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Transcription-induced Plectonemic Supercoiled DNA

Periodic Reporting for period 1 - TiPS-DNA (Transcription-induced Plectonemic Supercoiled DNA)

Reporting period: 2018-03-01 to 2020-02-29

Interestingly, DNA is not simply an passive storage device to store genetic information, but is a dynamic physical substrate, whose spatial structure plays an active part in the decoding process. This project aimed to study how 3D structure of genome influences cellular functions in cells. Specifically, I studied the regulatory role of DNA supercoiling, that is the coiling up of DNA due to applied twisting, in the process of gene expression using single-molecule visualization techniques. The major aim was to monitor transcription-induced DNA supercoil generation process in real-time by making time-laps videos. The biological questions that this project aimed to address is a key information for understanding the fundamental architecture of genome, that is critical to not only for the field of biology but for medical research, since perturbing this DNA topology can lead to fatal processes like mis-regulated gene expression, cancer, and developmental and neurodegenerative disorders.
This project has led breakthrough discoveries: firstly, we experimentally verified the DNA looping function of condensin complexes (one of SMCs) via single-molecule imaging [Science, 2018], which previously remained only as a hypothesis. This work had far-reaching impacts on both scientific community and general public, as can be estimated by high citation records (>100 per year) and high altmetric scores (580, top 5% of all the research outputs). Furthermore, I recently discovered that these condensins cooperate to form a novel type of DNA looping structure, named ‘Z-loop’, a mechanism which can drive highly efficient chromosomal compaction compared to single loops [Nature, 2020].
Currently, I am extending this study into several different directions. Firstly, I am investigating the interplay of SMC-driven loop extrusion and DNA supercoiling, the two major DNA structures which consist of chromosomes for all domains of life. My preliminary results show a wealth of intriguing phenomena on how DNA topology can significantly influence the molecular functions of active proteins, which has help me to setup my future research questions as detailed below. Secondly, I am studying the mechanism of loop extrusion on nucleosome bound DNA in order to simulate cellular conditions. My preliminary results discovered unexpected function of SMC proteins which can bypass protein roadblocks as big as its own sizes.

I believe that the potential impact of this proposal is significant and long-standing. The understanding of the spatial structure of chromosomes is one of the hottest field in science right now. And for good reasons: Resolving the spatial architecture of genomes profoundly impacts the core of biology, namely, how information is transferred to biological function. It has remained a tantalizing mystery how chromosomes self organize into specific architectures that vary over the life cycle of a cell. If indeed, as we genuinely expect, will succeed to resolve the basic looping structure of DNA and disentangle the fundamental structure of chromosomes, it may be considered a ground-breaking milestone in science, because it addresses a key element of living cells, the basic packaging structure of the genome which directly governs its biological function.
Schematic of DNA supercoiling present in cells