Development and functioning of higher organisms critically depends on properly regulated gene expression. Regulation of gene expression occurs primarily at the initial step (transcription) and involves DNA sequences, protein factors and dynamic changes in structure of DNA-protein complexes (chromatin). The major research goal in my laboratory is to understand the molecular mechanisms and regulation of the vital process of eukaryotic transcription in chromatin, and the role of the factors involved in cancer development and human aging (e.g. hFACT and hPARP1) in this process. This goal will be achieved using a combination of molecular genetics, genomics, biochemical, single-particle, structural and computational modeling approaches. Currently our efforts are focused in two primary directions: 1. The mechanisms of gene regulation over a distance (by enhancers & insulators), and 2. The mechanisms and regulation of transcript elongation through chromatin by RNA polymerase II. 

Distant regulation of gene transcription initiation is mediated by direct interaction between proteins bound at communicating DNA elements and involves looping of intervening DNA/chromatin regions (1). Our research focuses on the following critical questions: What features of DNA/chromatin template allow efficient communication over a distance? What are distinct features of the regulatory elements that are capable of action over a distance? We have adopted relatively simple, highly purified and efficient experimental systems for quantitative analysis of enhancer action over a distance in vitro (2). This simple experimental system allowed us to identify elements of DNA and chromatin structure, as well as protein factors that mediate distant gene regulation (unpublished).

Since 1998 our studies have been focused on analysis of histone survival during transcription by Pol II (funded by NIH RO1). We have established a “minimal” experimental system that maintains single- and multiple-round transcription through various defined mono- and polynucleosomes by yeast and human RNA polymerase II (3). This system faithfully recapitulates numerous features of transcribed chromatin described in vivo and allows their molecular analysis in vitro. Using this system, we have discovered a novel Pol II-specific mechanism involving survival of core histones and their modifications without even transient histone dissociation from DNA (4). These features of the mechanism suggest that it is likely used for maintenance of chromatin structure and the “histone code” that is particularly important during genomic transcription (5,6). It is also important for chromatin-specific DNA repair (7). The most recent focus of our studies is on the mechanism of action of various elongation factors (TFIIS) and histone chaperones (hFACT & hPARP1) facilitating histone survival during Pol II transcription. Importantly, both hFACT & hPARP-1 are involved in carcinogenesis and are important targets for anti-cancer drugs.