Knowledge Base

SIRT6 is an upstream regulator of DNA DSB repair

We demonstrated that SIRT6 recruited to the DSB repair sites within seconds Van Meter et al, Cell Reports, 2016 and mediates recruitment of PARP1, then SIRT6 mono-ADP ribosylates PARP1 on K521 and stimulates PARP1 activity. SIRT6 acts upstream of the separation between NHEJ and HR, and overexpression of SIRT6 stimulates both pathways of DNA DSB repair several fold Mao et al, Science, 2011. SIRT6 is phosphorylated by JNK on S10, and this phosphorylation stimulates SIRT6 mono-ADP-ribosylation activity and promotes recruitment of PARP1 to DSBs (vanMeter et al, Cell Reports, 2016). Together, the findings described above outline a model of how SIRT6 promotes DSB repair.

SIRT6 rescues senescence-related decline of DSB repair and BER

We showed that DNA DSB repair by HR declines as human fibroblasts cells approach replicative senescence. SIRT6, but not any other HR repair enzymes tested, was able to rescue senescence-related decline of HR (Mao et al, PNAS, 2012). We also showed that SIRT6 rescues age-related decline in base excision repair Xu et al, Cell Cycle, 2015.

SIRT6 promotes epigenome stability during aging

In addition to its role in DSB repair, we demonstrated that SIRT6 promotes epigenome stability by silencing retrotransposons Van Meter et al, Nature Communications, 2014. Importantly, L1s become de-repressed during aging and cellular senescence, leading us to propose that redistribution of SIRT6 on chromatin contributes to age-related activation of L1s. We demonstrated that L1 elements become highly active in SIRT6 KO mice leading to activation of type I interferon response. Treatment of the mice with reverse transcriptase inhibitors that inhibit L1 reverse transcription completely rescues the interferon response and extends the lifespan of SIRT6 KO mice by two-fold.

Naked mole rat has more stable epigenome

While generating naked mole rat iPSCs, we observed that the reprogramming efficiency of naked mole rat fibroblasts in response to OSKM was drastically lower than that of mouse fibroblasts Tan et al, Stem Cell Rep. 2017. Inactivation of Rb alone, but not p53, was sufficient to improve reprogramming efficiency, suggesting that naked mole rat chromatin may be refractory to reprogramming. Analysis of the global histone landscape revealed that naked mole rats had higher levels of repressive H3K27 methylation marks and lower levels of activating H3K27 acetylation marks than mouse. ATAC-seq revealed that in naked mole rat, promoters of reprogramming genes were more closed than mouse promoters, while expression of LT led to massive opening of the naked mole rat promoters. These results suggest that the naked mole rat displays a more stable epigenome that resists de-differentiation, contributing to the cancer resistance and longevity of this species.

Naked mole rat has unique ribosomal structure and enhanced translational fidelity

We discovered that naked mole rat has a unique split 28S ribosomal RNA. To understand how this may impact protein translation we developed new tools for analysis of translation fidelity Azpurua et al, PNAS, 2014, using these novel reporters we demonstrated that naked mole rat has more accurate protein synthesis. We then expanded this observation to sow that fidelity of protein synthesis co-evolves with maximum lifespan Ke et al, Aging Cell, 2017, which provides new meaning to the error catastrophe theory of aging.

Naked mole rat INK4 locus encodes a unique isoform

We identified novel isoform, pALT, encoded by the naked mole rat INK4 locus that consists of the first exon of p15 and the second and third exons of p16. This novel protein functions as cyclin dependent kinase inhibitor and has stronger ability to promote cell cycle arrest than either p15 or p16 Tian et al, PNAS, 2015.

Somatic mutations in single cells

We recently developed a highly accurate, single cell multiple displacement amplification (SCMDA) procedure to comprehensively determine the full spectrum of base substitutions in a single somatic cell Dong et al, Nature Methods, 2017. Using SCMDA to compare mouse and human germline and somatic mutation frequencies we found, first, that the observed somatic mutation frequencies in both human and mouse fibroblasts were 10-100 times higher than the germline mutation rate in these species. This underscores the disposable nature of somatic cells and is in keeping with the idea that aging is caused by the accumulation of unrepaired damage. Second, we found that both germline and somatic mutation frequencies were significantly higher in mice than in humans Milholland et al, Nature Communications, 2017.

Single-cell DNA methylation analysis

Changes in DNA methylation have been implicated in both cancer and aging. To analyze stochastic variation with age in DNA methylation in the overall genome, single cell assays are necessary. We, and others have recently developed such single cell methylomics assays using bisulfite sequencing. To analyze heterogeneity in 5mC patterns among the isolated mouse hepatocytes, we performed whole genome bisulfite sequencing of at least two cells from each animal as well as bulk DNA, which served as the reference. Epivariation frequency in the hepatocytes appeared to be remarkably high, i.e., in the order of 3.3 % of all CpG sites analyzed. This is more than three orders of magnitude higher than the frequency of somatic DNA sequence mutations and very similar to our previous promoter-based estimates Gravina, Genome Biology, 2016.

Longevity signatures based on gene expression

After analyzing RNA-seq-based gene expression liver, kidney, and brain of 33 diverse species of mammals, we uncovered parallel evolution of gene expression and lifespan, as well as the associated life-history traits, and identified the processes and pathways involved. We also reported these patterns across primary skin fibroblasts isolated from 16 species of mammals. Fushan et al, Aging Cell, 2015 MacRae et al, Aging, 2015 Ma et al, eLife, 2016

Longevity signatures based on metabolites and chemical elements

We identified metabolite patterns that define longevity across mammals (based on 26 species, 4 organs), mouse models of longevity (5 models, 2 organs), and primary fibroblasts of rodents (15 species). Ma et al, Cell Metabolism, 2015 We also examined 18 elements in the brain, heart, kidney, and liver of 26 mammalian species and identified the elemental composition of these organs, the patterns of utilization across the species, and their correlation with body mass and longevity. Ma et al, Cell Reports, 2015

Naked mole rat induced pluripotent stem cells

We generated induced pluripotent stem cells (iPSCs) from NMR fibroblasts and characterized their contribution to mouse-NMR chimeric embryos. Efficient reprogramming could be observed under N2B27+2i conditions. The iPSCs displayed a characteristic morphology, expressed pluripotent markers, formed embryoid bodies, and showed typical differentiation patterns. Lee et al, Stem Cell Reports, 2017

DNA methylation clock in mice

The DNA methylation levels of certain CpG sites are thought to reflect the pace of human aging. We developed a robust predictor of mouse biological age based on 90 CpG sites derived from partial blood DNA methylation profiles. The resulting clock correctly determines the age of mouse cohorts, detects the longevity effects of calorie restriction and gene knockouts, and reports rejuvenation of fibroblast-derived iPSCs. The data show that mammalian DNA methylomes are characterized by CpG sites that may represent the organism’s biological age. They are scattered across the genome, they are distinct in human and mouse, and their methylation gradually changes with age. The clock derived from these sites represents a biomarker of aging and can be used to determine the biological age of organisms and evaluate interventions that alter the rate of aging. Petkovich et al, Cell Metabolism, 2017