Carnegie Mellon

Chakrabarti Group


RNA Biology

RNA Genomics and Bioinformatics

Our laboratory has a broad interest in comparative and evolutionary genomics of RNAs in various eukaryotic pathogens. We are particularly interested in the identification and functional significance of species-specific non-coding RNA sequences. We characterize these RNAs based on various genetic and molecular studies, such as the RNA-protein interaction assays, analysis of the patterns of expression and the subcellular location of the ncRNAs under analysis.

RNA Genomics and RNA Genomics and Bioinformatics

Telomerase RNA

One of our major research goals in the lab is to characterize telomerase RNA from eukaryotic pathogens using RNA biochemistry and cell biology approaches. Telomerase RNA is an integral catalytic component of telomerase holoenzyme that synthesizes DNA repeats to protect ends of eukaryotic chromosomes. We suggest that targeting telomerase ribonucleoprotein enzyme should provide significant therapeutic clues for malaria and many other diseases caused by protozoan pathogens (e.g. Trypanosoma, Leishmania, Toxoplasma etc) since the majority of their virulence genes are located in the telomeric and subtelomeric regions of the chromosomes. We are working on elucidation of the mechanism of telomerase RNA-protein interactions in this pathogen which will facilitate the design and search for additional telomerase-specific inhibitors.

Telomerase RNA localized with telomeric DNA repeats in malaria parasite P. falciparum.

RNAs of unknown function (RUFs)

Apart from telomerase work, we are also engaged in biochemical characterization of several new RNAs that were recently identified in the malaria genome (see publications). Some RNAs are important components of essential biological processes in human pathogens, such as pre-mRNA splicing and ribosomal RNA (rRNA) biogenesis. In other instances, the mechanisms of action of many of these RNAs are as of yet unknown. Therefore, our goal is to take cross-disciplinary measures involving chemistry and biology to (1) functionally characterize these novel RNAs, (2) comprehensively identify the essential components of their molecular interactions, and (3) develop assays to screen chemical compounds that can potentially block the small RNA functions and disease pathogenesis.