Prediction of MiRNA Interactions With Candidate Atherosclerosis Gene MRNAs

Overview

Journal Front Genet

Date 2020 Dec 17

PMID 33329752

Citations 13

Authors

Dina Mukushkina

Dana Aisina

Anna Pyrkova

Alma Ryskulova

Siegfried Labeit

Anatoliy Ivashchenko

Affiliations

Soon will be listed here.

Abstract

The involvement of genes and miRNAs in the development of atherosclerosis is a challenging problem discussed in recent publications. It is necessary to establish which miRNAs affect the expression of candidate genes. We used known candidate atherosclerosis genes to predict associations. The quantitative characteristics of interactions of miRNAs with mRNA candidate genes were determined using the program, which identifies the localization of miRNA binding sites in mRNA, the free energy interaction of miRNA with mRNA. In mRNAs of and candidate genes, binding sites of 21 miRNAs and of 15 miRNAs, respectively, were identified. In mRNA binding sites of 25 miRNAs were located in a cluster of 41 nt. In , and mRNAs, clusters of miR-466, ID00436.3p-miR, and ID01030.3p-miR BS were identified. The organization of overlapping miRNA binding sites in clusters led to their compaction and caused competition among the miRNAs. The binding of 53 miRNAs to the mRNAs of 14 candidate genes with free energy interactions greater than -130 kJ/mole was determined. The miR-619-5p was fully complementary to and mRNAs, ID01593.5p-miR to mRNA, ID01935.5p-miR to , and miR-5096 to mRNA. Associations of miRNAs and candidate atherosclerosis genes are proposed for the early diagnosis of this disease.

Citing Articles

Circulating microRNAs in Carotid Atherosclerosis: Complex Interplay and Possible Associations with Atherothrombotic Stroke.

Tanashyan M, Shabalina A, Annushkin V, Mazur A, Kuznetsova P, Raskurazhev A Int J Mol Sci. 2024; 25(18).

PMID: 39337512 PMC: 11432131. DOI: 10.3390/ijms251810026.

Editorial: Bioinformatics of genome regulation and systems biology, Volume III.

Anashkina A, Orlova N, Ignatov A, Chen M, Orlov Y Front Genet. 2023; 14:1215987.

PMID: 37274783 PMC: 10233740. DOI: 10.3389/fgene.2023.1215987.

Endogenous piRNAs Can Interact with the Omicron Variant of the SARS-CoV-2 Genome.

Rakhmetullina A, Akimniyazova A, Niyazova T, Pyrkova A, Kamenova S, Kondybayeva A Curr Issues Mol Biol. 2023; 45(4):2950-2964.

PMID: 37185717 PMC: 10136802. DOI: 10.3390/cimb45040193.

New Insight into Mechanisms of Cardiovascular Diseases: An Integrative Analysis Approach to Identify TheranoMiRNAs.

Sessa F, Salerno M, Esposito M, Cocimano G, Pisanelli D, Malik A Int J Mol Sci. 2023; 24(7).

PMID: 37047756 PMC: 10095439. DOI: 10.3390/ijms24076781.

piRNA and miRNA Can Suppress the Expression of Multiple Sclerosis Candidate Genes.

Kamenova S, Sharapkhanova A, Akimniyazova A, Kuzhybayeva K, Kondybayeva A, Rakhmetullina A Nanomaterials (Basel). 2023; 13(1).

PMID: 36615932 PMC: 9823834. DOI: 10.3390/nano13010022.

References

Ivashchenko A, Berillo O, Pyrkova A, Niyazova R, Atambayeva S . The properties of binding sites of miR-619-5p, miR-5095, miR-5096, and miR-5585-3p in the mRNAs of human genes. Biomed Res Int. 2014; 2014:720715. PMC: 4137733. DOI: 10.1155/2014/720715. View

Li Q, Cui H, Yang Y, Li X, Chen G, Tian X . Quantitative Proteomics Analysis of Ischemia/Reperfusion Injury-Modulated Proteins in Cardiac Microvascular Endothelial Cells and the Protective Role of Tongxinluo. Cell Physiol Biochem. 2017; 41(4):1503-1518. DOI: 10.1159/000470806. View

Feinberg M, Moore K . MicroRNA Regulation of Atherosclerosis. Circ Res. 2016; 118(4):703-20. PMC: 4762069. DOI: 10.1161/CIRCRESAHA.115.306300. View

Atambayeva S, Niyazova R, Ivashchenko A, Pyrkova A, Pinsky I, Akimniyazova A . The Binding Sites of miR-619-5p in the mRNAs of Human and Orthologous Genes. BMC Genomics. 2017; 18(1):428. PMC: 5452331. DOI: 10.1186/s12864-017-3811-6. View

