MicroRNA Transcriptomes Reveal Prevalence of Rare and Species-Specific Arm Switching Events During Zebrafish Ontogenesis
Open accessAbstract
In metazoans, microRNAs (miRNAs) are essential regulators of gene expression, affecting critical cellular processes from differentiation and proliferation, to homeostasis. During miRNA biogenesis, the miRNA strand that loads onto the RNA-induced Silencing Complex (RISC) can vary, leading to changes in gene targeting and modulation of biological pathways. To investigate the impact of these “arm switching” events on gene regulation, we analyzed a diverse range of tissues and developmental stages in zebrafish by comparing 5p and 3p arms accumulation dynamics between embryonic developmental stages, adult tissues, and sexes. We also compared variable arm usage patterns observed in zebrafish to other vertebrates including arm switching data from fish, birds, and mammals. Our comprehensive analysis revealed that variable arm usage events predominantly take place during embryonic development. It is also noteworthy that isomiR occurrence correlates to changes in arm selection evidencing an important role of microRNA distinct isoforms in reinforcing and modifying gene regulation by promoting dynamics switches on miRNA 5p and 3p arms accumulation. Our results shed new light on the emergence and coordination of gene expression regulation and pave the way for future investigations in this field.
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- Authors
- Oliveira, A. C. D., Bovolenta, L. A., Figueiredo, L., Ribeiro, A. D. O., Pereira, B. J. A., de Almeida, T. R. A., Campos, V. F., Patton, J. G., & Pinhal, D.
- Affiliations
- Universidade Estadual Paulista (Unesp) (BR)
- Department of Chemical and Biological Sciences, Institute of Biosciences of Botucatu, São Paulo State University-UNESP, Botucatu, São Paulo, Brazil
- Laboratory of Structural Genomics, Postgraduate Program in Biotechnology, Center for Technological Development, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
- Vanderbilt University (US)
- Corresponding author
- Pinhal, Danillo
- ORCID
- Venue
- Evolutionary Bioinformatics
- Publisher
- SAGE Publications
- Published
- 2024-01
- Volume
- 20
- Pages
- 11769343241263230-11769343241263230
- ISSN
- 1176-9343 (ISSN-L)
- PMC
- PMC11271096
- OpenAlex
- W4400954353
- Semantic Scholar
- 366e72274ad082eee1aec6beda343bad7d924e1b
- Cited by
- 2
- References
- 72
- Citations by year
- 2025: 2
- FWCI
- 0.30
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Evolutionary Bioinformatics (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (publishedVersion, other-oa)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (Finance Code 001)
- Fundação de Amparo à Pesquisa do Estado de São Paulo (#2017/17510-2, #2018/05484-0, #2019/15494-5)
- Conselho Nacional de Desenvolvimento Científico e Tecnológico (#136152/2018-0, #167444/2017-4, #315139/2020-0, #433746/2018-1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › MicroRNA in disease regulation
- Life Sciences › Agricultural and Biological Sciences › Plant Science › Plant Molecular Biology Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Keywords
- isomiRs, microRNA biogenesis, RNA-induced silencing complex, zebrafish embryonic development, ontogeny, sex differences, gene expression regulation, microRNA transcriptome
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