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Dynamic Molecular Systems: Westlake x Science Joint Online Symposium #4
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On March 31st 2023, over 33,600 viewers from around the world enjoyed the fourth part of our live, online symposium series jointly organized by Science/AAAS and Westlake University, entitled “Dynamic Molecular Systems”.
World-renowned researchers Dr. Daniel R. Larson (NIH/NCI), Dr. Anders Sejr Hansen (MIT) and Dr. Allon Moshe Klein (Harvard University) divulged and discussed at length their research, latest insights and technology in the dynamic molecular behaviors that underlie the essential functions of all living systems. The symposium was co-chaired by Dr. Yihan Wan (Westlake University) and by Dr. Bryan Ray (Science/AAAS) who facilitated the discussions and provided greater depth to the dialogue and Q&A sections.
The online symposium series promotes a platform for open dialogue and a discussion of topics and cutting-edge ideas. Global audience members comprised of fellow researchers, academics, scientists and students from universities, hospitals, scientific research institutions and pharmaceutical companies, who were actively encouraged to submit their questions and ideas surrounding the future directions of the research field to the speakers.
Dr. Daniel R. Larson, National Institutes of Health / National Cancer Institute
Topic: “The Dynamic Spliceosome”
Dr. Anders Sejr Hansen, Massachusetts Institute of Technology
Topic: “Dynamics of 3D Genome Structure and Function”
Dr. Allon Moshe Klein, Harvard University
Topic: “Learning cell dynamics and fate biases from single cell transcriptomics and lineage tracing”
Dr. Yihan Wan, Principal Investigator, School of Life Sciences, Westlake University
Dr. Bryan Ray, Senior Editor of Science/American Association for the Advancement of Science
Dynamic molecular behaviors underlie the function of all living systems. Understanding the nature of dynamic molecular behaviors can reveal mechanisms explaining how biological macromolecules perform their functions and regulate cellular activities. Traditional biochemical analyses have taken snapshots at a particular moment in time of the biochemical properties of cells. Only recently have technologies in microscopy and the development of molecular probes, computer modeling, and the like allowed us to follow processes like gene regulation in real-time in living cells.
Dr. Daniel R. Larson, Senior Investigator in the Laboratory of Receptor Biology and Gene Expression at the National Institutes of Health / National Cancer Institute, opened the symposium with his talk focusing on the ‘Dynamic Spliceosome’.
Dynamic imaging of nascent RNAs provides new perspectives on the transcription and splicing of endogenous human genes. Dr. Larson's lab achieved high-throughput single-molecule imaging of nascent RNAs to trace transcription dynamics. They revealed the general principle of transcription kinetics and the stochasticity of splice site selection. To further illustrate the spliceosome and splicing dynamics, Larson’s lab focuses on one of the spliceosomal protein -- U2AF1. U2AF1 is an important protein during spliceosome assembly and is crucial in 3' splice site recognition. Using 3D orbital tracking microscopy, Larson’s lab measured the binding dynamics of U2AF protein and recorded the splicing dynamics of nascent RNA simultaneously. Their results indicate a kinetic proofreading process during E-complex and A-complex conversion. As the cryo-EM has gradually resolved the structure and assembly process of the spliceosome, the single-molecule live cell imaging techniques are bringing new perspectives on the dynamics of splicing processes.
The next speaker, Dr. Anders Sejr Hansen from the Department of Biological Engineering at Massachusetts Institute of Technology, discussed the 'Dynamics of 3D Genome Structure and Function'.
Mammalian genomes are folded into topologically associating domains (TADs) by cohesin and CTCF through the "loop extrusion" process. The 3D genome structure regulates gene expression, somatic cell recombination, and DNA repair. However, the real-time dynamics of loop formation and stability are still unknown.
Dr. Hansen started by asking how the genome connects enhancers to corresponding genes. Two existing models explain this problem to a certain extent. One is the "TAD model" based on the 3D structure of chromatin, and the enhancer-promoter interaction in TAD promotes specific gene expression; the second is the classical model, including like-kind interactions and many-to-many interactions. To verify the "TAD model," Dr. Hansen marked the TAD containing the Fbn2 gene in mouse embryonic stem cells and used super-resolution live cell imaging to track and simulate the dynamics of chromatin loops in real-time. They observed that only 3% ~ 6% of the time the TAD was fully looped, and the loops only lasted about 10 to 30 minutes.
