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High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection

ABSTRACT: Small RNA deep sequencing analysis was conducted on primary human fibroblasts infected with human cytomegalovirus (HCMV). HCMV-encoded miRNAs accumulated to ~20% of the total smRNA population at late stages of infection, and our analysis led to improvements in viral miRNA annotations and identification of novel HCMV miRNAs. Through crosslinking and immunoprecipitation of Argonaute-bound RNAs from infected cells, followed by high-throughput sequencing (Ago CLIP-seq), we obtained direct evidence for incorporation of all HCMV miRNAs into the endogenous host silencing machinery. Additionally, significant upregulation was observed during infection for a host miRNA cluster containing miR-96, miR-182 and miR-183. We also identified novel non-miRNA forms of virus-derived smRNAs, revealing greater complexity within the smRNA population during HCMV infection.

ORGANISM(S): Homo sapiens

PROVIDER: GSE33584 | GEO | 2011/11/10

SECONDARY ACCESSION(S): PRJNA148583

REPOSITORIES: GEO

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High-resolution profiling and analysis of viral and host small RNAs during human cytomegalovirus infection

Project description:Small RNA deep sequencing analysis was conducted on primary human fibroblasts infected with human cytomegalovirus (HCMV). HCMV-encoded miRNAs accumulated to ~20% of the total smRNA population at late stages of infection, and our analysis led to improvements in viral miRNA annotations and identification of novel HCMV miRNAs. Through crosslinking and immunoprecipitation of Argonaute-bound RNAs from infected cells, followed by high-throughput sequencing (Ago CLIP-seq), we obtained direct evidence for incorporation of all HCMV miRNAs into the endogenous host silencing machinery. Additionally, significant upregulation was observed during infection for a host miRNA cluster containing miR-96, miR-182 and miR-183. We also identified novel non-miRNA forms of virus-derived smRNAs, revealing greater complexity within the smRNA population during HCMV infection. High-throughput profiling of smRNAs, Ago1-, and Ago2-associated miRNAs from HCMV-infected fibroblast cells. Wild-type HCMV Towne (Genbank FJ616285.1) was used for these studies.

2011-11-10 | E-GEOD-33584 | biostudies-arrayexpress

Characterization of AGO1-/AGO4-associated smRNAs

2011-04-19 | GSE28591 | GEO

Characterization of AGO1-/AGO4-associated smRNAs

Project description:To fully characterize smRNAs associated with AGO1 and AGO4, we developed a two-step protocol to purify AGO/smRNA complexes from flowers, leaves, roots and seedlings with enhanced purity, and sequenced the smRNAs by IlluminaM-CM-"M-BM-^@M-BM-^Ys technology. We identified some additional miRNAs, collateral miRNAs encoded in known miRNA precursors, phased smRNA clusters and nat-siRNAs. Organ specific sequencing provided digital expression profiles of all obtained smRNAs, especially miRNAs. We used extracts from Arabidopsis flowers, leaves and roots as well as ten-day old seedlings to purify smRNAs associated with AGO1 and AGO4 protein complexes using a two-step immunoprecipitation method.

2011-04-19 | E-GEOD-28591 | biostudies-arrayexpress

Human cytomegalovirus infection perturbs neural progenitor cell fate via the expression of viral microRNAs

Project description:Congenital human cytomegalovirus (HCMV) infection is the leading infectious cause of birth defects, including neurodevelopmental disorders. HCMV infection mainly targets neural progenitor cells (NPCs) in fetal brains, inducing abnormal differentiation by altering key regulatory pathways. HCMV expresses a series of viral miRNAs during infection, but their roles, particularly in NPCs, are not fully understood. In this study, we characterized expression profiles of both cellular and viral miRNAs in HCMV-infected NPCs by microarray analysis during early infection time points and investigated the primary effects of these miRNAs on regulating NPC fate. While expression of most cellular miRNAs was unaffected by HCMV infection, one cellular miRNA was upregulated and six were downregulated from 2 to 24 h post infection. Moreover, of 17 HCMV miRNAs evaluated, six were differentially expressed in HCMV-infected NPCs during early infection time points.

