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| Status |
Public on Mar 15, 2017 |
| Title |
Hyper- and hypo- nutrition studies of the hepatic transcriptome and epigenome suggest that PPARα regulates anaerobic glycolysis |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
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.
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| Overall design |
RNA-seq analysis of mouse liver maintained on normal chow diet, high-fat diet or calorie restricted diet, ChIP-seq on RXRα and PPARα from mouse liver maintained on calorie restricted or high-fat diets, DNase-seq on mouse liver maintained on normal chow, high-fat, or calorie restricted diets.
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| Contributor(s) |
Motola S, Slotis AR, Vernia S, Ng CW, Kennedy NJ, Dalin S, Matthews BJ, Davis RJ, Fraenkel E |
| Citation(s) |
28282965 |
| Submission date |
Jun 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Shmulik Motola |
| Organization name |
MIT
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| Street address |
77 Mass Ave.
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
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| Platforms (1) |
| GPL9250 |
Illumina Genome Analyzer II (Mus musculus) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA208469 |
| SRA |
SRP026039 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE47954_CR_PPARa.bed.gz |
72.6 Kb |
(ftp)(http) |
BED |
| GSE47954_DNase_union.bed.gz |
705.4 Kb |
(ftp)(http) |
BED |
| GSE47954_PPARa_HFD.bed.gz |
174.4 Kb |
(ftp)(http) |
BED |
| GSE47954_RAW.tar |
4.6 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE47954_RXRa_CR.bed.gz |
204.0 Kb |
(ftp)(http) |
BED |
| GSE47954_RXRa_HFD.bed.gz |
442.4 Kb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
| Processed data provided as supplementary file |
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