Špela Mikec1, Martin Šimon1, Nicholas M Morton2, Santosh S Atanur3,4, Janez Konc5, Peter Dovč1, Simon Horvat6, Tanja Kunej7. 1. Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia. 2. The Queen's Medical Research Institute, Centre for Cardiovascular Science, University of Edinburgh, Edinburgh, UK. 3. Centre for Genomic and Experimental Medicine, University of Edinburgh, Edinburgh, UK. 4. Department of Metabolism, Digestion, and Reproduction, Faculty of Medicine, Imperial College London, London, UK. 5. Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia. 6. Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia. simon.horvat@bf.uni-lj.si. 7. Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domžale, Slovenia. tanja.kunej@bf.uni-lj.si.
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.
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.
Authors: Olga Gealekman; Nina Guseva; Celia Hartigan; Sarah Apotheker; Matthew Gorgoglione; Kunal Gurav; Khan-Van Tran; Juerg Straubhaar; Sarah Nicoloro; Michael P Czech; Michael Thompson; Richard A Perugini; Silvia Corvera Journal: Circulation Date: 2011-01-03 Impact factor: 29.690
Authors: S Fujisaka; I Usui; M Ikutani; A Aminuddin; A Takikawa; K Tsuneyama; A Mahmood; N Goda; Y Nagai; K Takatsu; K Tobe Journal: Diabetologia Date: 2013-03-15 Impact factor: 10.122