MIREyA: a computational approach to detect miRNA-directed gene activation [version 2; peer review: 1 approved, 2 approved with reservations]

• Published in: F1000 research Vol. 10; p. 249
• Main Authors: Elizarova, Anna, Ozturk, Mumin, Guler, Reto, Medvedeva, Yulia A
• Format: Journal Article
• Language: English
• Published: London Faculty of 1000 Ltd 2021; F1000 Research Limited; F1000 Research Ltd
• Subjects: Algorithms; Chromatin remodeling; Computer applications; Cytokines; Datasets; Gene expression; Genetic engineering; Genomes; Immune response; Infections; Macrophages; MicroRNAs; miRNA; Names; Pipelines; Seeds; Software Tool; Tuberculosis; enhancer; non-coding RNA; tuberculosis; microRNA; miRNA; regulator; macrophage
• ISSN: 2046-1402; 2046-1402
• DOI: 10.12688/f1000research.28142.2

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