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Functional and molecular dissection of viral lncRNAs throughout HCMV life cycle

ABSTRACT: Functional and molecular dissection of viral lncRNAs throughout HCMV life cycle

PROVIDER: PRJNA900198 | ENA |

REPOSITORIES: ENA

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Functional and molecular dissection of viral lncRNAs throughout HCMV life cycle

Project description:Small, compact genomes confer a selective advantage to viruses, yet human cytomegalovirus (HCMV) expresses the long non-coding RNAs (lncRNAs) RNA1.2, RNA2.7, RNA4.9, and RNA5.0. These lncRNAs account for majority of the viral transcriptome, but their functions remain largely unknown. Here, we showed that HCMV lncRNAs, except for RNA5.0, are required throughout the entire viral life cycle. Deletion of each lncRNA resulted in a decrease in viral progeny during lytic replication and failing to efficiently establish latent reservoirs and reactivate. Nanopore direct RNA sequencing of native lncRNA molecules revealed that each lncRNA exhibited a dynamic modification landscape, depending on the state of infection. Global analysis of the lncRNA interactome identified 32, 11, and 89 host factors that specifically bind to RNA1.2, RNA2.7, and RNA4.9, respectively. Moreover, 52 proteins commonly bound to the three lncRNAs were identified, including 11 antiviral immunity-related proteins. Our molecular analyses found that three lncRNAs are modified with N⁶-methyladenosine (m6A) and interact with m6A readers in all infection states. In-depth functional analysis revealed that m6A–mediated lncRNA stabilization as the key mechanism by which lncRNAs are maintained at high levels. Our study lays the groundwork for understanding viral lncRNA–mediated regulation of host-virus interaction throughout the HCMV life cycle.

2022-11-14 | PXD034587 | Pride

Functional and molecular dissection of viral lncRNAs throughout HCMV life cycle [longread]

Project description: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.

2022-11-16 | GSE217710 | GEO

Functional and molecular dissection of viral lncRNAs throughout HCMV life cycle [shortread]

2022-11-16 | GSE217713 | GEO

Functional and molecular dissection of viral lncRNAs throughout HCMV life cycle [longread]

Project description:Functional and molecular dissection of viral lncRNAs throughout HCMV life cycle [longread]

| PRJNA900202 | ENA

Functional and molecular dissection of viral lncRNAs throughout HCMV life cycle [shortread]

Project description:Functional and molecular dissection of viral lncRNAs throughout HCMV life cycle [shortread]

| PRJNA900204 | ENA

Functional and molecular dissection of viral lncRNAs throughout HCMV life cycle

Project description:This SuperSeries is composed of the SubSeries listed below.

2022-11-16 | GSE217714 | GEO

HCMV infection of human neural precursor cells: HCMV expression

Project description:HCMV treated and control human primary adult neural precursor cells (isolated from hippocampus) were used at passages 2-4 for infection with HCMV and RNA was harvested at indicated times

2012-07-22 | GSE31141 | GEO

Role of the HCMV immediate early proteins in controlling the HCMV transcriptome

Project description:Purpose: to investigate the role of the HCMV immediate early genes in controlling the HCMV and cellular transcriptomes

2022-12-21 | GSE171521 | GEO

Transcription profiling of soybean cyst nematode (Heterodera glycines) throughout the nematode life cycle

Project description:Expression profiling of 7,530 Heterodera glycines probesets present on the Affymetrix Soybean Genome Array GeneChip throughout the life cycle of the nematode (egg, infective J2, parasitic J2, J3, J4, adult female).

2007-10-20 | E-MEXP-1110 | biostudies-arrayexpress

Role of the HCMV immediate early proteins in controlling the HCMV and cellular epigenomes

Project description:Purpose: to investigate the role of the HCMV immediate early proteins in controlling the HCMV and cellular epigneomes during lytic infectioin

2022-12-21 | GSE171518 | GEO

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