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Genetic variants of the hypoxia‐inducible factor 3 alpha subunit (Hif3a) gene in the Fat and Lean mouse selection lines

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Abstract

Background

Adipose tissue hypoxia and members of the hypoxia-inducible factor alpha (HIFA) are involved in development of obesity. However, the mechanism and functions of HIF3A, one of three HIFA paralogs, in fat deposition have not been sufficiently studied.

Methods and results

In the present study, we investigated whether Hif3a sequence variants are associated with divergent fat deposition in mouse selection lines for fatness and leanness. Sequencing and RFLP were used to analyse sequence variants within Hif3a. To identify candidate regulatory variants, we performed literature screening and used databases and bioinformatics tools like Ensembl, MethPrimer, TargetScanMouse, miRDB, PolyAsite, RISE, LncRRIsearch, RNAfold, PredictProtein, CAIcal, and switches.ELM Resource. There are 90 sequence variants in Hif3a between the two mouse lines. While most Fat line variants locate within intronic regions, Lean line variants are mainly in 3′ UTR. We constructed a map of Hif3a potential regulatory regions and identified 39 regulatory variants by integrating data on constrained and regulatory elements, CpGs, and miRNAs and lncRNAs binding sites. Moreover, 3′ UTR and two exonic variants may influence mRNA stability, translation rate and protein functionality. We propose as priority candidates for further functional studies a missense (rs37398126) and synonymous (rs37739792) variants, and intronic (rs47471302) variant that overlap conserved element in promoter region and predicted lncRNAs binding site.

Conclusion

The results indicate a potential involvement of Hif3a in fat deposition. Additionally, approach used in the present study may serve as a general guideline for constructing an integrative gene map for prioritizing candidate gene variants with phenotypic effects.

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Acknowledgements

The authors also want to thank Dr Tim J. Aitman (Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, United Kingdom) for the help with WGS.

Funding

The authors acknowledge the study was financially supported by the Slovenian Research Agency under the postgraduate research program Young researchers (ŠM), P4-0220 research program and J4-2548 research project.

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Author notes

  1. Špela Mikec and Martin Šimon have contributed equally to this work.

Authors and Affiliations

  1. Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia

    Špela Mikec, Martin Šimon, Peter Dovč, Simon Horvat & Tanja Kunej

  2. The Queen’s Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK

    Nicholas M. Morton

  3. Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK

    Santosh S. Atanur

  4. Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, UK

    Santosh S. Atanur

  5. Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia

    Janez Konc

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  1. Špela Mikec
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Contributions

ŠM and MŠ: Formal analysis, Writing—original draft preparation. NMM: Formal analysis. Writing – review & editing. SSA: Formal analysis. JK: Resources. PD: Resources. SH and TK: Conceptualization, Writing – review & editing, Supervision.

Corresponding authors

Correspondence to Simon Horvat or Tanja Kunej.

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All authors have read and approved the final version of the manuscript for submission and declare that they have no competing interests.

Ethical approval

The FLI (Fat) and FHI (Lean) selection lines have been maintained in our laboratory for more than 70 generations. All mice used in this study were maintained according to local ethical and EU regulatory guidelines under the Veterinary Administration of Republic of Slovenia permit No. U34401-23/2020/6.

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Mikec, Š., Šimon, M., Morton, N.M. et al. Genetic variants of the hypoxia‐inducible factor 3 alpha subunit (Hif3a) gene in the Fat and Lean mouse selection lines. Mol Biol Rep 49, 4619–4631 (2022). https://doi.org/10.1007/s11033-022-07309-0

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