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Biophysical Modeling of 3-D Genome Organization (Leonid Mirny)
저장한 시리즈 ("피드 비활성화" status)
When? This feed was archived on September 02, 2022 22:36 (). Last successful fetch was on July 28, 2022 16:40 ()
Why? 피드 비활성화 status. 잠시 서버에 문제가 발생해 팟캐스트를 불러오지 못합니다.
What now? You might be able to find a more up-to-date version using the search function. This series will no longer be checked for updates. If you believe this to be in error, please check if the publisher's feed link below is valid and contact support to request the feed be restored or if you have any other concerns about this.
Manage episode 263639865 series 2369335
In this episode of the Epigenetics Podcast, we caught up with Leonid Mirny, Ph.D., from MIT to talk about his work on biophysical modeling of the 3-D structure of chromatin.
Leonid Mirny was part of the initial Hi-C paper titled "Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome" that was published in 2009 in the journal Science. Since then, technology has evolved and Dr. Mirny's group has developed a method called Micro-C that improves the Hi-C protocol by using MNase digestion to increase the resolution to nucleosomal level. This led to the visualization of interactions that were already predicted by his previous biophysical models.
Furthermore, Leonid Mirny worked on finding the mechanism by which chromatin loops are formed. He and his team proposed that loop extrusion underlies TAD formation. In this process, factors like cohesin and CTCF form progressively larger loops but stall at TAD boundaries due to interactions of CTCF with TAD boundaries. He used polymer simulations to show that this model produces TADs and finer-scale features of Hi-C data. Each TAD emerges from multiple loops dynamically formed through extrusion, contrary to typical illustrations of single static loops.
In this interview, we chatted with Dr. Mirny about the details of Hi-C, the development of Micro-C and how it compares to Hi-C, and how biophysical modeling helps to unravel the mechanisms behind loop extrusion.
References
- Grigory Kolesov, Zeba Wunderlich, … Leonid A. Mirny (2007) How gene order is influenced by the biophysics of transcription regulation (Proceedings of the National Academy of Sciences) DOI: 10.1073/pnas.0700672104
- Erez Lieberman-Aiden, Nynke L. van Berkum, … Job Dekker (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome (Science (New York, N.Y.)) DOI: 10.1126/science.1181369
- Geoffrey Fudenberg, Maxim Imakaev, … Leonid A. Mirny (2016) Formation of Chromosomal Domains by Loop Extrusion (Cell Reports) DOI: 10.1016/j.celrep.2016.04.085
- Johannes Nuebler, Geoffrey Fudenberg, … Leonid A. Mirny (2018) Chromatin organization by an interplay of loop extrusion and compartmental segregation (Proceedings of the National Academy of Sciences) DOI: 10.1073/pnas.1717730115
- Martin Falk, Yana Feodorova, … Leonid A. Mirny (2019) Heterochromatin drives compartmentalization of inverted and conventional nuclei (Nature) DOI: 10.1038/s41586-019-1275-3
Contact
- Active Motif on Twitter
- Epigenetics Podcast on Twitter
- Active Motif on Linked-In
- Active Motif on Facebook
- eMail: podcast@activemotif.com
80 에피소드
저장한 시리즈 ("피드 비활성화" status)
When? This feed was archived on September 02, 2022 22:36 (). Last successful fetch was on July 28, 2022 16:40 ()
Why? 피드 비활성화 status. 잠시 서버에 문제가 발생해 팟캐스트를 불러오지 못합니다.
What now? You might be able to find a more up-to-date version using the search function. This series will no longer be checked for updates. If you believe this to be in error, please check if the publisher's feed link below is valid and contact support to request the feed be restored or if you have any other concerns about this.
Manage episode 263639865 series 2369335
In this episode of the Epigenetics Podcast, we caught up with Leonid Mirny, Ph.D., from MIT to talk about his work on biophysical modeling of the 3-D structure of chromatin.
Leonid Mirny was part of the initial Hi-C paper titled "Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome" that was published in 2009 in the journal Science. Since then, technology has evolved and Dr. Mirny's group has developed a method called Micro-C that improves the Hi-C protocol by using MNase digestion to increase the resolution to nucleosomal level. This led to the visualization of interactions that were already predicted by his previous biophysical models.
Furthermore, Leonid Mirny worked on finding the mechanism by which chromatin loops are formed. He and his team proposed that loop extrusion underlies TAD formation. In this process, factors like cohesin and CTCF form progressively larger loops but stall at TAD boundaries due to interactions of CTCF with TAD boundaries. He used polymer simulations to show that this model produces TADs and finer-scale features of Hi-C data. Each TAD emerges from multiple loops dynamically formed through extrusion, contrary to typical illustrations of single static loops.
In this interview, we chatted with Dr. Mirny about the details of Hi-C, the development of Micro-C and how it compares to Hi-C, and how biophysical modeling helps to unravel the mechanisms behind loop extrusion.
References
- Grigory Kolesov, Zeba Wunderlich, … Leonid A. Mirny (2007) How gene order is influenced by the biophysics of transcription regulation (Proceedings of the National Academy of Sciences) DOI: 10.1073/pnas.0700672104
- Erez Lieberman-Aiden, Nynke L. van Berkum, … Job Dekker (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome (Science (New York, N.Y.)) DOI: 10.1126/science.1181369
- Geoffrey Fudenberg, Maxim Imakaev, … Leonid A. Mirny (2016) Formation of Chromosomal Domains by Loop Extrusion (Cell Reports) DOI: 10.1016/j.celrep.2016.04.085
- Johannes Nuebler, Geoffrey Fudenberg, … Leonid A. Mirny (2018) Chromatin organization by an interplay of loop extrusion and compartmental segregation (Proceedings of the National Academy of Sciences) DOI: 10.1073/pnas.1717730115
- Martin Falk, Yana Feodorova, … Leonid A. Mirny (2019) Heterochromatin drives compartmentalization of inverted and conventional nuclei (Nature) DOI: 10.1038/s41586-019-1275-3
Contact
- Active Motif on Twitter
- Epigenetics Podcast on Twitter
- Active Motif on Linked-In
- Active Motif on Facebook
- eMail: podcast@activemotif.com
80 에피소드
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