Analysis of 3D Chromatin Structure Using Super-Resolution Imaging (Alistair Boettiger)

<p>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.</p> <p>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.</p> <p class="md-end-block md-p"> </p> <p class="md-end-block md-p">References</p> <ul class="ul-list"><li class="md-list-item"> <p class="md-end-block md-p">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'>https://doi.org/10.1038/nature16496</a></p> </li> <li class="md-list-item"> <p class="md-end-block md-p">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'>10.1126/science.aau1783</a></p> </li> <li class="md-list-item"> <p class="md-end-block md-p">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'>https://doi.org/10.1038/s41596-020-00478-x</a></p> </li> <li class="md-list-item"> <p class="md-end-block md-p">Rajpurkar, A.R., Mateo, L.J., Murphy, S.E. et al. Deep learning connects DNA traces to transcription to reveal predictive features beyond