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| Status |
Public on Apr 01, 2014 |
| Title |
Site-Specific Association with Host and Viral Chromatin by KSHV LANA and its Reversal during Lytic Reactivation |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
Latency-associated nuclear antigen (LANA), a multifunctional protein expressed by the Kaposi sarcoma-associated herpesvirus (KSHV) in latently-infected cells, is required for stable maintenance of the viral episome. This is mediated by two interactions: LANA binds to specific sequences (LBS1 and 2) on viral DNA, and also engages host histones, tethering the viral genome to host chromosomes in mitosis. LANA has also been suggested to affect host gene expression, but both the mechanism(s) and role of this dysregulation in KSHV biology remain unclear. Here we have examined LANA interactions with host chromatin on a genome-wide scale using ChIP-seq, and show that LANA predominantly targets human genes near their transcriptional start sites (TSSs). These host LANA-binding sites are generally found within transcriptionally active promoters and display striking overrepresentation of a consensus DNA sequence virtually identical to the LBS1 motif in KSHV DNA. Comparison of the ChIP-seq profile with whole transcriptome (RNA-seq) data reveals that few of the genes that are differentially regulated in latent infection are occupied by LANA at their promoters. This suggests that direct LANA binding to promoters is not the prime determinant of altered host transcription in KSHV-infected cells. Most surprisingly, the association of LANA to both host and viral DNA is strongly disrupted during the lytic cycle of KSHV. This disruption can be prevented by the inhibition of viral DNA synthesis, suggesting the existence of novel and potent regulatory mechanisms linked to either viral DNA replication or late gene expression.
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| Overall design |
Profiling of KSHV LANA positioning on the host genome and examination of gene expression from promoters bound by KSHV LANA.
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| Contributor(s) |
Mercier A, Arias C, Madrid AS, Holdorf MM, Ganem D |
| Citation(s) |
24696474 |
| Submission date |
Mar 24, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
ALEXANDRE MERCIER |
| Organization name |
NOVARTIS INSTITUTES FOR BIOMEDICAL RESEARCH
|
| Department |
INFECTIOUS DISEASES
|
| Lab |
DON GANEM
|
| Street address |
5300 CHIRON WAY
|
| City |
EMERYVILLE |
| State/province |
CA |
| ZIP/Postal code |
94608 |
| Country |
USA |
| |
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| Platforms (2) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
| GPL16791 |
Illumina HiSeq 2500 (Homo sapiens) |
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| Samples (33)
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| Relations |
| BioProject |
PRJNA242969 |
| SRA |
SRP040694 |
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