MIREyA: a computational approach to detect miRNA-directed gene activation

Anna Elizarova; Mumin Ozturk; Reto Guler; Yulia A Medvedeva

doi:10.12688/f1000research.28142.2

MIREyA: a computational approach to detect miRNA-directed gene activation

F1000Res. 2021 Mar 29:10:249. doi: 10.12688/f1000research.28142.2. eCollection 2021.

Authors

Anna Elizarova^{1

2}, Mumin Ozturk^{3

4}, Reto Guler^{3

4

5}, Yulia A Medvedeva^{1

2}

Affiliations

¹ Group of Regulatory Transcriptomics and Epigenomics, Research Center of Biotechnology, Institute of Bioengineering, Russian Academy of Sciences, Moscow, 117312, Russian Federation.
² Department of Biological and Medical Physics, Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, 141701, Russian Federation.
³ International Centre for Genetic Engineering and Biotechnology, Cape Town, Cape Town, 7925, South Africa.
⁴ Department of Pathology, University of Cape Town, Institute of Infectious Diseases and Molecular Medicine (IDM), Division of Immunology and South African Medical Research Council (SAMRC) Immunology of Infectious Diseases, Faculty of Health Sciences, Cape Town, 7925, South Africa.
⁵ Wellcome Centre for Infectious Diseases Research in Africa (CIDRI-Africa), Institute of Infectious Disease and Molecular Medicine (IDM), Faculty of Health Sciences, University of Cape Town, Cape Town, 7925, South Africa.

Abstract

Emerging studies demonstrate the ability of microRNAs (miRNAs) to activate genes via different mechanisms. Specifically, miRNAs may trigger an enhancer promoting chromatin remodelling in the enhancer region, thus activating the enhancer and its target genes. Here we present MIREyA, a pipeline developed to predict such miRNA-gene-enhancer trios based on an expression dataset which obviates the need to write custom scripts. We applied our pipeline to primary murine macrophages infected by Mycobacterium tuberculosis (HN878 strain) and detected Mir22, Mir221, Mir222, Mir155 and Mir1956, which could up-regulate genes related to immune responses. We believe that MIREyA is a useful tool for detecting putative miRNA-directed gene activation cases. MIREyA is available from: https://github.com/veania/MIREyA.

Keywords: enhancer; macrophage; miRNA; microRNA; non-coding RNA; regulator; tuberculosis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Macrophages
Mice
MicroRNAs* / genetics
Mycobacterium tuberculosis* / genetics
Regulatory Sequences, Nucleic Acid
Transcriptional Activation

Substances

MIRN222 microRNA, mouse
MicroRNAs