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At present, it is unknown how the locations of replication origins are determined in the human genome. Here we dissect the role of topologically associating domains (TADs)(3-6), subTADs(7)  and loops(8) in the positioning of replication initiation zones (IZs). We stratify TADs and subTADs by the presence of corner-dots indicative of loops and  the orientation of CTCF motifs. We find that high-efficiency, early replicating IZs localize to boundaries between adjacent corner-dot TADs anchored by high-density arrays of divergently and convergently oriented CTCF motifs. By contrast, low-efficiency IZs localize to weaker dotless boundaries. Following ablation of cohesin-mediated loop extrusion during G1, high-efficiency IZs become diffuse and delocalized at boundaries with complex CTCF motif orientations. Moreover, G1 knockdown of the cohesin unloading factor WAPL results in gained long-range loops and narrowed localization of IZs at the same boundaries. Finally, targeted deletion or insertion of specific boundaries causes local replication timing shifts consistent with IZ loss or gain, respectively. Our data support a model in which cohesin-mediated loop extrusion and stalling at a subset of genetically encoded TAD and subTAD boundaries is an essential determinant of the locations of replication origins in human S phase.", "@id": "/publications/ee8db237-9a92-4b72-8292-a66028a95b5b/", "ID": "PMID:35676475", "date_published": "2022-06-08", "display_title": "Emerson DJ et al. (2022) PMID:35676475", "authors": ["Emerson DJ", "Zhao PA", "Cook AL", "Barnett RJ", "Klein KN", "Saulebekova D", "Ge C", "Zhou L", "Simandi Z", "Minsk MK", "Titus KR", "Wang W", "Gong W", "Zhang D", "Yang L", "Venev SV", "Gibcus JH", "Yang H", "Sasaki T", "Kanemaki MT", "Yue F", "Dekker J", "Chen CL", "Gilbert DM", "Phillips-Cremins JE"], "url": "https://www.ncbi.nlm.nih.gov/pubmed/35676475", "short_attribution": "Emerson DJ et al. (2022)", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "pubs_using": [{"uuid": "f2b3b3fb-e9af-484d-abeb-fe4316ffdc1a", "display_title": "Gholamalamdari O et al. (2025) PMID:38712201", "@type": ["Publication", "Item"], "@id": "/publications/f2b3b3fb-e9af-484d-abeb-fe4316ffdc1a/", "status": "current", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "publications_of_set": [{"@type": ["Publication", "Item"], "@id": "/publications/f2b3b3fb-e9af-484d-abeb-fe4316ffdc1a/", "title": "Beyond A and B Compartments: how major nuclear locales define nuclear genome  organization and function.", "date_published": "2025-02-26", "status": "current", "ID": "PMID:38712201", "journal": "bioRxiv : the preprint server for biology", "display_title": "Gholamalamdari O et al. (2025) PMID:38712201", "authors": ["Gholamalamdari O", "van Schaik T", "Wang Y", "Kumar P", "Zhang L", "Zhang Y", "Gonzalez GAH", "Vouzas AE", "Zhao PA", "Gilbert DM", "Ma J", "van Steensel B", "Belmont AS"], "uuid": "f2b3b3fb-e9af-484d-abeb-fe4316ffdc1a", "abstract": "Models of nuclear genome organization often propose a binary division into active  versus inactive compartments yet typically overlook nuclear bodies. Here we  integrated analysis of sequencing and image-based data to compare genome  organization in four human cell types relative to three different nuclear  locales: the nuclear lamina, nuclear speckles, and nucleoli. Whereas gene  expression correlates mostly with nuclear speckle proximity, DNA replication  timing correlates with proximity to multiple nuclear locales. Speckle attachment  regions emerge as DNA replication initiation zones whose replication timing and  gene composition vary with their attachment frequency. Most facultative LADs  retain a partially repressed state as iLADs, despite their positioning in the  nuclear interior. Knock out of two lamina proteins, Lamin A and LBR, causes a  shift of H3K9me3-enriched LADs from lamina to nucleolus, and a reciprocal  relocation of H3K27me3-enriched partially repressed iLADs from nucleolus to  lamina. Thus, these partially repressed iLADs appear to compete with LADs for  nuclear lamina attachment with consequences for replication timing. The nuclear  organization in adherent cells is polarized with nuclear bodies and genomic  regions segregating both radially and relative to the equatorial plane. Together,  our results underscore the importance of considering genome organization relative  to nuclear locales for a more complete understanding of the spatial and  functional organization of the human genome.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, {"@type": ["Publication", "Item"], "@id": "/publications/ee8db237-9a92-4b72-8292-a66028a95b5b/", "title": "Cohesin-mediated loop anchors confine the locations of human replication origins.", "date_published": "2022-06-08", "status": "current", "ID": "PMID:35676475", "journal": "Nature", "display_title": "Emerson DJ et al. (2022) PMID:35676475", "authors": ["Emerson DJ", "Zhao PA", "Cook AL", "Barnett RJ", "Klein KN", "Saulebekova D", "Ge C", "Zhou L", "Simandi Z", "Minsk MK", "Titus KR", "Wang W", "Gong W", "Zhang D", "Yang L", "Venev SV", "Gibcus JH", "Yang H", "Sasaki T", "Kanemaki MT", "Yue F", "Dekker J", "Chen CL", "Gilbert DM", "Phillips-Cremins JE"], "uuid": "ee8db237-9a92-4b72-8292-a66028a95b5b", "abstract": "DNA replication occurs through an intricately regulated series of molecular events and is fundamental for genome stability(1,2). At present, it is unknown how the locations of replication origins are determined in the human genome. Here we dissect the role of topologically associating domains (TADs)(3-6), subTADs(7)  and loops(8) in the positioning of replication initiation zones (IZs). We stratify TADs and subTADs by the presence of corner-dots indicative of loops and  the orientation of CTCF motifs. We find that high-efficiency, early replicating IZs localize to boundaries between adjacent corner-dot TADs anchored by high-density arrays of divergently and convergently oriented CTCF motifs. By contrast, low-efficiency IZs localize to weaker dotless boundaries. Following ablation of cohesin-mediated loop extrusion during G1, high-efficiency IZs become diffuse and delocalized at boundaries with complex CTCF motif orientations. Moreover, G1 knockdown of the cohesin unloading factor WAPL results in gained long-range loops and narrowed localization of IZs at the same boundaries. Finally, targeted deletion or insertion of specific boundaries causes local replication timing shifts consistent with IZ loss or gain, respectively. 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