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Dr. Yathish J Achar
Home » Genome Architecture
Genome Architecture
Research Interests

Chromatin structural transitions play crucial role in facilitating numerous biological functions. DNA supercoiling is one such transition playing important role in compacting DNA, regulating protein-DNA association and gene expression. Supercoiling is a fundamental property of DNA and is modulated by polymerases, topoisomerases and DNA-bound protein complexes. Winding DNA around its axis in the same direction as helix, introduces positive supercoiling whereas winding in the opposite direction triggers negative supercoil accumulation, a phenomenon well connected with transcription as ‘twin supercoiled domain’. Efficiently transcribed genes are negatively supercoiled, while excessive positive supercoiling will repress the transcription. Since supercoiling of DNA is known to be dynamic, non-covalent and ambiguous topological modifications, tracking inside the nucleus has been challenging. How these topological and structural properties of DNA modulate chromatin function is an important direction to pursue as it also has implications in Genome architecture, Gene expression and DNA editing technologies.

Our main research question is to understand how much of our genomic DNA is double stranded? We wish to question the current thought of considering DNA to be a simple linear polymer molecule. Contrary, we believe, our DNA to be dynamic with regular deformation to its helical structure, generating supercoiling, bending and twisting. These mechanical and physical properties of chromatin along with alternative DNA structures (cruciform, Z-DNA, H-DNA), might play major role in chromosome organization and gene regulations. Variations among these DNA structures are commonly associated with human diseases, ranging from autism to cancer. Detailed understanding of DNA structural variations also provides therapeutical benefits, as genome engineering tools such as CRISPR-Cas are mechanically sensitive to DNA supercoiling.

Figure 1: Our working model, where negative supercoiled regions are melted and single strand regions are intertwined to form cruciform-like structures.

Our research interest is to unravel the link between DNA mechanics and genome organization with specific emphasis on cancer predisposition. Particularly, focuses on following two major themes:

(i) DNA supercoil role in chromatin remodelling during cancer development:

A key feature of the mammalian genome is topologically associated domains (TADs), which partition each interphase chromosomes into mega-base sized territories that exhibit intra-domain interactions but relatively rare inter-domain interactions. TADs are highly conserved among species, cell types and tissues and are notably stable and are non-disruptive during physiological activities. However, TADs can be subject to alterations, especially in the context of human diseases and cancer. TADs are limited by boundaries, enriched with CCCTC-binding factor (CTCF) and cohesion protein complexes which facilitate within DNA-DNA interactions. Deleting or mutating boundary element leads to fusion of two or more TADs or totally new TADs can be formed due to genome rearrangements. Understanding the events through which TADs form and control long-range interactions provide significant insights into how genomic rearrangements in cancer genomes can cause deregulation of oncogenes and tumour suppressors.

Figure 2: Loss of Negative supercoil reduces Top2 complexes, which stabilize and lock cohesin ring (upper panel). This suggests a possibility of loss of stable TAD by either transforming into unstable one or merging with neighbouring unstable TADs. Super-enhancer can activate oncogene as a result of merging of two independent TADs (lower panel.

During transformation into a cancer genome, stable TADs metamorphose into unstable ones. Major reason for such disarray could be due to alteration in DNA mechanics, where negative supercoiled structures could drastically change. Additionally, Cancer cells undergoing metastasis should compromise their 3-D genome architecture, where chromatin is deformed for the benefit of movement across tight spaces. Identifying TADs which are prone to alter its DNA mechanics will shed light of how hierarchical genome architecture is maintained and also provide therapeutic interests.

(ii) DNA structural role in dictating RNA splicing and transcription control:

Introns found to enhance gene expression at different stages of transcription and also translation. However, the cost and benefits of having introns is yet to be fully understood. Introns also contribute for alternative splicing, a phenomenon by which many varieties of mRNAs can be produced by single gene by either including or excluding particular intron. Generally accepted model for alternative splicing is that, the lower elongation rates increase chances of splicing compared to higher elongation rates. Alternative splicing can have prognostic value as most of cancer cells show general as well as cancer-specific variation in splicing events.

Figure 3: DNA supercoil at intron can form secondary DNA structures such as cruciform which are targets for DNA topoisomerase I

Our hypothesis is that exon and introns are distinguishable at DNA supercoil levels, suggesting for separable boundaries. Proteins such as Poly [ADP-ribose] polymerase-1 (PARP1) which are enriched at exon/intron (E/I) boundaries might play a role in supercoil distribution. PARP1 at E/I boundary slows down RNA pol2 at boundaries, suggesting that elongation rate is tightly regulated at the boundaries

We believe, our research topics will provide a decisive contribution in filling the existing gap between the current understandings between DNA in vitro studies and three-dimensional chromatin architecture. Moreover, understanding DNA supercoil and its associated structures at the genome levels would provide detailed insights to molecular understanding of chromatin-DNA beyond the nucleosomes and epigenetics. This offers a novel perspective for understanding cancer development and potential angles for exploring DNA as a therapeutic target.

Contact Information
E-mail: yathish<at>cdfd.org.in
Phone: +91-40-27216105
Fax: +91-40- 27216006
Last updated on: Wednesday, 28th July, 2021

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