Mapping Data

Experiment

• Experiment
  TEXT-QTL-Candidate Genes
• Chromosome
  15
• Reference
  J:240252 Beltram J, et al., Construction of an integrative regulatory element and variation map of the murine Tst locus. BMC Genet. 2016 Jun 11;17(1):77
• ID
  MGI:5905069

Genes

Gene	Assay Type
Fob3b2	reported elsewhere
Tst	reported elsewhere

Notes

• Experiment
  The current study developed a map of regulatory elements for the Tst locus in mice and identified candidate genetic variants with increased causal likelihood. The map provided a basis for experimental validation and functional analyses of this novel candidate leanness and anti-diabetic gene.
  
  The focus of the current study was on the nuclear-encoded mitochondrial thiosulfate sulfur-transferase gene (Tst, also known by synonym Rhodanese) that the authors recently identified in a positional cloning experiment as a causal gene for the Fob3b2 QTL phenotypic effect [22, J:236030]. The genetic variants responsible for upregulation of Tst expression in the Lean mice had not yet been identified.
  
  A main objective of the study was to integrate various genomic annotations in the Tst locus to construct a map of regulatory elements of the gene and to identify and prioritise the causal genetic variants between the Fat (F-line) and Lean (L-line) lines.
  
  First, to uncover polymorphisms that might be causal for the difference in expression of the Tst gene, a classical high resolution Sanger-sequencing of the entire Tst locus in Fat and Lean lines was undertaken. Bioinformatics analysis was performed on a 7400 bp-long segment of the mouse Tst gene, including the ~ 0.5 kb upstream and downstream regions.
  
  SNPs were categorized into variation consequence types - upstream gene variant, synonymous variant, intron variant, missense variant, nonsense variant, 5 or 3 untranslated region (UTR) variant and downstream gene variant.
  
  The identified genetic variants were then evaluated and prioritised using a regulatory element map of the Tst locus that integrated broad functional information from conserved polymorphisms in other strains, association studies, transcription factor binding site motifs, chromatin modification motifs and miRNA binding sites.
  
  In the case of Tst gene the comparative analysis of various regulatory features provided strong evidence of three regulatory genome segments located in the promotor, an intron, and the 3' UTR of the locus. The study concluded that SNPs rs251994838 and rs31534689 represented the highest priority candidate genetic variants for further experimental functional validation of their causality on the phneotype.
  
  The approach, to build a detailed integrative regulatory element map can be applied for evaluating and prioritising polymorphisms within candidate regions in any trait or species of interest. Reducing and prioritising the number of potential causal polymorphisms is essential for efficient planning of further experiments to prove or support causality of candidate genetic variants.