Biological variance within mRNA sequencing condition groups.

<p>The squared coefficient of variation (CV²) was plotted against Fragments Per Kilobase of exon per Million fragments mapped (log₁₀FPKM), representing the total distribution of mRNA sequence reads for each condition group, which are depicted as follows, 5 months AL (coral), 5 months CR (green), 15 months AL (blue), and 15 months CR (purple).</p

Differential gene expression via mRNA sequence analysis pairwise comparisons.

<p>The total number of differentially expressed transcripts identified by total mRNA sequencing within each pairwise comparison are indicated, along with the log₂ fold change (Log2FC) range and the number of upregulated (gray) and downregulated (white) targets (p<0.01, q<0.05).</p

CR upregulation of neuroprotective gene signatures is conserved at 5 and 15 months, despite divergent transcriptional profiles.

<p>(A) 102 genes are common to both the 15 and 5 month CR vs. AL differential expression mRNA sequencing profiles. Of the 102 common genes, 70/102 (69%) of significant changes occur in the opposite direction. (B) Normalized age- and diet-dependent FPKM levels for select protein folding and calcium buffering genes (*p<0.01, q<0.05); heat shock 70 kDa protein 5 (Hspa5), heat shock 70 kDa protein 1B (Hspa1b), calreticulin (Calr). (C) Log₂ fold change levels for the 32 conserved gene expression changes within 15 (blue) and 5 (red) month CR vs. AL expression profiles that occurred in the same direction are depicted (p<0.01, q<0.05).</p

Average body weight following sustained 30% CR or AL feeding.

<p>Beginning at approximately 2.5 months of age, wild-type female mice were maintained on 30% CR (purple) or AL (blue) diets and were sacrificed following 2.5 or 12.5 months of diet administration. Body weight was measured approximately twice weekly. Within the first 2 weeks of AL and CR feeding, mice maintained on the 30% CR diet lost an average of 12% of their body weight (t-test, p<0.001), which stabilized for the remainder of the study. For study days 1–85, n = 12–18, and for study days 85–365, n = 6–14, reflecting sacrifice of the first group of mice at 5 months of age; mean +/- SEM.</p

High fat diet and exercise lead to a disrupted and pathogenic DNA methylome in mouse liver

<p>High-fat diet consumption and sedentary lifestyle elevates risk for obesity, non-alcoholic fatty liver disease, and cancer. Exercise training conveys health benefits in populations with or without these chronic conditions. Diet and exercise regulate gene expression by mediating epigenetic mechanisms in many tissues; however, such effects are poorly documented in the liver, a central metabolic organ. To dissect the consequences of diet and exercise on the liver epigenome, we measured DNA methylation, using reduced representation bisulfite sequencing, and transcription, using RNA-seq, in mice maintained on a fast food diet with sedentary lifestyle or exercise, compared with control diet with and without exercise. Our analyses reveal that genome-wide differential DNA methylation and expression of gene clusters are induced by diet and/or exercise. A combination of fast food and exercise triggers extensive gene alterations, with enrichment of carbohydrate/lipid metabolic pathways and muscle developmental processes. Through evaluation of putative protective effects of exercise on diet-induced DNA methylation, we show that hypermethylation is effectively prevented, especially at promoters and enhancers, whereas hypomethylation is only partially attenuated. We assessed diet-induced DNA methylation changes associated with liver cancer-related epigenetic modifications and identified significant increases at liver-specific enhancers in fast food groups, suggesting partial loss of liver cell identity. Hypermethylation at a subset of gene promoters was associated with inhibition of tissue development and promotion of carcinogenic processes. Our study demonstrates extensive reprogramming of the epigenome by diet and exercise, emphasizing the functional relevance of epigenetic mechanisms as an interface between lifestyle modifications and phenotypic alterations.</p