Methods of MicroRNA Promoter Prediction and Transcription Factor Mediated Regulatory Network

Overview

Journal Biomed Res Int

Publisher Wiley

Specialties Biomedical Engineering
Biotechnology
General Medicine

Date 2017 Jun 29

PMID 28656148

Citations 28

Authors

Yuming Zhao

Fang Wang

Su Chen

Jun Wan

Guohua Wang

Affiliations

Soon will be listed here.

Abstract

MicroRNAs (miRNAs) are short (~22 nucleotides) noncoding RNAs and disseminated throughout the genome, either in the intergenic regions or in the intronic sequences of protein-coding genes. MiRNAs have been proved to play important roles in regulating gene expression. Hence, understanding the transcriptional mechanism of miRNA genes is a very critical step to uncover the whole regulatory network. A number of miRNA promoter prediction models have been proposed in the past decade. This review summarized several most popular miRNA promoter prediction models which used genome sequence features, or other features, for example, histone markers, RNA Pol II binding sites, and nucleosome-free regions, achieved by high-throughput sequencing data. Some databases were described as resources for miRNA promoter information. We then performed comprehensive discussion on prediction and identification of transcription factor mediated microRNA regulatory networks.

Citing Articles

Identification of Key Genes Related to Immune-Lipid Metabolism in Skin Barrier Damage and Analysis of Immune Infiltration.

Tu Y, Gu H, Li N, Sun D, Yang Z, He L Inflammation. 2024; .

PMID: 39465470 DOI: 10.1007/s10753-024-02174-4.

MicroRNA-138: an emerging regulator of skeletal development, homeostasis, and disease.

Brito V, Bell-Hensley A, McAlinden A Am J Physiol Cell Physiol. 2023; 325(6):C1387-C1400.

PMID: 37842749 PMC: 10861148. DOI: 10.1152/ajpcell.00382.2023.

Computational prediction of promotors in strain C58 by using the machine learning technique.

Zulfiqar H, Ahmed Z, Grace-Mercure B, Hassan F, Zhang Z, Liu F Front Microbiol. 2023; 14:1170785.

PMID: 37125199 PMC: 10133480. DOI: 10.3389/fmicb.2023.1170785.

The CXCR4/miR-1910-5p/MMRN2 Axis Is Involved in Corneal Neovascularization by Affecting Vascular Permeability.

Wang X, Cui Z, Chen X, Luo Q, Jiang Z, Liu X Invest Ophthalmol Vis Sci. 2023; 64(4):10.

PMID: 37040097 PMC: 10108737. DOI: 10.1167/iovs.64.4.10.

HLGNN-MDA: Heuristic Learning Based on Graph Neural Networks for miRNA-Disease Association Prediction.

Yu L, Ju B, Ren S Int J Mol Sci. 2022; 23(21).

PMID: 36361945 PMC: 9657597. DOI: 10.3390/ijms232113155.

References

He L, Hannon G . MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet. 2004; 5(7):522-31. DOI: 10.1038/nrg1379. View

Chien C, Sun Y, Chang W, Chiang-Hsieh P, Lee T, Tsai W . Identifying transcriptional start sites of human microRNAs based on high-throughput sequencing data. Nucleic Acids Res. 2011; 39(21):9345-56. PMC: 3241639. DOI: 10.1093/nar/gkr604. View

Corcoran D, Pandit K, Gordon B, Bhattacharjee A, Kaminski N, Benos P . Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS One. 2009; 4(4):e5279. PMC: 2668758. DOI: 10.1371/journal.pone.0005279. View

Landgraf P, Rusu M, Sheridan R, Sewer A, Iovino N, Aravin A . A mammalian microRNA expression atlas based on small RNA library sequencing. Cell. 2007; 129(7):1401-14. PMC: 2681231. DOI: 10.1016/j.cell.2007.04.040. View

Wang G, Wang Y, Teng M, Zhang D, Li L, Liu Y . Signal transducers and activators of transcription-1 (STAT1) regulates microRNA transcription in interferon gamma-stimulated HeLa cells. PLoS One. 2010; 5(7):e11794. PMC: 2909916. DOI: 10.1371/journal.pone.0011794. View

