Chromatin & transcriptional regulation


1) Roles of SET-9 & SET-26 in germline development and longevity

  • Dynamic regulations of histone modifications are known to be key to germline development and longevity but the molecular mechanisms remain largely unknown. We have investigated the roles of  the highly homologous paralogs SET-9 and SET-26 and found that they share redundant function in germline development, but only SET-26, not SET-9, plays a role in modulating lifespan and resistance to heat stress. We showed that SET-9 is only detectable in the germline whereas SET-26 is broadly expressed, and their differential expression patterns likely account for the different phenotypes associated with the loss of each gene. We demonstrated that SET-9 and SET-26 bind to H3K4me3 in vitro and in vivo, and that the loss of set-9 & set-26 results in broadening of H3K4me3 domains surrounding most SET-9 & SET-26 binding regions. Additionally, we found that SET-9 & SET-26 are able to regulate the RNA expression of a subset of their target genes, irrespective of their H3K4me3 status. We hypothesize that SET-9 and SET-26 are critical for organizing local chromatin environment and regulating the expression of specific target genes, and these two activities together contribute to their roles in germline development and longevity. Considering that SET-9 & SET-26 are highly homologous to human MLL5, a factor implicated in leukemia and glioblastoma, the findings reported here will provide important new insights into the functions and biological roles of MLL5, and may pave the way for future therapeutic development.

2) Roles of HCF-1 in germline stem cells and longevity

  • In supporting the close connection between stem cell function and aging, emerging research has highlighted a number of longevity determinants, including FOXO and HCF proteins, to have key roles in regulating stem cell function. HCF-1 is a highly conserved transcriptional co-regulator. We previously established a critical role of hcf-1 in longevity through genetic studies in C. elegans. HCF-1 regulates the key longevity determinant DAF-16/FOXO to modulate aging and lifespan in worms. Recently, C. elegans HCF-1 was found to regulate germline stem cell proliferation and our own data suggest HCF-1 is critical for maintaining germline immortality in worms, a clear indication that HCF-1 has an essential role in ensuring germline stem cell fidelity in C. elegans. In mammals, HCF-1 regulates the key stem cell pluripotency factor RONIN. The C. elegans germline has the ability to proliferate indefinitely and to establish all of the cells of the next generation, the two characteristics that impart stemness. Therefore, the C. elegans germline represents an easily manipulatable system for studying stem cell function.


3) Dynamic changes of histone modification patterns with aging

  • Currently not much is known about whether aging is accompanied by broad changes in the general chromatin landscape in C. elegans. We have profiled the genome-wide patterns of several key histone modifications through the aging process to uncover age-dependent patterns that can generate testable hypotheses for future studies. Findings from our  investigations will provide a much-needed framework for integrating emerging functional data to understand how the epigenome modulates aging and longevity in C. elegans.
  • We profiled the genome-wide pattern of tri-methylation of lysine 36 on histone 3 (H3K36me3) in the somatic cells of young and old C. elegans. We revealed a new role of H3K36me3 in maintaining gene expression stability through aging with important consequences on longevity. We found that genes with dramatic expression change during aging are marked with low or even undetectable levels of H3K36me3 in their gene-bodies, irrespective of their corresponding mRNA abundance. Interestingly, 3’-UTR length strongly correlates with H3K36me3 levels and age-dependent mRNA expression stability.  A similar negative correlation between H3K36me3 marking and mRNA expression change during aging is also observed in Drosophila melanogaster, suggesting a conserved mechanism for H3K36me3 in suppressing age-dependent mRNA expression change. Importantly, inactivation of the methyltransferase met-1 resulted in a decrease in global H3K36me3 marks, an increase in mRNA expression change with age, and a shortened lifespan, suggesting a causative role of the H3K36me3 marking in modulating age-dependent gene expression stability and longevity.
  • We also investigated the connection between H3K4me3 and gene expression regulation during aging by monitoring the age-dependent profiles of H3K4me3 and gene expression in somatic cells. Whereas the global H3K4me3 patterns remain largely stable with age, we uncovered around 30% of H3K4me3 enriched regions to show significant and reproducible changes with age. We further showed that these age-dynamic H3K4me3 regions largely mark gene-bodies and are acquired specifically during adult stages. We found that these adult-specific age-dynamic H3K4me3 regions are well-correlated with gene expression changes with age. Moreover, we found that global reduction of H3K4me3 levels, by depleting the methyltransferase complex component ASH-2, results in significant decreased RNA expression of genes that acquire H3K4me3 marking in their gene-bodies during adult stage. These data together suggest that altered H3K4me3 levels with age could result in age-dependent gene expression changes. Interestingly, the genes with dynamic changes in H3K4me3 and RNA levels with age are enriched for those involved in fatty acid metabolism, oxidation-reduction, and stress response. Therefore, our findings revealed divergent roles of H3K4me3 in gene expression regulation during aging, with important implications on physiological relevance.
  • We are currently investigating how the repressive marks such as H3K27me3 and H3K9me3 may change with aging.