“Genome folding in development, ” by Alistair Boettiger, Assistant Professor, Stanford School of Medicine, Department of Developmental Biology, Member of Stanford Bio-X, Member of Stanford Biophysics, Stanford University.
Establishment of different cell types during development requires precise interactions between genes and distal regulatory elements. However, our understanding of what these interactions look like in three dimensions, how they vary across cell types in complex tissue, and how they relate to transcriptional state remain limited. I will describe optical reconstruction of chromatin architecture (ORCA), a microscopy approach to follow the path of DNA in intact nuclei in thousands of cells. We have used this approach to the study the structure of the Hox complex in Drosophila embryos and mouse embryonic stem cells with nanoscale accuracy and genomic resolution as high as 2 kilobases. Simultaneous imaging of nascent transcription allowed direct correlation of DNA folding to RNA expression in single cells. These data can predict functional enhancers by identifying elements whose proximity to a promoter correlate to that promoter’s nascent transcription activity. They also provide new insights into the mechanisms of enhancer-promoter communication. Further, we find extensive cell-type specific 3D folding of the Hox-locus. These distinct folding patterns result in the formation of physical enhancer-promoter domains specifically in cell types containing the active, not inactive, enhancers. I will also describe our work using ORCA in mutant embryos to elucidate the molecular factors which drive this cell-type specific chromatin organization that provides robust control of these critical patterning genes. We believe this approach for high resolution single-cell DNA domain analysis and RNA expression in vivo support a prominent role for 3D chromatin organization in cell identity and will be broadly applicable in other developmental systems.
Monday, February 10, 2020 at 2:30 LSC#3
Host: Dr. Sheila Teves