Question

From the evidence of their impact on DNA methylation, discuss how both a calorie-restricted diet or a diet that includes rapamycin would likely affect aging?

Answer 1

Calorie restricted diet and diet rich in rapamycin have been known to increase lifespan in mice and invertebrates. Calorie restriction diet (CR) is a diet that has 10-30% less calories than normal diet. Rapamycin is an antibiotic that inhibit the mTORC1 signaling pathway.

Aging has been linked to several CpG islands that have DNA methylation states. DNA methylation is addition of methyl groups to cytosine residues in DNA by DNA methylases. DNA methylation is an important mechanism of epigenetic changes and mostly leads to gene silencing. Diet can affect epigenetic changes during aging by direct action of expression of genes, ligand based activation of nuclear receptors and effects on signaling via membrane receptors. Although aging causes decreased global DNA methylation, it can induce gene silencing by DNA methylation of specific target genes (local DNA methylation). CR diet will reverse this effect on DNA methylation of during aging. Proto-oncogenes such as RAS are increasingly methylated by CR. This results in reduced oxidative stress in the organism. CR diet also hypermethylates the E2F-1 binding site on a promoter of a p16INK4a. This p16INK4a gene is a tumor suppressor gene that is involved in aging. This hyper methylation will inhibit the binding of E2F1, a transcriptional activator of p16INK4a. As a result, there is down regulation of gene expression, leading to decreased aging related changes. CR diet is known to increase the activity of histone deacetylases (HDAC) that remove acetyl groups from histones and will thus, free the DNA for transcription. Enhanced activity of HDAC1 on p16INK4a will activate the gene expression due to loss of gene silencing. HDAC1 also deacetylates TERT (human reverse transcriptase) promoter region, which is involved in addition of telomere repeats to chromosomes. Thus, there is increased genome stability and less progression of aging. CR induces the expression of sirtuins like SIRT1, which will negatively influencing p53 transcription, thereby inhibiting apoptosis. SIRT1 deacetylates histone and non-histone substrates such as p53, p16INK4a, DNA repair Kup70 protein etc. Activation of Kup70 by SIRT1 causes the inactivation of BAX, thus leading to loss of apoptosis. Di and Tri-methylation of histone 3 by CR, can lead to activation of genes such as p16INK4a. Thu, CR diet can induce DNA methylation, histone methylation and histone deacetylation changes to reverse aging.

Rapamycin inhibit mTORC1 signaling (immediate effect) and mTORC2 signaling (chronic effect). The mTORC1 pathway is a redox sensing pathway and increases protein synthesis via S6K1 phosphorylation. mTORC1 also increases localization of ribosomes to mRNA cap by phosphorylating 4E-BP1. Phosphorylation by mTORC1 is via association through RAPTOR protein. Rapamycin causes increased genome wide occupancy of Rsc9. This Rsc 9 is a subunit of the RSC chromatin remodeling complex. Thus, chromatin can be remodeled due to alteration of nucleosome structure. TORC1 signaling allows occupancy of Esa1-histones acetyltransferase complex at promoters of genes for ribosomal protein genes. This action of mTORC1 will result in acetylation of histone 4, leading to increased transcription. When Rapamycin is added, the Rsa1 complex is released form the promoters of these genes. This results in gene silencing, causing reduced protein synthesis and growth. H3K56 is a target for mTORC1 signaling and shows increased acetylation. H3K56 acetylation is known to reduce longevity. Acetylation allows RNA pol I transcription and processing of rRNA. However, when rapamycin is present in yeast, acetylation of H3K56 is deacetylated locally at loci of ribosomal DNA. As a result, RNA pol 1 transcription and rRNA processing is inhibited.

Rapamycin will retard the epigenetic clock, leading to decreased aging. Rapamycin increases expression of H3K56ac, H3K36me3, H3K4me1 and H3K27ac (ac is acetylation, me is methylation). Increased DNA methylation by rapamycin can affect the metabolic cofactors such as citrate, succinate etc. Rapamycin reduces the turnover of 5 methylcytosine in DNA, thereby decreasing global DNA methylation. It also inhibits the incorporation of histones in cells that have undergone senescence via effects on linker histone 1.