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5 Janelia Publications

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    10/27/22 | Spatial organization of the 3D genome encodes gene co-expression programs in single cells
    Peng Dong , Shu Zhang , Liangqi Xie , Lihua Wang , Andrew L. Lemire , Arthur D. Lander , Howard Y. Chang , Zhe J. Liu
    bioRxiv. 2022 Oct 27:. doi: 10.1101/2022.10.26.513917

    Deconstructing the mechanism by which the 3D genome encodes genetic information to generate diverse cell types during animal development is a major challenge in biology. The contrast between the elimination of chromatin loops and domains upon Cohesin loss and the lack of downstream gene expression changes at the cell population level instigates intense debates regarding the structure-function relationship between genome organization and gene regulation. Here, by analyzing single cells after acute Cohesin removal with sequencing and spatial genome imaging techniques, we discover that, instead of dictating population-wide gene expression levels, 3D genome topology mediated by Cohesin safeguards long-range gene co-expression correlations in single cells. Notably, Cohesin loss induces gene co-activation and chromatin co-opening between active domains in cis up to tens of megabase apart, far beyond the typical length scale of enhancer-promoter communication. In addition, Cohesin separates Mediator protein hubs, prevents active genes in cis from localizing into shared hubs and blocks intersegment transfer of diverse transcriptional regulators. Together, these results support that spatial organization of the 3D genome orchestrates dynamic long-range gene and chromatin co-regulation in single living cells.

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    09/19/22 | The evolutionary dynamics of extrachromosomal DNA in human cancers.
    Lange JT, Rose JC, Chen CY, Pichugin Y, Xie L, Tang J, Hung KL, Yost KE, Shi Q, Erb ML, Rajkumar U, Wu S, Taschner-Mandl S, Bernkopf M, Swanton C, Liu Z, Huang W, Chang HY, Bafna V, Henssen AG, Werner B, Mischel PS
    Nature Genetics. 2022 Sep 19:. doi: 10.1038/s41588-022-01177-x

    Oncogene amplification on extrachromosomal DNA (ecDNA) is a common event, driving aggressive tumor growth, drug resistance and shorter survival. Currently, the impact of nonchromosomal oncogene inheritance-random identity by descent-is poorly understood. Also unclear is the impact of ecDNA on somatic variation and selection. Here integrating theoretical models of random segregation, unbiased image analysis, CRISPR-based ecDNA tagging with live-cell imaging and CRISPR-C, we demonstrate that random ecDNA inheritance results in extensive intratumoral ecDNA copy number heterogeneity and rapid adaptation to metabolic stress and targeted treatment. Observed ecDNAs benefit host cell survival or growth and can change within a single cell cycle. ecDNA inheritance can predict, a priori, some of the aggressive features of ecDNA-containing cancers. These properties are facilitated by the ability of ecDNA to rapidly adapt genomes in a way that is not possible through chromosomal oncogene amplification. These results show how the nonchromosomal random inheritance pattern of ecDNA contributes to poor outcomes for patients with cancer.

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    06/06/22 | Direct Observation of Compartment-Specific Localization and Dynamics of Voltage-Gated Sodium Channels.
    Liu H, Wang H, Pitt GS, Liu ZJ
    Journal of Neuroscience. 2022 Jun 06:. doi: 10.1523/JNEUROSCI.0086-22.2022

    Brain enriched voltage-gated sodium channel (VGSC) Na1.2 and Na1.6 are critical for electrical signaling in the central nervous system. Previous studies have extensively characterized cell-type specific expression and electrophysiological properties of these two VGSCs and how their differences contribute to fine-tuning of neuronal excitability. However, due to lack of reliable labeling and imaging methods, the sub-cellular localization and dynamics of these homologous Na1.2 and Na1.6 channels remain understudied. To overcome this challenge, we combined genome editing, super-resolution and live-cell single molecule imaging to probe subcellular composition, relative abundances and trafficking dynamics of Na1.2 and Na1.6 in cultured mouse and rat neurons and in male and female mouse brain. We discovered a previously uncharacterized trafficking pathway that targets Na1.2 to the distal axon of unmyelinated neurons. This pathway utilizes distinct signals residing in the intracellular loop 1 (ICL1) between transmembrane domain I and II to suppress the retention of Na1.2 in the axon initial segment (AIS) and facilitate its membrane loading at the distal axon. As mouse pyramidal neurons undergo myelination, Na1.2 is gradually excluded from the distal axon as Na1.6 becomes the dominant VGSC in the axon initial segment and nodes of Ranvier. In addition, we revealed exquisite developmental regulation of Na1.2 and Na1.6 localizations in the axon initial segment and dendrites, clarifying the molecular identity of sodium channels in these subcellular compartments. Together, these results unveiled compartment-specific localizations and trafficking mechanisms for VGSCs, which could be regulated separately to modulate membrane excitability in the brain.Direct observation of endogenous voltage-gated sodium channels reveals a previously uncharacterized distal axon targeting mechanism and the molecular identity of sodium channels in distinct subcellular compartments.

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    05/29/22 | Plasticity-induced actin polymerization in the dendritic shaft regulates intracellular AMPA receptor trafficking.
    V. C. Wong , P.R. Houlihan , H. Liu , D. Walpita , M.C. DeSantis , Z. Liu , E. K. O’Shea
    bioRxiv. 2022 May 29:. doi: 10.1101/2022.05.29.493906

    AMPA-type receptors (AMPARs) are rapidly inserted into synapses undergoing long-term potentiation (LTP) to increase synaptic transmission, but how AMPAR-containing vesicles are selectively trafficked to these synapses during LTP is not known. Here we developed a strategy to label AMPAR GluA1 subunits expressed from the endogenous loci of rat hippocampal neurons such that the motion of GluA1-containing vesicles in time-lapse sequences can be characterized using single-particle tracking and mathematical modeling. We find that GluA1-containing vesicles are confined and concentrated near sites of stimulation-induced plasticity. We show that confinement is mediated by actin polymerization, which hinders the active transport of GluA1-containing vesicles along the length of the dendritic shaft by modulating the rheological properties of the cytoplasm. Actin polymerization also facilitates myosin-mediated transport of GluA1-containing vesicles to exocytic sites. We conclude that neurons utilize F-actin to increase vesicular GluA1 reservoirs and promote exocytosis proximal to the sites of neuronal activity.

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    04/11/22 | BRD2 compartmentalizes the accessible genome.
    Xie L, Dong P, Qi Y, Hsieh TS, English BP, Jung S, Chen X, De Marzio M, Casellas R, Chang HY, Zhang B, Tjian R, Liu Z
    Nature Genetics. 2022 Apr 11;54(4):481-491. doi: 10.1038/s41588-022-01044-9

    Mammalian chromosomes are organized into megabase-sized compartments that are further subdivided into topologically associating domains (TADs). While the formation of TADs is dependent on cohesin, the mechanism behind compartmentalization remains enigmatic. Here, we show that the bromodomain and extraterminal (BET) family scaffold protein BRD2 promotes spatial mixing and compartmentalization of active chromatin after cohesin loss. This activity is independent of transcription but requires BRD2 to recognize acetylated targets through its double bromodomain and interact with binding partners with its low-complexity domain. Notably, genome compartmentalization mediated by BRD2 is antagonized on the one hand by cohesin and on the other hand by the BET homolog protein BRD4, both of which inhibit BRD2 binding to chromatin. Polymer simulation of our data supports a BRD2-cohesin interplay model of nuclear topology, in which genome compartmentalization results from a competition between loop extrusion and chromatin-state-specific affinity interactions.

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