TRmir: A Comprehensive Resource for Human Transcriptional Regulatory Information of MiRNAs

Yu Gao; Chenchen Feng; Yuexin Zhang; Chao Song; Jiaxin Chen; Yanyu Li; Ling Wei; Fengcui Qian; Bo Ai; Yuejuan Liu; Jiang Zhu; Xiaojie Su; Chunquan Li; Qiuyu Wang

doi:10.3389/fgene.2022.808950

TRmir: A Comprehensive Resource for Human Transcriptional Regulatory Information of MiRNAs

Front Genet. 2022 Feb 4:13:808950. doi: 10.3389/fgene.2022.808950. eCollection 2022.

Authors

Yu Gao¹, Chenchen Feng¹, Yuexin Zhang^{1

2}, Chao Song^{1

2}, Jiaxin Chen¹, Yanyu Li¹, Ling Wei¹, Fengcui Qian^{1

2}, Bo Ai¹, Yuejuan Liu¹, Jiang Zhu¹, Xiaojie Su³, Chunquan Li^{1

2

4

5

6

7

8

9}, Qiuyu Wang^{1

2

4

5

6

7}

Affiliations

¹ School of Medical Informatics, Harbin Medical University, Daqing, China.
² The First Affiliated Hospital, Department of Cardiology, Hengyang Medical School, University of South China, Daqing, China.
³ College of Medical Laboratory Science and Technology, Harbin Medical University, Daqing, China.
⁴ The First Affiliated Hospital, Institute of Cardiovascular Disease, Hengyang Medical School, University of South China, Hengyang, China.
⁵ School of Computer, University of South China, Hengyang, China.
⁶ The First Affiliated Hospital, Cardiovascular Lab of Big Data and Imaging Artificial Intelligence, Hengyang Medical School, University of South China, Hengyang, China.
⁷ Hunan Provincial Base for Scientific and Technological Innovation Cooperation, University of South China, Hengyang, China.
⁸ General Surgery Department, Beijing Friendship Hospital, Capital Medical University, Beijing, China.
⁹ Guangxi Key Laboratory of Diabetic Systems Medicine, Guilin Medical University, Guilin, China.

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs, which play important roles in regulating various biological functions. Many available miRNA databases have provided a large number of valuable resources for miRNA investigation. However, not all existing databases provide comprehensive information regarding the transcriptional regulatory regions of miRNAs, especially typical enhancer, super-enhancer (SE), and chromatin accessibility regions. An increasing number of studies have shown that the transcriptional regulatory regions of miRNAs, as well as related single-nucleotide polymorphisms (SNPs) and transcription factors (TFs) have a strong influence on human diseases and biological processes. Here, we developed a comprehensive database for the human transcriptional regulation of miRNAs (TRmir), which is focused on providing a wealth of available resources regarding the transcriptional regulatory regions of miRNAs and annotating their potential roles in the regulation of miRNAs. TRmir contained a total of 5,754,414 typical enhancers/SEs and 1,733,966 chromatin accessibility regions associated with 1,684 human miRNAs. These regions were identified from over 900 human H3K27ac ChIP-seq, ATAC-seq, and DNase-seq samples. Furthermore, TRmir provided detailed (epi)genetic information about the transcriptional regulatory regions of miRNAs, including TFs, common SNPs, risk SNPs, linkage disequilibrium (LD) SNPs, expression quantitative trait loci (eQTLs), 3D chromatin interactions, and methylation sites, especially supporting the display of TF binding sites in the regulatory regions of over 7,000 TF ChIP-seq samples. In addition, TRmir integrated miRNA expression and related disease information, supporting extensive pathway analysis. TRmir is a powerful platform that offers comprehensive information about the transcriptional regulation of miRNAs for users and provides detailed annotations of regulatory regions. TRmir is free for academic users and can be accessed at http://bio.liclab.net/trmir/index.html.

Keywords: chromatin accessibility; genetics and epigenetics; microRNA; super-enhancer/typical enhancer; transcriptional regulation.