{"lab": {"@type": ["Lab", "Item"], "correspondence": [{"contact_email": "dG9tb2tvLnlhbWFkYUBub3J0aHdlc3Rlcm4uZWR1", "@id": "/users/3b5a8696-b152-4a12-bcf1-69186d6bb510/", "display_title": "Tomoko Yamada"}], "status": "current", "display_title": "Tomoko Yamada, NW", "uuid": "4e87e04c-6a49-4a71-8240-5fdae2f04b24", "@id": "/labs/tomoko-yamada-lab/", "title": "Tomoko Yamada, NW", "pi": {"error": "no view permissions"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin", "role.lab_submitter", "submits_for.4e87e04c-6a49-4a71-8240-5fdae2f04b24"]}}, "award": {"center_title": "Yamada", "@type": ["Award", "Item"], "description": "NI-OFHHD: The long-term goals of the proposed research are to elucidate mechanisms of three-dimensional genome architecture in the control of neuronal connectivity in the brain. It has recently been found that physiological stimuli including sensory experience or developmental signals remodel neuronal genome architecture in vivo. Strikingly, it's found that long-distance genome interactions massively increase in the developing cerebellum in mice. The discovery of these long-distance interactions formed between genes critical for neuronal differentiation unveils novel nuclear mechanisms by which genome architecture may play a role in the wiring of the brain. These findings raise fundamental questions on the mechanisms and biological functions of these interactions in the brain, which will be addressed in this grant. First, the organizing principles of long-distance genome interactions in the brain will be elucidated. Based on the in vivo findings, the hypothesis that long-distance genomic interactions are organized by specific epigenetic and transcriptional features will be tested. In addition, the study will also test the hypothesis that anchors of long-distance interactions assemble into higher-ordered subnuclear structures including nuclear speckles or Mediator condensates, which function as transcriptionally active hubs. Second, the projcet will define mechanisms by which long-distance interactions are formed in development. The BAF chromatin remodeling complex alters the genome environment to activate or repress transcription and is required for brain development in mice and humans, and its dysregulation results in human neurodevelopmental disorders, including Coffin\u2013Siris syndrome and autism. Based on our preliminary findings, the hypothesis that the BAF complex transiently inhibits formation of long-distance genome interactions in immature neurons of the developing brain will be tested. Following early development, the inhibition of the long-distance interactions might be relieved by the recruitment of specific sets of transcription factors that drive terminal neuron differentiation. This project will test the hypothesis that these transcription regulators, identified using DNA motif analyses, promote the formation of the long-distance genome interactions. Finally, this study will also test the hypothesis that the formation of long-distance genome interactions is necessary for the maturation of neurons in vivo, including making proper connections with their pre- and post-synaptic partners. The proposed research is significant as it will advance our understanding of the mechanisms regulating genome architecture to control neuronal differentiation in mammalian brain. 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It was developed in 2014 as an improvement over the dilution Hi-C method. Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. 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Compared to standard dilution Hi-C, this technique reduces the frequency of random ligation because the ligation is performed <i>in situ</i> inside the nucleus, a constrained space, instead of in solution, where DNA fragments are floating freely. In addition, this protocol can be done more quickly in the lab and was the first to introduce the use of 4-cutter restriction enzymes as opposed to the previous 6-cutters, providing higher resolution.\n</p>\n<p>\nThe protocol involves cross-linking the cells with formaldehyde to form links between physically adjacent DNA regions. The cells are then permeabilized with their nuclei intact. A 4-cutter restriction enzyme is used to digest the chromatin into multiple DNA fragments. The resulting fragments are biotinylated by end filling of the fragments ends. The fragments are then ligated and the DNA is purified and sheared. 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Among these interactions, we identify a nuclear  subcompartment enriched for near-megabase long enhancers and their associated  neuronal long genes encoding synaptic or signaling proteins. Neuronal long genes  are differentially recruited to this enhancer-dense subcompartment to help shape  the transcriptional identities of granule neuron subtypes in the cerebellum.  SPRITE analyses of higher-order genomic interactions, together with IGM-based 3D  genome modeling and imaging approaches, reveal that the enhancer-dense  subcompartment forms prominent nuclear structures, which we term mega-enhancer  bodies. These novel nuclear bodies reside in the nuclear periphery, away from  other transcriptionally active structures, including nuclear speckles located in  the nuclear interior. Together, our findings define additional layers of  higher-order 3D genome organization closely linked to neuronal maturation and  identity in the brain.", "uuid": "dee249a4-3f69-4a9e-b7e2-51c643b449a3", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [], "publications_of_set": [{"ID": "doi:10.1101/2023.07.19.549737", "display_title": "Zhao Z et al. (2023) doi:10.1101/2023.07.19.549737", "journal": "bioRxiv : the preprint server for biology", "abstract": "Dynamic regulation of gene expression plays a key role in establishing the  diverse neuronal cell types in the brain. Recent findings in genome biology  suggest that three-dimensional (3D) genome organization has important, but  mechanistically poorly understood functions in gene transcription. Beyond local  genomic interactions between promoters and enhancers, we find that cerebellar  granule neurons undergoing differentiation in vivo exhibit striking increases in  long-distance genomic interactions between transcriptionally active genomic loci,  which are separated by tens of megabases within a chromosome or located on  different chromosomes. Among these interactions, we identify a nuclear  subcompartment enriched for near-megabase long enhancers and their associated  neuronal long genes encoding synaptic or signaling proteins. Neuronal long genes  are differentially recruited to this enhancer-dense subcompartment to help shape  the transcriptional identities of granule neuron subtypes in the cerebellum.  SPRITE analyses of higher-order genomic interactions, together with IGM-based 3D  genome modeling and imaging approaches, reveal that the enhancer-dense  subcompartment forms prominent nuclear structures, which we term mega-enhancer  bodies. These novel nuclear bodies reside in the nuclear periphery, away from  other transcriptionally active structures, including nuclear speckles located in  the nuclear interior. Together, our findings define additional layers of  higher-order 3D genome organization closely linked to neuronal maturation and  identity in the brain.", "date_published": "2023-07-25", "status": "current", "uuid": "dee249a4-3f69-4a9e-b7e2-51c643b449a3", "@type": ["Publication", "Item"], "authors": ["Zhao Z", "Parra OP", "Musella F", "Scrutton-Alvarado N", "Fujita SI", "Alber F", "Yang Y", "Yamada T"], "title": "Mega-Enhancer Bodies Organize Neuronal Long Genes in the Cerebellum.", "@id": "/publications/dee249a4-3f69-4a9e-b7e2-51c643b449a3/", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "number_of_experiments": 3, "@context": "/terms/", "aggregated-items": {"badges": []}, "validation-errors": []}