Rodriguez I, Coto E, Reguero J, Gonzalez P, Andres V, Lozano I . Role of the CDKN1A/p21, CDKN1C/p57, and CDKN2A/p16 genes in the risk of atherosclerosis and myocardial infarction. Cell Cycle. 2007; 6(5):620-5. DOI: 10.4161/cc.6.5.3927. View

Solly E, Dimasi C, Bursill C, Psaltis P, Tan J . MicroRNAs as Therapeutic Targets and Clinical Biomarkers in Atherosclerosis. J Clin Med. 2019; 8(12). PMC: 6947565. DOI: 10.3390/jcm8122199. View

Wiese C, Zhong J, Xu Z, Zhang Y, Ramirez Solano M, Zhu W . Dual inhibition of endothelial miR-92a-3p and miR-489-3p reduces renal injury-associated atherosclerosis. Atherosclerosis. 2019; 282:121-131. PMC: 7484899. DOI: 10.1016/j.atherosclerosis.2019.01.023. View

Chen F, Ye X, Jiang H, Zhu G, Miao S . MicroRNA-151 Attenuates Apoptosis of Endothelial Cells Induced by Oxidized Low-density Lipoprotein by Targeting Interleukin-17A (IL-17A). J Cardiovasc Transl Res. 2020; 14(3):400-408. DOI: 10.1007/s12265-020-10065-w. View

Lemieux S, Major F . RNA canonical and non-canonical base pairing types: a recognition method and complete repertoire. Nucleic Acids Res. 2002; 30(19):4250-63. PMC: 140540. DOI: 10.1093/nar/gkf540. View

10.

Wang Y, Zhu J, Handberg A, Overvad K, Tjonneland A, Rimm E . Association between plasma CD36 levels and incident risk of coronary heart disease among Danish men and women. Atherosclerosis. 2018; 277:163-168. DOI: 10.1016/j.atherosclerosis.2018.08.045. View

11.

Maitrias P, Metzinger-Le Meuth V, Massy Z, Mbaya-Moutoula E, Reix T, Caus T . MicroRNA deregulation in symptomatic carotid plaque. J Vasc Surg. 2015; 62(5):1245-50.e1. DOI: 10.1016/j.jvs.2015.06.136. View

12.

Cipollone F, Felicioni L, Sarzani R, Ucchino S, Spigonardo F, Mandolini C . A unique microRNA signature associated with plaque instability in humans. Stroke. 2011; 42(9):2556-63. DOI: 10.1161/STROKEAHA.110.597575. View

13.

Orom U, Nielsen F, Lund A . MicroRNA-10a binds the 5'UTR of ribosomal protein mRNAs and enhances their translation. Mol Cell. 2008; 30(4):460-71. DOI: 10.1016/j.molcel.2008.05.001. View

14.

Lu Y, Thavarajah T, Gu W, Cai J, Xu Q . Impact of miRNA in Atherosclerosis. Arterioscler Thromb Vasc Biol. 2018; 38(9):e159-e170. PMC: 6795547. DOI: 10.1161/ATVBAHA.118.310227. View

15.

Chen W, Yu F, Di M, Li M, Chen Y, Zhang Y . MicroRNA-124-3p inhibits collagen synthesis in atherosclerotic plaques by targeting prolyl 4-hydroxylase subunit alpha-1 (P4HA1) in vascular smooth muscle cells. Atherosclerosis. 2018; 277:98-107. DOI: 10.1016/j.atherosclerosis.2018.08.034. View

16.

Shoeibi S . Diagnostic and theranostic microRNAs in the pathogenesis of atherosclerosis. Acta Physiol (Oxf). 2019; 228(1):e13353. DOI: 10.1111/apha.13353. View

17.

Toba H, Cortez D, Lindsey M, Chilton R . Applications of miRNA technology for atherosclerosis. Curr Atheroscler Rep. 2014; 16(2):386. PMC: 4362664. DOI: 10.1007/s11883-013-0386-9. View

18.

Friedman R, Farh K, Burge C, Bartel D . Most mammalian mRNAs are conserved targets of microRNAs. Genome Res. 2008; 19(1):92-105. PMC: 2612969. DOI: 10.1101/gr.082701.108. View

19.

Li X, He X, Wang J, Wang D, Cong P, Zhu A . The Regulation of Exosome-Derived miRNA on Heterogeneity of Macrophages in Atherosclerotic Plaques. Front Immunol. 2020; 11:2175. PMC: 7511579. DOI: 10.3389/fimmu.2020.02175. View

20.

Wang C, Yang W, Liang X, Song W, Lin J, Sun Y . MicroRNA-761 modulates foam cell formation and inflammation through autophagy in the progression of atherosclerosis. Mol Cell Biochem. 2020; 474(1-2):135-146. DOI: 10.1007/s11010-020-03839-y. View