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Mistargeted SHM activities can lead to mutations and chromosomal translocations that contribute to the development of B cell lymphoma. Recent studies suggest that the three-dimensional (3D) organization of the genome regulates SHM targeting and mistargeting. However, it is largely unknown how the genome is spatially organized across multiple length scales in GC B cell development and lymphoma, and how 3D genome architecture mechanistically affects the targeting and mistargeting of SHM. Conventional approaches cannot address these questions in the primary GC tissue environment due to technical limitations. Here, we propose to apply a new method recently developed by our team, termed Multiplexed Imaging of Nucleome Architectures (MINA), to primary human tonsil tissue samples and malignant GC-derived human B cell lymphomas. We will investigate and test the association between SHM susceptibility and a variety of 3D nucleome architectures, including topologically associating domain (TAD) architecture, phase separation, and nuclear positioning of genomic regions relative to nuclear lamina, nucleoli, and nuclear pores. Through targeted genomic perturbations in human B cell lymphomas, we will test specific hypotheses linking SHM targeting elements to elevated chromatin looping interactions, TAD phase separation, nuclear pore proximity, and mutation vulnerability. Our study will significantly advance our understanding of the role of 3D genome architecture and nuclear organization in GC B cells undergoing SHM in both the developmental and tumorigenesis contexts. 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"Yale-Wang_lab_MINA_Nikon_Eclipse_Ti2-U_Jellyfish_Config2", "@id": "/microscope-configurations/f0172a96-2bf5-4e6a-938d-f205c6e728c9/", "status": "released", "uuid": "f0172a96-2bf5-4e6a-938d-f205c6e728c9", "title": "Yale-Wang_lab_MINA_Nikon_Eclipse_Ti2-U_Jellyfish_Config2", "@type": ["MicroscopeConfiguration", "UserContent", "Item"], "microscope": {"Name": "Yale-Wang_lab_MINA_Nikon_Eclipse_Ti2-U_Jellyfish_Config2"}, "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "@id": "/experiments-mic/4DNEXC5WYC84/", "@type": ["ExperimentMic", "Experiment", "Item"], "uuid": "f6c78a64-a5ad-4ed8-84b9-7414ae343363", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}, "display_title": "multiplexed FISH on IMR-90 - 4DNEXC5WYC84", "external_references": [], "experiment_sets": [{"status": "released", "experimentset_type": "replicate", "@id": "/experiment-set-replicates/4DNES82IH3OG/", "uuid": "0458bcc5-c5a7-4833-a67a-0b8332ea5e62", "@type": ["ExperimentSetReplicate", "ExperimentSet", "Item"], "display_title": "4DNES82IH3OG", "accession": "4DNES82IH3OG", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "produced_in_pub": {"journal": "Genome biology", "status": "current", "authors": ["Cheng Y", "Liu M", "Hu M", "Wang S"], "@id": "/publications/9c1ed2e4-0c1d-48c1-85fb-a1b5d5a6db8b/", "ID": "PMID:34749781", "short_attribution": "Cheng Y et al. (2021)", "title": "TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations.", "uuid": "9c1ed2e4-0c1d-48c1-85fb-a1b5d5a6db8b", "@type": ["Publication", "Item"], "display_title": "Cheng Y et al. (2021) PMID:34749781", "abstract": "BACKGROUND: Topologically associating domains (TADs) are important building blocks of three-dimensional genome architectures. The formation of TADs has been  shown to depend on cohesin in a loop-extrusion mechanism. Recently, advances in an image-based spatial genomics technique known as chromatin tracing lead to the  discovery of cohesin-independent TAD-like structures, also known as single-cell domains, which are highly variant self-interacting chromatin domains with boundaries that occasionally overlap with TAD boundaries but tend to differ among single cells and among single chromosome copies. Recent computational modeling studies suggest that epigenetic interactions may underlie the formation of the single-cell domains. RESULTS: Here we use chromatin tracing to visualize in female human cells the fine-scale chromatin folding of inactive and active X chromosomes, which are known to have distinct global epigenetic landscapes and distinct population-averaged TAD profiles, with inactive X chromosomes largely devoid of TADs and cohesin. We show that both inactive and active X chromosomes possess highly variant single-cell domains across the same genomic region despite the fact that only active X chromosomes show clear TAD structures at the population level. These X chromosome single-cell domains exist in distinct cell lines. Perturbations of major epigenetic components and transcription mostly do not affect the frequency or strength of the single-cell domains. Increased chromatin compaction of inactive X chromosomes occurs at a length scale above that of the single-cell domains. CONCLUSIONS: In sum, this study suggests that single-cell domains are genome architecture building blocks independent of the tested major epigenetic components.", "date_published": "2021-11-08", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"authors": ["Cheng Y", "Liu M", "Hu M", "Wang S"], "ID": "PMID:34749781", "display_title": "Cheng Y et al. (2021) PMID:34749781", "date_published": "2021-11-08", "journal": "Genome biology", "@id": "/publications/9c1ed2e4-0c1d-48c1-85fb-a1b5d5a6db8b/", "status": "current", "abstract": "BACKGROUND: Topologically associating domains (TADs) are important building blocks of three-dimensional genome architectures. The formation of TADs has been  shown to depend on cohesin in a loop-extrusion mechanism. Recently, advances in an image-based spatial genomics technique known as chromatin tracing lead to the  discovery of cohesin-independent TAD-like structures, also known as single-cell domains, which are highly variant self-interacting chromatin domains with boundaries that occasionally overlap with TAD boundaries but tend to differ among single cells and among single chromosome copies. Recent computational modeling studies suggest that epigenetic interactions may underlie the formation of the single-cell domains. RESULTS: Here we use chromatin tracing to visualize in female human cells the fine-scale chromatin folding of inactive and active X chromosomes, which are known to have distinct global epigenetic landscapes and distinct population-averaged TAD profiles, with inactive X chromosomes largely devoid of TADs and cohesin. We show that both inactive and active X chromosomes possess highly variant single-cell domains across the same genomic region despite the fact that only active X chromosomes show clear TAD structures at the population level. These X chromosome single-cell domains exist in distinct cell lines. Perturbations of major epigenetic components and transcription mostly do not affect the frequency or strength of the single-cell domains. Increased chromatin compaction of inactive X chromosomes occurs at a length scale above that of the single-cell domains. CONCLUSIONS: In sum, this study suggests that single-cell domains are genome architecture building blocks independent of the tested major epigenetic components.", "@type": ["Publication", "Item"], "short_attribution": "Cheng Y et al. (2021)", "uuid": "9c1ed2e4-0c1d-48c1-85fb-a1b5d5a6db8b", "title": "TAD-like single-cell domain structures exist on both active and inactive X chromosomes and persist under epigenetic perturbations.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "28 consecutive 30-kb loci on chrX, XIST transcript", "combined": "Target: 28 consecutive 30-kb loci on chrX, XIST transcript"}, "experiment_summary": "multiplexed FISH on IMR-90", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSMYIICTY/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample missing Cell Culture Details"], "badge": {"commendation": null, "warning": "Biosample Metadata Incomplete", "uuid": "2b2cc7ff-b7a8-4138-9a6c-22884fc71690", "@id": "/badges/biosample-metadata-incomplete/", "badge_icon": "/static/img/badges/biosample-icon.svg", "description": "Biosample is missing metadata information required as part of the standards implemented by the 4DN Samples working group."}}}]}, "validation-errors": []}