generated. Here, we identified numerous CRCs using two identification methods and detailed the landscape of the CRCs driven by SEs in large cell/tissue samples. The comprehensive biological analyses, including sequence conservation, CRC activity and genome binding affinity were conducted for common TFs, moderate TFs, and specific TFs, which exhibit different biological features. The local module located from the common CRC network highlighted the essential functions and prognostic performance. The tissue-specific CRC network was highly related to cell identity. Core TFs in tissue-specific CRC networks exhibited disease markers, and had regulatory potential for cancer immunotherapy. Moreover, a user-friendly resource named CRCdb (http://www.licpathway.net/crcdb/index.html) was developed, which contained the detailed information of CRCs and core TFs used in this study, as well as other interesting results, such as the most representative CRC, frequency of TFs, and indegree/outdegree of TFs.

摘要
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/7ec9/10149290/4be22571ee7a/fx1.jpg

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