Research
 
The hallmark of mammalian spermiogenesis is the dramatic chromatin remodeling process wherein the nucleosomal histones are replaced first by the transition proteins, TP1, TP2 and TP4 and subsequently by the protamines P1 and P2. Our lab is focused on understanding the various processes of Chromatin Remodeling during Mammalian Spermatogenesis. We are also interested in studying the meiotic recombination events, DNA damage, Cancer Genetics and role of non-coding RNA in cellular differentiation and disease and System Biology.

Chromatin Structure and Function
  The various DNA transaction processes like replication, transcription and recombination encounter chromatin and not naked DNA as the template. Chromatin undergoes extensive reorganization during mammalian spermatogenesis. In our laboratory, we have been working over the last decade on the structural features of this chromatin reorganization brought about by testis specific histone variants and unique basic proteins TP1 and TP2, which appear transiently during spermiogenesis.
 
TP2 is a DNA condensing protein with two atoms of zinc bound per molecule. It condenses DNA with a GC rich sequence preference and recognizes mammalian CpG island sequence in a zinc dependent manner. We have carried out a detailed site directed mutagenesis analysis of rat TP2 and identified two zinc finger modules involving 4 histidine and 4 cysteine residues respectively. The modular structures of the two zinc fingers identified in TP2 define a new class of zinc finger proteins that do not fall into any of the known classes of zinc fingers. Transfection experiments with COS-7 cells using wild type and the two zinc finger pocket mutants have shown that TP2 preferentially localizes to nucleolus. The nuclear localization signal in TP2 was identified to be GKVSKRKAV present in the C-terminal, third of TP2 as a part of an extended NLS sequence. Interestingly, TP1 also shows preferential localization of nucleolus.
 
 
 

Meiotic Recombination
  We had recently identified and characterized a DNA repair locus from pachytene spermatocytes of rat. A detailed theoretical and experimental analysis of this site indicates that it displays considerable secondary structure. The principal elements that appear to confer this feature to the meiotic repair site are DNA unwinding elements, intrinsically bent DNA and nuclear scaffold or matrix associated regions. The meiotic repair site with its several potential SC binding and recombination motifs co-habits with a MAR/ORI and occurs at the base of chromosomal loop.
This locus seems to be highly conserved within rodents and also in humans. A large locus of 17 kb has been isolated from mouse and characterized. It has also been found that, mouse hotspot region encodes a novel non-coding RNA. The functionality of the transcript w.r.t to its localization is being assessed.
 

DNA Repair
  The mismatch repair system has been highly conserved in various species. In eukaryotic cells, the Mut S and Mut L homologs play crucial roles in both DNA mismatch repair and meiotic recombination. Expression analysis of rat MLH1, MSH2, MSH3 and MSH6 in the testes of rats of different ages showed differential expression of these genes as a function of developmental maturation of the testes.
These studies have indicated that MSH3 may have a more predominant role in the meiotic recombination process. Studies are underway to identify the interacting proteins of MLH1.
 
 

Non-coding RNA in Cellular Development and Differentiation
  Our group has discovered a novel non-coding RNA encoded in the mouse genome flanking a recombination hotspot. This non-coding RNA is processed and restricted to the nucleus. mrhl is poorly conserved across different species and significant homology is found only in the rat genome. Studies in lab are focused on exploring the biological role of this RNA.
 
 
 

Cancer Biology and Genetics
  Astrocytoma is the most common type of brain cancer constituting more than half all brain tumors. We found several genes known to be involved in malignancy including Achate-Scute complex like-1 (Drosophila) (ASCL1) and Adedipocyte Enhancer binding Protein-1 (AEBP1) by microarray analysis. Studies are in underway to understand the biology of few of the genes that have shown to get differentially expressed in these cancers with respect to disease progression.

System Level Studies
  In post genomic era, it is clear that biological processes need precise interactions between molecules to execute cellular functions. To address this, we need a comprehensive understanding of the biological system. To uncover these biological networks in the cell, system biology approach is applied. Our group utilizes this approach to understand the complex interactions that lead to tumor development, regulation by non coding RNAs etc.