2023-06-30 | GSE206370 | GEO

Selective degradation of the miR-17 family members of the miR-17-92 cluster by human Cytomegalovirus

Project description:miRNA microarrays were used to investigate host miRNA expression profiles during HCMV clinical strain infection. Human foreskin fibroblasts (HFFs) were infected with the HCMV clinical strain Toledo. To mimic the attenuated strain, we used ToledoM-NM-^T15kb, which lacks the 15-kb genomic segment in the UL/bM-bM-^@M-^Y region. Changes in miRNA expression upon HCMV infection. Human foreskin fibroblasts (HFFs) were infected with Toledo-WT or ToledoM-NM-^T15kb for miRNA microarray (5 MOI). The miRNA expression levels of virus-infected HFFs at 24 or 72 hpi have been compared with those for the noninfected control.

2013-05-09 | E-GEOD-43761 | biostudies-arrayexpress

Selective degradation of the miR-17 family members of the miR-17-92 cluster by human Cytomegalovirus

2013-05-09 | GSE43761 | GEO

miRNA-mediated targeting of human cytomegalovirus reveals biological host and viral targets of IE2

Project description:We introduce target sites for the microRNA (miRNA) miR-142 into the 3’-untranslated region of the human cytomegalovirus (HCMV) IE2 to study the transcriptional effect of IE2 knock-down on both viral and host genes in cells that express miR-142. When comparing transcriptional data from miR-142 expressing macrophages infected with HCMV to macrophages infected with IE2-miR-142 targeted HCMV, we see a knock-down of IE2 and differential regulation of predicted viral targets of IE2 including IE1, vIL-10 and US29. We then generated fibroblasts expressing miR-142 to study the knock-down of IE2 in a different cellular system and find drastic differences in loss of IE2 on the host transcriptional profile in the two different cell types.

2017-12-28 | GSE107680 | GEO

Expression profile of EV71-infection-responsive miRNAs

Project description:We attempted to identify potential miRNAs that can regulate viral replication by screening host miRNAs in EV71-infected RD cells. To compare the differential expression of miRNAs in EV71-infected cells at different time points, miRNA expression profiles were analyzed using Agilent Human MicroRNA Array chips. At 5 h p.i., the expression levels of most miRNAs in EV71-infected cells were not different from those of mock-infected cells. However, five miRNAs (miR-574-3p, miR-574-5p, miR-181d, miR-197, and miR-939) showed a miRNAs (miR-193a-3p and miR-324-5p) exhibited a increase in expression level in response to EV71 infection at 10 h p.i.

2016-01-01 | GSE75455 | GEO

Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male sterile line by deep sequencing (Degradome-Seq)

Project description:The male sterility of thermosensitive genic male sterile (TGMS) lines of wheat (Triticum aestivum) is strictly controlled by temperature. The early phase of anther development is especially susceptible to cold stress. MicroRNAs (miRNA) play an important role in plant development and in responses to environmental stress. In this study, deep sequencing of small RNA (smRNA) libraries obtained from spike tissues of the TGMS line under cold and control conditions identified a total of 81 unique miRNA sequences from 30 families, and trans-acting small interfering RNAs (tasiRNAs) derived from two TAS3 genes. To identify smRNA targets in the wheat TGMS line, we applied the degradome sequencing method, which globally and directly identifies the remnants of smRNA-directed target cleavage. We identified 26 targets of 16 miRNA families and three targets of tasiRNAs. Comparing smRNA sequencing datasets and TaqMan qPCR results, we identified six miRNAs and one tasiRNA (tasiRNA-ARF) as cold stress-responsive smRNAs in spike tissues of the TGMS line. We also determined the expression profiles of target genes that encode transcription factors in response to cold stress. Interestingly, expressions of cold-stress responsive smRNAs integrated in the auxin-signaling pathway and their target genes were largely anticorrelated. We investigated tissue-specific expression of smRNAs using a tissue microarray approach. Our data indicated that miR167 and tasiRNA-ARF play roles in regulating the auxin-signaling pathway, and possibly in the developmental response to cold stress. These data provide evidence that smRNA regulatory pathways are linked with male sterility in the TGMS line during cold stress.

2012-04-11 | GSE37134 | GEO

Uncovering small RNA-mediated responses to cold stress in a wheat thermosensitive genic male sterile line by deep sequencing (Degradome-Seq)

2012-04-11 | E-GEOD-37134 | biostudies-arrayexpress

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