Analysis of Roquin targetome during HCMV infection
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ABSTRACT:
PROVIDER: PRJNA545893 | ENA |
REPOSITORIES: ENA
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Project description:To investigate how Roquin regulates cellular transcripts during Human cytomegalovirus (HCMV) infection, we examined the levels of cellular transcripts in cells treated control or Roquin-targeting siRNA during HCMV replication. Also, we performed Roquin crosslinking and immunoprecipitation followed by high-throughput sequencing (Roquin CLIP-seq) in HCMV-infected cells to identify which transcripts are directly bound by Roquin.
2019-08-15 | GSE132081 | GEO
Project description:To elucidate miRNA-mediated temporal crosstalk during productive infection, we identified genome-wide miRNA target sites using Argonaute-crosslinking and immunoprecipitation followed by high-throughput sequencing (AGO-CLIPseq) in human cytomegalovirus (HCMV)-infected cells and evaluated the targeting efficacy by applying our new AGO-CLIPseq enrichment (ACE)-scoring algorithm. To uncover the miRNA targetome in uninfected or infected human foreskin fibroblasts with HCMV (24, 48 and 72 post-infection hour) were subjected to take AGO-CLIPseq as well as mRNAseq/smallRNAseq.
2014-12-03 | E-GEOD-63797 | biostudies-arrayexpress
Project description:To elucidate miRNA-mediated temporal crosstalk during productive infection, we identified genome-wide miRNA target sites using Argonaute-crosslinking and immunoprecipitation followed by high-throughput sequencing (AGO-CLIPseq) in human cytomegalovirus (HCMV)-infected cells and evaluated the targeting efficacy by applying our new AGO-CLIPseq enrichment (ACE)-scoring algorithm.
2014-12-03 | GSE63797 | GEO
Project description:SIRT3 has been shown to inhibit HCMV infection, but the mechanism under the antiviral effect is not clear. To identify the mediator of SIRT3 antiviral function, we aim to identify and quantify SIRT3 interactions during HCMV infection. A set of large-scale IPs were performed to determine the specific interactions with SIRT3 during infection, while small-scale IPs were conducted to determine the temporal interactions over the life cycle of infection. The mitochondrial proteome was used to characterize the changes of protein abundances after infection, and it was used for the normalization of acetylation.
2021-04-01 | PXD018995 | Pride
Project description:Purpose: to investigate expression of HCMV and cellular RNAs at early times post-infection in a lytic model
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Project description:Purpose: to investigate occupancy of Pol II and H3K27Ac on the HCMV and cellular genomes at early times post-infection in a lytic model
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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
Project description:Infection with Human cytomegalovirus (HCMV) can result in either productive or non-productive infection, the latter potentially leading to establishment of latency, but the molecular factors that dictate these different infection outcomes are elusive. Macrophages are known targets of HCMV and considered to be permissive for productive infection, while monocytes, their precursors, are thought to support latent infection. Here we reveal that infection of macrophages is more complex than previously appreciated and can result in either productive or non-productive infection. By analyzing the progression of HCMV infection in c and macrophages using single cell transcriptomics, we uncover that the key characteristics that define productive and non-productive cells are the onset of viral gene expression, and activation of Interferon-stimulated genes (ISGs), respectively. We show that the level of viral gene expression, and specifically the expression of the major immediate early factor, IE1, is the principle barrier for establishing productive infection. On the cellular side, induction of ISGs in response to infection surprisingly does not dictate infection outcome, but we find that the cell intrinsic ISG levels is a main determinant of infection outcome. Indeed, intrinsic ISG level is downregulated with monocyte differentiation. We further show that, compared to monocytes, non-productive macrophages maintain slightly higher levels of viral transcripts and are able to reactivate, raising the possibility that they can serve as latency reservoirs in tissues. Moreover, we find that productive infection perturbs macrophage identity and function, likely affecting their immunological role during active infection. Overall, by harnessing the tractable system of monocyte differentiation we decipher the underlying principles that control HCMV infection outcome, and propose macrophages as a new potential HCMV reservoir in tissues.
2023-01-05 | GSE189581 | GEO
Project description:HCMV infection of human neural precursor cells: HCMV expression
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Project description:We employed RNA-seq to map the transcriptome of human MRC5 fibroblasts during HCMV infection with AD169. These data will highlight the ways in which the HCMV infection alters RNA levels during infection.
2022-08-14 | GSE210989 | GEO