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Quantification of interaction strength between a synthetic enhancer-promoter pair with Region Capture Micro-C

ABSTRACT: To quantify the interaction strength between a synthetic enhancer-promoter (E-P) pair investigated in this study, we applied Region Capture Micro-C (RCMC) to a ~1.9 Mb region containing the engineered E-P pair. We mapped the 3D genomic structure of these loci across multiple clonal mouse embryonic stem cell (mESC) lines featuring varying E-P genomic distances and CTCF binding site configurations, along with control lines with either the enhancer or the entire E-P pair deleted. Furthermore, we profiled E-P interactions under acute depletion of CTCF and/or cohesin subunit RAD21. For the 339 kb E-P pair flanked by convergent CTCF binding sites, we assessed three perturbations: CTCF depletion (via dTAG-13), RAD21 depletion (via 5-ph-IAA), and simultaneous CTCF and RAD21 co-depletion. RAD21 depletion was also performed on the 339 kb E-P pair lacking CTCF binding sites.

ORGANISM(S): Mus musculus

PROVIDER: GSE335363 | GEO | 2026/06/15

REPOSITORIES: GEO

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Project description:Chromatin-organizing factors, like CTCF and cohesins, have been implicated in the control of complex viral regulatory programs. We investigated the role of CTCF and cohesin in the control of the latent to lytic switch for Kaposi's Sarcoma-Associated Herpesvirus (KSHV). We found that cohesin subunits, but not CTCF, were required for the repression of KSHV immediate early gene transcription. Depletion of cohesin subunits Rad21, SMC1, or SMC3 resulted in lytic cycle gene transcription and viral DNA replication. In contrast, depletion of CTCF failed to induce lytic transcription or DNA replication. ChiP-Seq analysis revealed that cohesins and CTCF bound to several sites within the immediate early control regions for ORF50 and more distal 5' sites that also regulate the divergently transcribed ORF45-46-47 gene cluster. Rad21 depletion led to a robust increase in ORF45 and ORF47 transcripts, with similar kinetics to that observed with chemical induction by sodium butyrate. During latency, the chromatin between the ORF45 and ORF50 transcription start sites was enriched in histone H3K4me3 with elevated H3K9ac at the ORF45 promoter and elevated H3K27me3 at the ORF50 promoter. A paused form of RNA pol II was loosely associated with the ORF45 promoter region during latency, but was converted to an active elongating form upon reactivation induced by Rad21 depletion. Butyrate-induced transcription of ORF45 and ORF47 was resistant to cyclohexamide, suggesting that these genes have immediate early features similar to ORF50. Butyrate-treatment caused the rapid dissociation of cohesins and loss of CTCF binding at the immediate early gene locus, suggesting that cohesins may be a direct target of butyrate-mediated lytic induction. Our findings implicate cohesins as a major repressor of KSHV lytic gene activation, and function coordinately with CTCF to regulate the switch between latent and lytic gene activity. Study of chromatin-organizing factors, like CTCF and cohesins.

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Quantification of interaction strength between a synthetic enhancer-promoter pair with Region Capture Micro-C

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