Hypothalamic transcriptomes of 99 mouse strains reveal trans eQTL hotspots, splicing QTLs and novel non-coding genes

Elife. 2016 Sep 13;5:e15614. doi: 10.7554/eLife.15614.


Previous studies had shown that the integration of genome wide expression profiles, in metabolic tissues, with genetic and phenotypic variance, provided valuable insight into the underlying molecular mechanisms. We used RNA-Seq to characterize hypothalamic transcriptome in 99 inbred strains of mice from the Hybrid Mouse Diversity Panel (HMDP), a reference resource population for cardiovascular and metabolic traits. We report numerous novel transcripts supported by proteomic analyses, as well as novel non coding RNAs. High resolution genetic mapping of transcript levels in HMDP, reveals both local and trans expression Quantitative Trait Loci (eQTLs) demonstrating 2 trans eQTL 'hotspots' associated with expression of hundreds of genes. We also report thousands of alternative splicing events regulated by genetic variants. Finally, comparison with about 150 metabolic and cardiovascular traits revealed many highly significant associations. Our data provide a rich resource for understanding the many physiologic functions mediated by the hypothalamus and their genetic regulation.

Keywords: RNA-Seq; eQTL; evolutionary biology; genomics; high fat diet; hypothalamus; mouse; neuroscience; obesity; trans-eQTL.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, N.I.H., Extramural

MeSH terms

  • Alternative Splicing
  • Animals
  • Cardiovascular Diseases / genetics
  • Chromosome Mapping
  • Genetic Association Studies
  • Hypothalamus / physiology*
  • Metabolic Diseases / genetics
  • Mice
  • Proteome / analysis
  • Quantitative Trait Loci*
  • RNA, Untranslated / analysis
  • Sequence Analysis, RNA
  • Transcriptome*


  • Proteome
  • RNA, Untranslated