Unlike the snapshot captured chromatin loops in previous studies, the dynamic loop extrusion model suggests that enhancer-promoter interactions may depend more on cohesin-mediated incomplete looping within TADs, rather than a complete CTCF-CTCF loop.
To verify the second model, Dr. Hansen developed the RCMC technology, which generates ultra-high-resolution 3D genomic association map. RCMC defines the newly discovered microcompartments that regulates enhancer-promoter and promoter-promoter interactions, and this mechanism is largely independent of "loop extrusion" and transcription. Finally, Dr. Hansen suggested that the insulator model and many-to-many enhancer-promoters may jointly determine the gene expression promoted by distal enhancers. By developing dynamic chromatin loop imaging technology and new 3D genome capture technology, Dr. Hansen discovered the chromatin loop dynamics and new structures of the 3D genome. His labs’ work improved the enhancer-promoter interaction model from a dynamic perspective, which has helped us to understand how mammalian gene expression is regulated.
The final speaker, Dr. Allon Moshe Klein, Associate Professor of Systems Biology at Harvard University, shared his research surrounding ‘Learning cell dynamics and fate biases from single cell transcriptomics and lineage tracing’.
Dr. Klein's group applied single-cell transcriptome sequencing technology to study cell fate determination in the hematopoietic system. Through single-time point sampling analysis, they obtained the potential developmental trajectories of the hematopoietic system. However, Dr. Klein found ambiguous regions in the developmental trajectory re-constructed by the transcriptome at a single time point. For example, due to overlap in the fate determination trajectory between monocytes and neutrophils, it cannot determine the exact time of cell fate determination and whether there is a period of dynamic changes in cell fate. Therefore, they developed the LARRY technology, where each cell was given a specific barcode. The differentiation potential and differentiation process of the stem cell were inferred by comparing the cells with the same barcode.
Comparing the fate-time dynamic information with the single-cell transcriptome analysis sampled at a single time point, they came to the following conclusions: First, LARRY can show the predetermined fate decision stage. Second, differentiation trajectories of different stem cell clones could converge. Third, Dr. Klein pointed out that only 60% of cases of cell fate determination can be predicted by single-cell transcriptome analysis at fixed time points.
Hence, Dr. Klein concluded: first, simple transcriptome analysis cannot fully illustrate the occurrence of cell fate determination; second, the differentiation of cells is not a "tree diagram" with only one path, but the convergence of multiple trajectories; third, there are some "hidden variables" in addition to the transcriptome data that determine the fate of cells. Finally, Dr. Klein also briefly introduced his group's latest algorithm, Cospar, which combines lineage and transcriptome information for cell fate prediction.
The symposium concluded with an open Q&A discussion section whereby insightful and innovative ideas were shared between the speakers and co-chairs. To enjoy the full playback and open discussion of ‘Dynamic Molecular Systems’ jointly organized by Science/AAAS and Westlake University, please visit: https://live.vhall.com/v3/lives/watch/703086320
We would like to sincerely thank the three distinguished guest speakers Dr. Daniel R. Larson, Dr. Anders Sejr Hansen, Dr. Allon Moshe Klein for their time and openness in sharing their latest research and ideas in the field of ‘dynamic molecular systems’, as well as co-chairs Dr. Yihan Wan and Dr. Bryan Ray for their expertise and added insights. We would also like to extend our sincere thanks to all audience members who joined live and helped facilitate an informative and engaging symposium shared across the world.
Please check out our previous parts to this symposium series and we very much look forward to you joining us in our upcoming parts, as we work towards an open and global platform for scientific discussion and innovation.
Science/AAAS and Westlake University Symposium Series
Part 1 | Gene Editing | https://live.vhall.com/v3/lives/watch/925591016
Part 2 | Biomolecular Condensates | https://live.vhall.com/v3/lives/watch/340760384
Part 3 | Protein Engineering | https://live.vhall.com/v3/lives/watch/537973129
Part 4 | Dynamic Molecular Systems | https://live.vhall.com/v3/lives/watch/703086320
Part 5 | New Insights into Host–Virus Interactions | 08:30-10:30am, Wednesday, 26 April 2023 (US Eastern Time) // 20:30-22:30pm, Wednesday, 26 April 2023 (UTC+8)
Dynamic Molecular Systems: Westlake x Science Joint Online Symposium #4
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