Researcher working with sample

Genome replication and its role in aging

More than half of the human genome consists of repetitive DNA that replicates late and is transcriptionally silenced, shrouded by heterochromatin. Recent studies show these repeated sequences open up for transcription during carcinogenesis and aging, tending to serve more readily as replication origins. Because they make up such a large portion of the overall genome, chromatin shifts in these regions could upset the balance of replication resources, competing with other parts of the genome for limiting replication factors.

We use S. cerevisiae as a model to understand:

  1. Which features of heterochromatin suppress the activation of replication origins within these repetitive sequences.
  2. How excessive allocation of replication resources to these repetitive sequences compromises replication elsewhere in the genome.
  3. The relationship between genome replication failure and aging.

Related publications in PDF:

Foss EJ, et al. SIR2 suppresses replication gaps and genome instability by balancing replication between repetitive and unique sequencesProc Natl Acad Sci USA 114(3):552-557, 2017.

Kwan EX, et al. A natural polymorphism in rDNA replication origins links origin activation with calorie restriction and lifespanPLoS Genet 9(3):e1003329, 2013.

Yeast cells
Yeast cells, with many in various stages of budding. Lifespan of yeast is defined as how many daughter cells bud from one single mother cell.
binding locations of replication factors
The binding locations of replication factors, as visualized from data gathered via high-throughput deep-genome sequencing.
Mother and daughter yeast cells budding
A close-up picture of mother and daughter cells budding, this time visualized with fluorescent microscopy.

Sirtuin inhibitors to treat cancer

Histones and other nuclear proteins can be modified by acetylation, the addition of an acetyl group to lysine residues. These acetyl groups can be removed by several classes of histone deacetylases (HDACs). Class III HDACs, known as NAD-dependent deacetylases or sirtuins, comprise of seven members in humans (SIRT1-7).  We identified the first sirtuin inhibitors using a phenotypic screen in yeast and subsequently discovered that this class of agents exhibit potent anticancer activity.

In collaboration with Julian Simon’s laboratory, we seek to optimize inhibitors of SIRT2, with the goal of increasing their selectivity and potency. We are testing this class of agents as novel antilymphoma therapeutics and for dissecting molecular pathways by which sirtuin inhibition exerts anticancer activity.

Related publications in PDF:

Leko V, et al. Enterocyte-specific inactivation of SIRT1 reduces tumor load in the APC(+/min) mouse modelPLoS One 8(6):e66283, 2013.

Mahajan SS, et al. Development of pyrazolone and isoxazol-5-one cambinol analogues as sirtuin inhibitorsJ Med Chem 57(8):3283-94, 2014.

Heltweg B, et al. Antitumor activity of a small-molecule inhibitor of human silent information regulator 2 enzymesCancer Res 66(8):4368-77, 2006.

Bedalov A, et al. Identification of a small molecule inhibitor of Sir2pProc Natl Acad Sci USA 98(26):15113-8, 2001.

The structure of splitomicin
The structure of splitomicin, one of the original sirtuin inhibitors discovered by Bedalov, et al. and published in a 2001 paper. It is named in honor of Dr. Bedalov's hometown of Split, Croatia.

X-chromosome inactivation and Rett syndrome

X-chromosome inactivation is an epigenetic phenomenon that renders one of the two X-chromosomes in female cells transcriptionally silent, ensuring that X-linked gene dosage matches that in males, who have only one X chromosome. Rett syndrome is a neurodevelopmental disorder present in females who are heterozygous for a mutation in the X-linked gene MeCP2. Because cells in these individuals will be missing MeCP2 function only when the wild type copy of the gene is on the inactive X, reactivation of the silenced copy of MeCP2 presents a potential therapeutic strategy for this disease.

We are interested in molecular events that keep X-chromosome in the inactive state and are devising genetic and pharmacologic means to activate genes on the inactive X-chromosome.

Our research is supported in part by the Rett Syndrome Research Trust.

Related publications in PDF:

Sripathy S, et al. Screen for reactivation of MeCP2 on the inactive X chromosome identifies the BMP/TGF-β superfamily as a regulator of XIST expressionProc Natl Acad Sci USA ePub before print, 2017.

Wang J, et al. Wild-type microglia do not reverse pathology in mouse models of Rett syndromeNature521(7552):E1-4, 2015.

Calico cat
Calico cats get their distinctive colors from random X-inactivation, due to the coloration gene being located on the X chromosome.