Academic Background

Paul Kaufman received his A.B. in Biochemistry from the University of California, Berkeley and his Ph.D. in Biology from MIT. He was a postdoctoral fellow at Cold Spring Harbor Laboratory, where he was supported by the Life Sciences Research Foundation. He went on to become a Career Staff Scientist at the Lawrence Berkeley National Laboratory and Associate Adjunct Professor of Biochemistry and Molecular Biology at the University of California, Berkeley. Dr. Kaufman joined the Program in Gene Function and Expression at the University of Massachusetts Medical School as an Associate Professor in 2005 and was promoted to Full Professor in 2011.

Assembly and Function of Eukaryotic Chromosomes

We study several different classes of chromatin proteins used by eukaryotic cells to regulate gene expression and chromosome structure. We study these processes in the pathogenic yeast Candida albicans and in human cells, using biochemical, genetic, genomic, and cell biological techniques.

Current Projects

Introduction

In eukaryotes, DNA is assembled into a nucleoprotein complex called chromatin. The fundamental repeating unit of chromatin is the nucleosome, which consists of 146 bp of DNA wrapped around an octamer of core histone proteins, comprised of two H2A/H2B dimers flanking an inner (H3/H4)2 tetramer. In addition to their role in compacting the genome and occluding access to trans-acting proteins, core histone proteins affect all aspects of chromosome function via a wide variety of post-translational modifications.

We are investigating several aspects of chromatin biology. First, we are using our expertise with a fungal histone acetyltransferase enzyme to search for novel candidate antifungal compounds. Second, we are exploring how the transcriptional and spatial regulation of repetitive DNA in human cells is regulated.

Histone H3-K56 acetylation by the fungal-specific enzyme Rtt109 is required for fungal pathogenesis

In fungal cells, histone H3 lysine 56 is quantitatively acetylated on newly synthesized molecules by an enzyme termed Rtt109. H3-K56 acetylation promotes subsequent deposition onto DNA and is required for normal rates of histone turnover. Notably, cells lacking H3-K56 acetylation are very sensitive to genotoxic agents, including DNA alkylating chemicals and hydrogen peroxide. An important feature of this pathway is that it is fungal-specific; in other eukaryotes, H3-K56 acetylation is much less abundant than in fungal cells, and its biological role is not clear. Further, there is no close mammalian homolog of Rtt109; although the p300 enzyme is a distant relative, it is distinct in its active site properties and in its mechanism.

An important way that mammals fight off fungal pathogens is via phaogcytic engulfment and attack with reactive oxygen species. We therefore reasoned that fungal cells that lack H3-K56 acetylation would be poor pathogens because they would be killed more easily by phagocytic cells such as macrophages. We tested this idea in Candida albicans, the most prevalent fungal pathogen of humans (Lopes da Rosa et al., PNAS 2010). Indeed, C. albicans cells lacking Rtt109 are much less lethal to mice upon systemic infection of the bloodstream. Further, these cells are more easily killed by macrophages, in a manner that depends on generation of reactive oxygen species. Because Rtt109 lacks close mammalian homologs, we concluded that Rtt109 is a good candidate target for novel antifungal therapeutics.

In collaboration with the Broad Institute as part of the NIH Molecular Libraries Program, we have screened over 300,000 small molecules in an in vitro assay for histone acetylation by Rtt109. Characterization of candidate inhibitors is in progress.

Regulation of human repetitive DNA by chromatin proteins and remodeling enzymes

We are exploring how human nucleosome remodeling enzymes and other chromatin proteins regulate the transcriptional output and three-dimensional organization of repetitive elements in the genome. These studies are facilitated by our development of a versatile family of retroviral and lentiviral vectors for protein overexpression and depletion, and by the microscopy, high throughput sequencing and bioinformatics resources at UMMS.