Enhancers and genome conformation provide complex transcriptional control of a herpesviral gene
Abstract Complex transcriptional control is a conserved feature of both eukaryotes and the viruses that infect them. Despite viral genomes being smaller and more gene dense than their hosts, we generally lack a sense of scope for the features governing the transcriptional output of individual viral...
Saved in:
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Springer Nature
2024-11-01
|
| Series: | Molecular Systems Biology |
| Subjects: | |
| Online Access: | https://doi.org/10.1038/s44320-024-00075-0 |
| Tags: |
Add Tag
No Tags, Be the first to tag this record!
|
| _version_ | 1841559003177418752 |
|---|---|
| author | David W Morgens Leah Gulyas Xiaowen Mao Alejandro Rivera-Madera Annabelle S Souza Britt A Glaunsinger |
| author_facet | David W Morgens Leah Gulyas Xiaowen Mao Alejandro Rivera-Madera Annabelle S Souza Britt A Glaunsinger |
| author_sort | David W Morgens |
| collection | DOAJ |
| description | Abstract Complex transcriptional control is a conserved feature of both eukaryotes and the viruses that infect them. Despite viral genomes being smaller and more gene dense than their hosts, we generally lack a sense of scope for the features governing the transcriptional output of individual viral genes. Even having a seemingly simple expression pattern does not imply that a gene’s underlying regulation is straightforward. Here, we illustrate this by combining high-density functional genomics, expression profiling, and viral-specific chromosome conformation capture to define with unprecedented detail the transcriptional regulation of a single gene from Kaposi’s sarcoma-associated herpesvirus (KSHV). We used as our model KSHV ORF68 – which has simple, early expression kinetics and is essential for viral genome packaging. We first identified seven cis-regulatory regions involved in ORF68 expression by densely tiling the ~154 kb KSHV genome with dCas9 fused to a transcriptional repressor domain (CRISPRi). A parallel Cas9 nuclease screen indicated that three of these regions act as promoters of genes that regulate ORF68. RNA expression profiling demonstrated that three more of these regions act by either repressing or enhancing other distal viral genes involved in ORF68 transcriptional regulation. Finally, we tracked how the 3D structure of the viral genome changes during its lifecycle, revealing that these enhancing regulatory elements are physically closer to their targets when active, and that disrupting some elements caused large-scale changes to the 3D genome. These data enable us to construct a complete model revealing that the mechanistic diversity of this essential regulatory circuit matches that of human genes. |
| format | Article |
| id | doaj-art-2fcdc7064be84947abdabdf1a5f30ecb |
| institution | Kabale University |
| issn | 1744-4292 |
| language | English |
| publishDate | 2024-11-01 |
| publisher | Springer Nature |
| record_format | Article |
| series | Molecular Systems Biology |
| spelling | doaj-art-2fcdc7064be84947abdabdf1a5f30ecb2025-01-05T12:50:42ZengSpringer NatureMolecular Systems Biology1744-42922024-11-01211305810.1038/s44320-024-00075-0Enhancers and genome conformation provide complex transcriptional control of a herpesviral geneDavid W Morgens0Leah Gulyas1Xiaowen Mao2Alejandro Rivera-Madera3Annabelle S Souza4Britt A Glaunsinger5Department of Plant and Microbial Biology, UC BerkeleyDepartment of Plant and Microbial Biology, UC BerkeleyDepartment of Plant and Microbial Biology, UC BerkeleyDepartment of Molecular and Cell Biology, UC BerkeleyDepartment of Molecular and Cell Biology, UC BerkeleyDepartment of Plant and Microbial Biology, UC BerkeleyAbstract Complex transcriptional control is a conserved feature of both eukaryotes and the viruses that infect them. Despite viral genomes being smaller and more gene dense than their hosts, we generally lack a sense of scope for the features governing the transcriptional output of individual viral genes. Even having a seemingly simple expression pattern does not imply that a gene’s underlying regulation is straightforward. Here, we illustrate this by combining high-density functional genomics, expression profiling, and viral-specific chromosome conformation capture to define with unprecedented detail the transcriptional regulation of a single gene from Kaposi’s sarcoma-associated herpesvirus (KSHV). We used as our model KSHV ORF68 – which has simple, early expression kinetics and is essential for viral genome packaging. We first identified seven cis-regulatory regions involved in ORF68 expression by densely tiling the ~154 kb KSHV genome with dCas9 fused to a transcriptional repressor domain (CRISPRi). A parallel Cas9 nuclease screen indicated that three of these regions act as promoters of genes that regulate ORF68. RNA expression profiling demonstrated that three more of these regions act by either repressing or enhancing other distal viral genes involved in ORF68 transcriptional regulation. Finally, we tracked how the 3D structure of the viral genome changes during its lifecycle, revealing that these enhancing regulatory elements are physically closer to their targets when active, and that disrupting some elements caused large-scale changes to the 3D genome. These data enable us to construct a complete model revealing that the mechanistic diversity of this essential regulatory circuit matches that of human genes.https://doi.org/10.1038/s44320-024-00075-0Capture Hi-CCRISPR InterferenceGene RegulationHerpesvirusKSHV |
| spellingShingle | David W Morgens Leah Gulyas Xiaowen Mao Alejandro Rivera-Madera Annabelle S Souza Britt A Glaunsinger Enhancers and genome conformation provide complex transcriptional control of a herpesviral gene Molecular Systems Biology Capture Hi-C CRISPR Interference Gene Regulation Herpesvirus KSHV |
| title | Enhancers and genome conformation provide complex transcriptional control of a herpesviral gene |
| title_full | Enhancers and genome conformation provide complex transcriptional control of a herpesviral gene |
| title_fullStr | Enhancers and genome conformation provide complex transcriptional control of a herpesviral gene |
| title_full_unstemmed | Enhancers and genome conformation provide complex transcriptional control of a herpesviral gene |
| title_short | Enhancers and genome conformation provide complex transcriptional control of a herpesviral gene |
| title_sort | enhancers and genome conformation provide complex transcriptional control of a herpesviral gene |
| topic | Capture Hi-C CRISPR Interference Gene Regulation Herpesvirus KSHV |
| url | https://doi.org/10.1038/s44320-024-00075-0 |
| work_keys_str_mv | AT davidwmorgens enhancersandgenomeconformationprovidecomplextranscriptionalcontrolofaherpesviralgene AT leahgulyas enhancersandgenomeconformationprovidecomplextranscriptionalcontrolofaherpesviralgene AT xiaowenmao enhancersandgenomeconformationprovidecomplextranscriptionalcontrolofaherpesviralgene AT alejandroriveramadera enhancersandgenomeconformationprovidecomplextranscriptionalcontrolofaherpesviralgene AT annabellessouza enhancersandgenomeconformationprovidecomplextranscriptionalcontrolofaherpesviralgene AT brittaglaunsinger enhancersandgenomeconformationprovidecomplextranscriptionalcontrolofaherpesviralgene |