Dr. Madhulika Srivastava

Role of enhancers in genome organization and function: Enhancers are the vanguards of tissue specific gene regulation but the mechanisms underlying their ability to activate specific cognate promoters are diverse and not completely understood. Our recent studies have demonstrated an unambiguous role of enhancer Eb in defining TCRb location relative to chromosome territory. The ability to reposition the target locus relative to chromosome territory highlights a novel aspect pertaining to activity of enhancers which may contribute to their ability to regulate gene expression and adds to the diversity of mechanisms underlying enhancer activity. Further, enhancers are well known as critical regulators of chromatin accessibility. Our observations support the idea that enhancers also influence intranuclear movements of loci relative to chromosome territory. This has implications for understanding the role of enhancers in three-dimensional genome organization and function and provides a useful start point to gain insights in understanding how intranuclear positions of genes change during development. 

Role of CTCF in chromatin organization : CTCF, a DNA binding protein with multifunctional attributes, is an important contributor to chromatin organization. Global analysis by ChIP-Seq and ChIA-PET has demonstrated the presence of several thousand CTCF binding sites in the human and mouse genomes and emphasized their importance in defining chromatin looping patterns critical for specific regulation of genes.  Understanding about the role and mechanisms of CTCF based higher order chromatin organization has emerged based on quest to understand transcriptional regulation. In addition, higher order chromatin organization is also critically important for VDJ recombination at antigen receptor loci (Igh, Igk, TCRa/d and TCRb) in developing B-cells and T-cells and each of these loci have several CTCF binding sites. Considering the diverse and multifunctional attributes of CTCF, current efforts in the lab focus on understanding different aspects underlying CTCF based regulation of transcription and VDJ recombination. Our chromosome conformation capture analysis indicated that CTCF plays an important role in VDJ recombination at TCRb locus. It mediates long-range chromatin looping interactions important for establishment of recombination center as well as facilitates the spatial proximity of TCRb variable gene segments to the recombination center. Our analysis also suggests that even mild changes in the CTCF-based chromatin organization, that may arise due to mutations or epigenetic aberrations, can have profound functional consequences for gene expression.