All Publications

  • Polycomb-mediated genome architecture enables long-range spreading of H3K27 methylation. Proceedings of the National Academy of Sciences of the United States of America Kraft, K., Yost, K. E., Murphy, S. E., Magg, A., Long, Y., Corces, M. R., Granja, J. M., Wittler, L., Mundlos, S., Cech, T. R., Boettiger, A. N., Chang, H. Y. 2022; 119 (22): e2201883119


    SignificanceThe relationship between long-range Polycomb-associated chromatin contacts and the linear propagation of histone H3 lysine 27 trimethylation (H3K27me3) by Polycomb repressive complex 2 (PRC2) is not well-characterized. Here, we nominate a role for developmental loci as genomic architectural elements that enable long-range spreading of H3K27me3. Polycomb-associated loops are disrupted upon loss of PRC2 binding and deletion of loop anchors results in alterations of H3K27me3 deposition and ectopic gene expression. These results suggest that Polycomb-mediated genome architecture is important for gene repression during embryonic development.

    View details for DOI 10.1073/pnas.2201883119

    View details for PubMedID 35617427

  • Deep learning connects DNA traces to transcription to reveal predictive features beyond enhancer-promoter contact. Nature communications Rajpurkar, A. R., Mateo, L. J., Murphy, S. E., Boettiger, A. N. 2021; 12 (1): 3423


    Chromatin architecture plays an important role in gene regulation. Recent advances in super-resolution microscopy have made it possible to measure chromatin 3D structure and transcription in thousands of single cells. However, leveraging these complex data sets with a computationally unbiased method has been challenging. Here, we present a deep learning-based approach to better understand to what degree chromatin structure relates to transcriptional state of individual cells. Furthermore, we explore methods to "unpack the black box" to determine in an unbiased manner which structural features of chromatin regulation are most important for gene expression state. We apply this approach to an Optical Reconstruction of Chromatin Architecture dataset of the Bithorax gene cluster in Drosophila and show it outperforms previous contact-focused methods in predicting expression state from 3D structure. We find the structural information is distributed across the domain, overlapping and extending beyond domains identified by prior genetic analyses. Individual enhancer-promoter interactions are a minor contributor to predictions of activity.

    View details for DOI 10.1038/s41467-021-23831-4

    View details for PubMedID 34103507

  • The lysine demethylase KDM4A controls the cell-cycle expression of replicative canonical histone genes BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS Van Rechem, C., Ji, F., Mishra, S., Chakraborty, D., Murphy, S. E., Dillingham, M. E., Sadreyev, R., Whetstine, J. R. 2020; 1863 (10): 194624


    Chromatin modulation provides a key checkpoint for controlling cell cycle regulated gene networks. The replicative canonical histone genes are one such gene family under tight regulation during cell division. These genes are most highly expressed during S phase when histones are needed to chromatinize the new DNA template. While this fact has been known for a while, limited knowledge exists about the specific chromatin regulators controlling their temporal expression during cell cycle. Since histones and their associated mutations are emerging as major players in diseases such as cancer, identifying the chromatin factors modulating their expression is critical. The histone lysine tri-demethylase KDM4A is regulated over cell cycle and plays a direct role in DNA replication timing, site-specific rereplication, and DNA amplifications during S phase. Here, we establish an unappreciated role for the catalytically active KDM4A in directly regulating canonical replicative histone gene networks during cell cycle. Of interest, we further demonstrate that KDM4A interacts with proteins controlling histone expression and RNA processing (i.e., hnRNPUL1 and FUS/TLS). Together, this study provides a new function for KDM4A in modulating canonical histone gene expression.

    View details for DOI 10.1016/j.bbagrm.2020.194624

    View details for Web of Science ID 000574417000005

    View details for PubMedID 32798738

  • 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-+
  • 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