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(2025)", "journal": "bioRxiv", "date_published": "2025-10-03", "ID": "doi:10.1101/2025.10.01.679912", "title": "Acidic transcription factors position the genome at nuclear speckles through transcription dependent and independent mechanisms", "status": "current", "@type": ["Publication", "Item"], "display_title": "Chaturvedi P et al. (2025) doi:10.1101/2025.10.01.679912", "authors": ["Chaturvedi P", "Ghosh P", "Zhang L", "Zhang M", "Zhao H", "Belmont AS"], "abstract": "A small fraction of the genome positions reproducibly near nuclear speckles (NS), increasing expression and/or splicing efficiency of NS-associated genes. How specific genomic regions target to NS remains unclear. Here, we demonstrate that establishment of genome-wide NS-association occurs independent of active transcription. We show that DNA sequences derived from NS-associated regions integrated as transgenes autonomously target to NS. By systematically dissecting one such genomic locus, the COL1A1-SGCA locus, we identified redundant NS-targeting cis regulatory elements, including a ~600 bp fragment with 17 binding motifs for 8 transcription factors (TFs). Four NS-targeting TFs within this fragment contain acidic activation domains (AADs) that provide both chromatin-context and transcription-dependent NS-targeting, a property that appears common among several other tested AADs. A subset of acidic activator TFs contain an additional, transcription-independent NS-targeting activity. Our findings establish diverse and partially redundant NS-targeting activities, which may facilitate dynamic gene positioning at NS periphery for context-specific transcriptional responses.", "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}, "publications_of_exp": [{"short_attribution": "Chaturvedi P et al. (2025)", "ID": "doi:10.1101/2025.10.01.679912", "authors": ["Chaturvedi P", "Ghosh P", "Zhang L", "Zhang M", "Zhao H", "Belmont AS"], "display_title": "Chaturvedi P et al. (2025) doi:10.1101/2025.10.01.679912", "uuid": "5cd0982a-1e4b-41aa-a87c-e1f951fc614d", "abstract": "A small fraction of the genome positions reproducibly near nuclear speckles (NS), increasing expression and/or splicing efficiency of NS-associated genes. How specific genomic regions target to NS remains unclear. Here, we demonstrate that establishment of genome-wide NS-association occurs independent of active transcription. We show that DNA sequences derived from NS-associated regions integrated as transgenes autonomously target to NS. By systematically dissecting one such genomic locus, the COL1A1-SGCA locus, we identified redundant NS-targeting cis regulatory elements, including a ~600 bp fragment with 17 binding motifs for 8 transcription factors (TFs). Four NS-targeting TFs within this fragment contain acidic activation domains (AADs) that provide both chromatin-context and transcription-dependent NS-targeting, a property that appears common among several other tested AADs. A subset of acidic activator TFs contain an additional, transcription-independent NS-targeting activity. Our findings establish diverse and partially redundant NS-targeting activities, which may facilitate dynamic gene positioning at NS periphery for context-specific transcriptional responses.", "date_published": "2025-10-03", "@id": "/publications/5cd0982a-1e4b-41aa-a87c-e1f951fc614d/", "status": "current", "journal": "bioRxiv", "title": "Acidic transcription factors position the genome at nuclear speckles through transcription dependent and independent mechanisms", "@type": ["Publication", "Item"], "principals_allowed": {"view": ["system.Everyone"], "edit": ["group.admin"]}}], "experiment_categorizer": {"field": "Target", "value": "SON protein", "combined": "Target: SON protein"}, "experiment_summary": "TSA-seq against SON protein on RPE-hTERT (Tier 2)", "@context": "/terms/", "aggregated-items": {"badges": [{"parent": "/biosamples/4DNBSIP4IZY6/", "embedded_path": "biosample.badges", "item": {"messages": ["Biosample receives gold status for being a 4DN Tier 1 or Tier 2 cell line that follows the approved SOP and contains all of the pertinent metadata information as required by the 4DN Samples working group."], "badge": {"commendation": "Gold Biosample", "warning": null, "uuid": "6c2b7409-4478-4e15-aabc-1a0df6b883e9", "@id": "/badges/gold-biosample/", "badge_icon": "/static/img/badges/biosample-badge-gold-star.svg", "description": "Gold biosample"}}}]}, "validation-errors": []}