All Publications

  • Advances in Chromatin Imaging at Kilobase-Scale Resolution. Trends in genetics : TIG Boettiger, A., Murphy, S. 2020


    It is now widely appreciated that the spatial organization of the genome is nonrandom, and its complex 3D folding has important consequences for many genome processes. Recent developments in multiplexed, super-resolution microscopy have enabled an unprecedented view of the polymeric structure of chromatin - from the loose folds of whole chromosomes to the detailed loops of cis-regulatory elements that regulate gene expression. Facilitated by the use of robotics, microfluidics, and improved approaches to super-resolution, thousands to hundreds of thousands of individual cells can now be analyzed in an individual experiment. This has led to new insights into the nature of genomic structural features identified by sequencing, such as topologically associated domains (TADs), and the nature of enhancer-promoter interactions underlying transcriptional regulation. We review these recent improvements.

    View details for DOI 10.1016/j.tig.2019.12.010

    View details for PubMedID 32007290

  • Visualizing DNA folding and RNA in embryos at single-cell resolution NATURE Mateo, L. J., Murphy, S. E., Hafner, A., Cinquini, I. S., Walker, C. A., Boettiger, A. N. 2019; 568 (7750): 49-+
  • Visualizing DNA folding and RNA in embryos at single-cell resolution. Nature Mateo, L. J., Murphy, S. E., Hafner, A. n., Cinquini, I. S., Walker, C. A., Boettiger, A. N. 2019


    The establishment of cell types during development requires precise interactions between genes and distal regulatory sequences. We have a limited understanding of how these interactions look in three dimensions, vary across cell types in complex tissue, and relate to transcription. Here we describe optical reconstruction of chromatin architecture (ORCA), a method that can trace the DNA path in single cells with nanoscale accuracy and genomic resolution reaching two kilobases. We used ORCA to study a Hox gene cluster in cryosectioned Drosophila embryos and labelled around 30 RNA species in parallel. We identified cell-type-specific physical borders between active and Polycomb-repressed DNA, and unexpected Polycomb-independent borders. Deletion of Polycomb-independent borders led to ectopic enhancer-promoter contacts, aberrant gene expression, and developmental defects. Together, these results illustrate an approach for high-resolution, single-cell DNA domain analysis in vivo, identify domain structures that change with cell identity, and show that border elements contribute to the formation of physical domains in Drosophila.

    View details for PubMedID 30886393

  • Cross-talk between Lysine-Modifying Enzymes Controls Site-Specific DNA Amplifications. Cell Mishra, S. n., Van Rechem, C. n., Pal, S. n., Clarke, T. L., Chakraborty, D. n., Mahan, S. D., Black, J. C., Lawrence, M. S., Daniels, D. L., Whetstine, J. R. 2018


    Acquired chromosomal DNA amplifications are features of many tumors. Although overexpression and stabilization of the histone H3 lysine 9/36 (H3K9/36) tri-demethylase KDM4A generates transient site-specific copy number gains (TSSGs), additional mechanisms directly controlling site-specific DNA copy gains are not well defined. In this study, we uncover a collection of H3K4-modifying chromatin regulators that function with H3K9 and H3K36 regulators to orchestrate TSSGs. Specifically, the H3K4 tri-demethylase KDM5A and specific COMPASS/KMT2 H3K4 methyltransferases modulate different TSSG loci through H3K4 methylation states and KDM4A recruitment. Furthermore, a distinct chromatin modifier network, MLL1-KDM4B-KDM5B, controls copy number regulation at a specific genomic locus in a KDM4A-independent manner. These pathways comprise an epigenetic addressing system for defining site-specific DNA rereplication and amplifications.

    View details for DOI 10.1016/j.cell.2018.06.018

    View details for PubMedID 30057114