BBS Faculty Member - Dipanjan Chowdhury

Dipanjan Chowdhury

Division of Genomic Stability and DNA Repair
Department of Radiation Oncology

Dana Farber Cancer Institute
HIM Building, Room 223
4 Blackfan Circle
Boston, MA 02115
Tel: 617-582-8639
Fax: 617-582-8213
Visit my lab page here.

DNA damage response- phosphatases and non-coding RNA

We are interested in the role of two ‘new’ players, phosphatases and non-coding RNA in the ‘old’ process of DNA repair. Phosphorylation signaling networks have primarily been studied from an activation perspective, with phosphatases viewed as simple counter-balances that functioned passively in the wake of kinase activity. This dogma has persisted in the field of DNA repair for many decades. However recent large-scale, phosphoproteomic analysis of the DNA damage response (DDR) revealed that over one-third of observed phosphorylation sites were down-regulated within minutes of DNA damage. These data suggest that protein phosphatases not only play a role in counter-acting DNA damage-induced phosphorylation events, but also play a primary role in initiating the repair process. Consistent with these results, we recently identified a functional role for the PP2A family (PP2A, PP4 and PP6) of protein serine/threonine phosphatases in DDR. We have demonstrated that phosphatases participate in multiple steps of the DDR, which includes facilitating DNA repair in the context of the cell cycle phase, restoration of chromatin structure and regulating checkpoints. We now have evidence that dephosphorylation of specific phospho-residues of DNA repair proteins is necessary for their participation in DDR. A comprehensive identification of proteins that undergo dephosphorylation in the course of the DDR by any individual phosphatase has not been conducted. In fact, there are limited examples in the literature where a systematic genome-wide method has been utilized to identify proteins dephosphorylated by an individual Ser/Thr phosphatase. We have developed a novel phospho-proteomic strategy based on the rationale that phosphoproteins enriched in the absence of a phosphatase are putative substrates. Our goal is to continue these studies and systematically investigate the role of phosphatases in DSB repair.

A ground-breaking discovery in the past few decades has been the role of evolutionarily conserved non-coding RNAs in cell/tissue development and human disease. There has been an explosion of research on non-coding RNAs, specifically microRNA (miRNA)s, with a large volume of emerging data documenting their influence on almost every cellular process and signaling pathway. Until recent times the research on DDR has been surprisingly impervious to this new class of regulators. However, in the past few years there is increasing evidence of non-coding RNAs being induced by DNA breaks and potentially contributing to DDR. We have shown that important DNA repair proteins like H2AX and BRCA1 are regulated by miRNAs during differentiation and in various stages of the cell cycle. We adapted a biochemical strategy of co-immunoprecipitating miRNA/mRNA interactions to identify physiologically relevant targets (including DDR proteins) of miRNAs. Using cross-linking/immunoprecipitation and RNA-Seq we now have evidence that other non-coding RNA species maybe associated with DNA repair factors and directly impact the repair process. These results not only provide the ‘proof-of principle’ regarding a broad role for miRNAs and other non-coding RNAs in DNA repair, but also open up a plethora of questions regarding the molecular details of their precise function in various aspects of DDR. Understanding the details of DNA repair is fundamentally important for both DNA replication and recombination, and almost nothing is known about non-coding RNAs in either of these processes.

Last Update: 1/22/2016


For a complete listing of publications click here.



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