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| Status |
Public on Nov 16, 2022 |
| Title |
Functional and molecular dissection of viral lncRNAs throughout HCMV life cycle [shortread] |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Small, compact genomes confer a selective advantage to viruses, yet human cyto-megalovirus (HCMV) expresses the long non-coding RNAs (lncRNAs); RNA1.2, RNA2.7, RNA4.9, and RNA5.0. Little is known about the function of these lncRNAs in the virus life cycle. Here, we dissected the functional and molecular landscape of HCMV lncRNAs. We found that HCMV lncRNAs occupy ~30 % and 50~60 % of to-tal and poly(A)+ viral transcriptome, respectively, throughout virus life cycle. RNA1.2, RNA2.7, and RNA4.9, the three abundantly expressed lncRNAs, appear to be es-sential in all infection states. Among these three lncRNAs, depletion of RNA2.7 and RNA4.9 results in the greatest defect in maintaining latent reservoir and promoting lytic replication, respectively. Moreover, we delineated the global post-transcriptional nature of HCMV lncRNAs by nanopore direct RNA sequencing and interactome analysis. We revealed that the lncRNAs are modified with N⁶-methyladenosine (m6A) and interact with m6A readers in all infection states. In-depth analysis demonstrated that m6A machineries stabilize HCMV lncRNAs, which could account for the over-whelming abundance of viral lncRNAs. Our study lays the groundwork for under-standing the viral lncRNA–mediated regulation of host-virus interaction throughout the HCMV life cycle.
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| Overall design |
Comparative viral gene expression profiling of RNA-seq and DRS data for HCMV latency, reactivation, and lytic infection sample.
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| Contributor(s) |
Lee S, Kim H, Hong A, Song J, Chang H, Ahn K |
| Citation(s) |
36369338 |
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| Submission date |
Nov 10, 2022 |
| Last update date |
Nov 16, 2022 |
| Contact name |
Hyeshik Chang |
| E-mail(s) |
hyeshik@snu.ac.kr
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| Organization name |
Seoul National University
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| Department |
School of Biological Sciences
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| Lab |
Hyeshik Chang Lab
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| Street address |
Building 203 Room 525, School of Biological Sciences, Seoul National University, 1 Gwanak-ro, Gwanak-gu
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| City |
Seoul |
| State/province |
South Korea |
| ZIP/Postal code |
08826 |
| Country |
South Korea |
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| Platforms (1) |
| GPL24676 |
Illumina NovaSeq 6000 (Homo sapiens) |
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| Samples (4)
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| GSM6725346 |
HCMV-infected Kasumi-3 latency, replicate 1 [shortread] |
| GSM6725347 |
HCMV-infected Kasumi-3 latency, replicate 2 [shortread] |
| GSM6725348 |
HCMV-infected Kasumi-3 reactivation, replicate 1 [shortread] |
| GSM6725349 |
HCMV-infected Kasumi-3 reactivation, replicate 2 [shortread] |
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| This SubSeries is part of SuperSeries: |
| GSE217714 |
Functional and molecular dissection of viral lncRNAs throughout HCMV life cycle |
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| Relations |
| BioProject |
PRJNA900204 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE217713_shortread-featurecount.tsv.gz |
5.1 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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