Wang G, Yu T, Zhang W . WordSpy: identifying transcription factor binding motifs by building a dictionary and learning a grammar. Nucleic Acids Res. 2005; 33(Web Server issue):W412-6. PMC: 1160252. DOI: 10.1093/nar/gki492. View

Zhao Y, Wang F, Juan L . MicroRNA Promoter Identification in Arabidopsis Using Multiple Histone Markers. Biomed Res Int. 2015; 2015:861402. PMC: 4573627. DOI: 10.1155/2015/861402. View

Lee Y, Kim M, Han J, Yeom K, Lee S, Baek S . MicroRNA genes are transcribed by RNA polymerase II. EMBO J. 2004; 23(20):4051-60. PMC: 524334. DOI: 10.1038/sj.emboj.7600385. View

Weis L, Reinberg D . Transcription by RNA polymerase II: initiator-directed formation of transcription-competent complexes. FASEB J. 1992; 6(14):3300-9. DOI: 10.1096/fasebj.6.14.1426767. View

10.

Georgakilas G, Vlachos I, Zagganas K, Vergoulis T, Paraskevopoulou M, Kanellos I . DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators. Nucleic Acids Res. 2015; 44(D1):D190-5. PMC: 4702888. DOI: 10.1093/nar/gkv1254. View

11.

Fujita S, Iba H . Putative promoter regions of miRNA genes involved in evolutionarily conserved regulatory systems among vertebrates. Bioinformatics. 2007; 24(3):303-8. DOI: 10.1093/bioinformatics/btm589. View

12.

Wang G, Zhang W . A steganalysis-based approach to comprehensive identification and characterization of functional regulatory elements. Genome Biol. 2006; 7(6):R49. PMC: 1779545. DOI: 10.1186/gb-2006-7-6-r49. View

13.

Lewis B, Burge C, Bartel D . Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell. 2005; 120(1):15-20. DOI: 10.1016/j.cell.2004.12.035. View

14.

Wang G, Wang Y, Shen C, Huang Y, Huang K, Huang T . RNA polymerase II binding patterns reveal genomic regions involved in microRNA gene regulation. PLoS One. 2010; 5(11):e13798. PMC: 2970572. DOI: 10.1371/journal.pone.0013798. View

15.

Wang X, Xuan Z, Zhao X, Li Y, Zhang M . High-resolution human core-promoter prediction with CoreBoost_HM. Genome Res. 2008; 19(2):266-75. PMC: 2652208. DOI: 10.1101/gr.081638.108. View

16.

Guo Z, Maki M, Ding R, Yang Y, Zhang B, Xiong L . Genome-wide survey of tissue-specific microRNA and transcription factor regulatory networks in 12 tissues. Sci Rep. 2014; 4:5150. PMC: 5381490. DOI: 10.1038/srep05150. View

17.

Zhao X, Zhang H, Li L . Identification and analysis of the proximal promoters of microRNA genes in Arabidopsis. Genomics. 2013; 101(3):187-94. DOI: 10.1016/j.ygeno.2012.12.004. View

18.

Zhou X, Ruan J, Wang G, Zhang W . Characterization and identification of microRNA core promoters in four model species. PLoS Comput Biol. 2007; 3(3):e37. PMC: 1817659. DOI: 10.1371/journal.pcbi.0030037. View

19.

Alexiou P, Vergoulis T, Gleditzsch M, Prekas G, Dalamagas T, Megraw M . miRGen 2.0: a database of microRNA genomic information and regulation. Nucleic Acids Res. 2009; 38(Database issue):D137-41. PMC: 2808909. DOI: 10.1093/nar/gkp888. View

20.

Rhead B, Karolchik D, Kuhn R, Hinrichs A, Zweig A, Fujita P . The UCSC Genome Browser database: update 2010. Nucleic Acids Res. 2009; 38(Database issue):D613-9. PMC: 2808870. DOI: 10.1093/nar/gkp939. View