Alistair Boettiger's guest appearances

Alistair Boettiger

Epigenetics Podcast

OwlTail

In this episode of the Epigenetics Podcast, we talked with Alistair Boettiger from Stanford University about his work on the analysis of 3D chromatin structure of single cells using super-resolution imaging. Alistair Boettiger and his team focus on developing advanced microscopy techniques to understand gene regulation at the level of 3D genome organization. They have developed Optical Reconstruction of Chromatin Architecture (ORCA), a microscopy approach to trace the 3-dimensional DNA path in the nucleus with genomic resolution down to 2 kb and a throughput of ~10,000 cells per experiment. These methods enable the identification of structural features with comparable resolution to Hi-C, while the advantages of microscopy such as single cell resolution and multimodal measurements remain.   References  Boettiger, A., Bintu, B., Moffitt, J. et al. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature 529, 418–422 (2016). https://doi.org/10.1038/nature16496   Bogdan Bintu et al., Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 362, eaau1783 (2018). DOI:10.1126/science.aau1783   Mateo, L.J., Sinnott-Armstrong, N. &amp; Boettiger, A.N. Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA. Nat Protoc 16, 1647–1713 (2021). https://doi.org/10.1038/s41596-020-00478-x   Rajpurkar, A.R., Mateo, L.J., Murphy, S.E. et al. Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer–promoter contact. Nat Commun 12, 3423 (2021). https://doi.org/10.1038/s41467-021-23831-4   Tzu-Chiao Hung, David M. Kingsley, &amp; Alistair Boettiger. (2023). Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development. BioRxiv, 2023.02.06.527380. https://doi.org/10.1101/2023.02.06.527380   Hafner, A., Park, M., Berger, S. E., Murphy, S. E., Nora, E. P., &amp; Boettiger, A. N. (2023). Loop stacking organizes genome folding from TADs to chromosomes. Molecular cell, 83(9), 1377–1392.e6. https://doi.org/10.1016/j.molcel.2023.04.008     Related Episodes  Hi-C and Three-Dimensional Genome Sequencing (Erez Lieberman Aiden)   Unraveling Mechanisms of Chromosome Formation (Job Dekker)   Biophysical Modeling of 3-D Genome Organization (Leonid Mirny)      Contact  Epigenetics Podcast on Twitter   Epigenetics Podcast on Instagram   Epigenetics Podcast on Mastodon   Active Motif on Twitter   Active Motif on LinkedIn   Email: podcast@activemotif.com   

In this episode of the Epigenetics Podcast, we talked with Alistair Boettiger from Stanford University about his work on the analysis of 3D chromatin structure of single cells using super-resolution imaging. Alistair Boettiger and his team focus on developing advanced microscopy techniques to understand gene regulation at the level of 3D genome organization. They have developed Optical Reconstruction of Chromatin Architecture (ORCA), a microscopy approach to trace the 3-dimensional DNA path in the nucleus with genomic resolution down to 2 kb and a throughput of ~10,000 cells per experiment. These methods enable the identification of structural features with comparable resolution to Hi-C, while the advantages of microscopy such as single cell resolution and multimodal measurements remain. References <ul><li> Boettiger, A., Bintu, B., Moffitt, J. et al. Super-resolution imaging reveals distinct chromatin folding for different epigenetic states. Nature 529, 418–422 (2016). <a href="https://doi.org/10.1038/nature16496" rel="nofollow" target="_blank">https://doi.org/10.1038/nature16496</a> </li> <li> Bogdan Bintu et al., Super-resolution chromatin tracing reveals domains and cooperative interactions in single cells. Science 362, eaau1783 (2018). DOI:<a href="https://doi.org/10.1126/science.aau1783" rel="nofollow" target="_blank">10.1126/science.aau1783</a> </li> <li> Mateo, L.J., Sinnott-Armstrong, N. &amp; Boettiger, A.N. Tracing DNA paths and RNA profiles in cultured cells and tissues with ORCA. Nat Protoc 16, 1647–1713 (2021). <a href="https://doi.org/10.1038/s41596-020-00478-x" rel="nofollow" target="_blank">https://doi.org/10.1038/s41596-020-00478-x</a> </li> <li> Rajpurkar, A.R., Mateo, L.J., Murphy, S.E. et al. Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer–promoter contact. Nat Commun 12, 3423 (2021). <a href="https://doi.org/10.1038/s41467-021-23831-4" rel="nofollow" target="_blank">https://doi.org/10.1038/s41467-021-23831-4</a> </li> <li> Tzu-Chiao Hung, David M. Kingsley, &amp; Alistair Boettiger. (2023). Boundary stacking interactions enable cross-TAD enhancer-promoter communication during limb development. BioRxiv, 2023.02.06.527380. <a href="https://doi.org/10.1101/2023.02.06.527380" rel="nofollow" target="_blank">https://doi.org/10.1101/2023.02.06.527380</a> </li> <li> Hafner, A., Park, M., Berger, S. E., Murphy, S. E., Nora, E. P., &amp; Boettiger, A. N. (2023). Loop stacking organizes genome folding from TADs to chromosomes. Molecular cell, 83(9), 1377–1392.e6. <a href="https://doi.org/10.1016/j.molcel.2023.04.008" rel="nofollow" target="_blank">https://doi.org/10.1016/j.molcel.2023.04.008</a> </li> </ul> Related Episodes <ul><li> <a href="https://www.activemotif.com/podcasts#erez-lieberman-aiden" rel="nofollow" target="_blank">Hi-C and Three-Dimensional Genome Sequencing (Erez Lieberman Aiden)</a> </li> <li> <a href="https://www.activemotif.com/podcasts#job-dekker" rel="nofollow" target="_blank">Unraveling Mechanisms of Chromosome Formation (Job Dekker)</a> </li> <li> <a href="https://www.activemotif.com/podcasts#leonid-mirny" rel="nofollow" target="_blank">Biophysical Modeling of 3-D Genome Organization (Leonid Mirny)</a> </li> </ul> <ul><li> Contact <ul><li> <a href="https://twitter.com/epigenetics_pod" rel="nofollow" target="_blank">Epigenetics Podcast on Twitter</a> </li> <li> <a href="https://www.instagram.com/epigenetics_pod/" rel="nofollow" target="_blank">Epigenetics Podcast on Instagram</a> </li> <li> <a href="https://podcasts.social/@epigenetics_pod" rel="nofollow" target="_blank">Epigenetics Podcast on Mastodon</a> </li> <li> <a href="https://twitter.com/activemotif" rel="nofollow" target="_blank">Active Motif on Twitter</a> </li> <li> <a href="https://www.linkedin.com/company-beta/35651/" rel="nofollow" target="_blank">Active Motif on LinkedIn</a> </li> <li> Email: <a href="mailto:podcast@activemotif.com">podcast@activemotif.com</a> </li> </ul> </li></ul>