title: Hyper- and hypo- nutrition studies of the hepatic transcriptome and epigenome suggest that PPARα regulates anaerobic glycolysis.
abstract: Diet plays a crucial role in shaping human health and disease. Diets promoting obesity and insulin resistance can lead to severe metabolic diseases, while calorie-restricted (CR) diets can improve health and extend lifespan. In this work, we fed mice either a chow diet (CD), a 16 week high-fat diet (HFD), or a CR diet to compare and contrast the effects of these diets on mouse liver biology. We collected transcriptomic and epigenomic datasets from these mice using RNA-Seq and DNase-Seq. We found that both CR and HFD induce extensive transcriptional changes, in some cases altering the same genes in the same direction. We used our epigenomic data to infer transcriptional regulatory proteins bound near these genes that likely influence their expression levels. In particular, we found evidence for critical roles played by PPARα and RXRα. We used ChIP-Seq to profile the binding locations for these factors in HFD and CR livers. We found extensive binding of PPARα near genes involved in glycolysis/gluconeogenesis and uncovered a role for this factor in regulating anaerobic glycolysis. Overall, we generated extensive transcriptional and epigenomic datasets from livers of mice fed these diets and uncovered new functions and gene targets for PPARα.
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
authors.forename: Anthony R
authors.identifier: 0000-0002-3394-1275
authors.initials: AR
authors.lastname: Soltis
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
authors.forename: Shmulik
authors.initials: S
authors.lastname: Motola
authors.affiliation: Howard Hughes Medical Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
authors.forename: Santiago
authors.initials: S
authors.lastname: Vernia
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
authors.forename: Christopher W
authors.initials: CW
authors.lastname: Ng
authors.affiliation: Howard Hughes Medical Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
authors.forename: Norman J
authors.initials: NJ
authors.lastname: Kennedy
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
authors.forename: Simona
authors.identifier: 0000-0001-5024-9718
authors.initials: S
authors.lastname: Dalin
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
authors.forename: Bryan J
authors.initials: BJ
authors.lastname: Matthews
authors.affiliation: Howard Hughes Medical Institute and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
authors.forename: Roger J
authors.initials: RJ
authors.lastname: Davis
authors.affiliation: Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA. fraenkel-admin@mit.edu.
authors.forename: Ernest
authors.initials: E
authors.lastname: Fraenkel
mesh_terms: D000693:Anaerobiosis; D000818:Animals; D031204:Caloric Restriction / Q000009:adverse effects*; D059305:Diet, High-Fat / Q000009:adverse effects*; D044127:Epigenesis, Genetic; D057890:Epigenomics / Q000379:methods*; D020869:Gene Expression Profiling / Q000379:methods*; D005786:Gene Expression Regulation; D006019:Glycolysis; D008099:Liver / Q000737:chemistry*; D008297:Male; D051379:Mice; D009752:Nutritional Status; D047493:PPAR alpha / Q000235:genetics*; D017422:Sequence Analysis, DNA; D017423:Sequence Analysis, RNA
chemical_list: D047493:PPAR alpha