Cohesin Subunit Rad21 Binds to the Herpes Simplex Virus 1 Genome near CTCF Insulator Sites during Latency In Vivo

• Published in: Journal of virology Vol. 95; no. 11
• Main Authors: Singh, Pankaj, Neumann, Donna M
• Format: Journal Article
• Language: English
• Published: 1752 N St., N.W., Washington, DC American Society for Microbiology 10-05-2021
• Subjects: Genome and Regulation of Viral Gene Expression; Genome Replication and Regulation of Viral Gene Expression; HSV-1; cohesin; Rad21; latency; HSV-1 latency; mouse ocular; CTCF; chromatin; insulator; epigenetics
• ISSN: 0022-538X; 1098-5514
• DOI: 10.1128/JVI.00364-21

Herpes simplex virus 1 (HSV-1) is a human pathogen that can establish a lifelong infection in the host. During latency, HSV-1 genomes are chromatinized and are abundantly associated with histones in sensory neurons, yet the mechanisms that govern the latent-lytic transition remain unclear. We hypothesize that the latent-lytic switch is controlled by CTCF insulators, positioned within the HSV-1 latent genome. CTCF insulators, together with the cohesin complex, can establish and maintain chromatin loops that allow distance-separated gene regions to be spatially oriented for transcriptional control. In the current study, we demonstrated that the cohesin subunit Rad21 was recruited to latent HSV-1 genomes near four of the CTCF insulators during latency. We showed that the CTCF insulator known as CTRS1/2, positioned downstream from the essential transactivating immediate-early (IE) region of ICP4, was only enriched in Rad21 prior to but not during latency, suggesting that the CTRS1/2 insulator is not required for the maintenance of latency. Further, deletion of the CTRL2 insulator, positioned downstream from the latency-associated transcript (LAT) enhancer, resulted in a loss of Rad21 enrichment at insulators flanking the ICP4 region at early times postinfection in mouse ganglia, suggesting that these insulators are interdependent. Finally, deletion of the CTRL2 insulator resulted in a loss of Rad21 enrichment at the CTRL2 insulator in a cell type-specific manner, and this loss of Rad21 enrichment was correlated with decreased LAT expression, suggesting that Rad21 recruitment to viral genomes is important for efficient gene expression. IMPORTANCE CTCF insulators are important for transcriptional control, and increasing evidence suggests that CTCF insulators, together with the cohesin complex, regulate viral transcription in DNA viruses. The CTCF-cohesin interaction is important for the formation of chromatin loops, structures that orient distance-separated elements in close spatial proximity for transcriptional control. Herpes simplex virus 1 (HSV-1) has seven putative CTCF insulators that flank the LAT and the IE, indicating that CTCF insulators play a role in the transition from latency to reactivation. Contributions from the work presented here include the finding that CTCF insulators in HSV-1 genomes are differentially enriched in the cohesin subunit Rad21, suggesting that CTCF-cohesin interactions are establishing and anchoring chromatin loop structures to control viral transcription.