Alteration in m6A methylome of goat lung under PPRV infection
Ontology highlight
ABSTRACT:
ORGANISM(S): Capra hircus
PROVIDER: GSE190718 | GEO | 2022/12/05
REPOSITORIES: GEO
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Project description:Peste des petits ruminants virus (PPRV) belongs to the genus Morbillivirus that causes an acute and highly contagious disease in goats and sheep. Virus infection can trigger the change in the cellular microRNA (miRNA) expression profile, which play important post-transcriptional regulatory roles in gene expression and can greatly influence viral replication and pathogenesis. Here, we employed deep sequencing technology to determine cellular miRNAs expression profile in goat peripheral blood mononuclear cells (PBMCs) infected with Nigeria 75/1 vaccine virus, a widely used vaccine strain for mass vaccination programs against Peste des petits ruminants (PPR). Expression analysis demonstrated that PPRV infection can elicit 316 significantly differentially expressed (DE) miRNAs including 103 known and 213 novel miRNAs candidates in infected PBMCs at 24 hours post-infection as compared with mock control. Target prediction and functional analysis of these DEmiRNAs revealed significant enrichment for several signaling pathways including TLR signaling pathways, PI3K-Akt, endocytosis, viral carcinogenesis, and JAK-STAT signaling pathways. This study provides a valuable basis for further investigation on the roles of miRNAs in PPRV replication and pathogenesis.
2020-08-18 | GSE156378 | GEO
Project description:The mRNA m6A reader YTHDF2 is overexpressed in a broad spectrum of human acute myeloid leukemias (AML). To understand the role of YTHDF2 in AML, we generated m6A meRIP-seq libraries form Ythdf2fl/fl (Ythdf2CTL) pre-leukemic cells.
2019-04-05 | E-MTAB-6791 | biostudies-arrayexpress
Project description:The mRNA m6A reader YTHDF2 is overexpressed in a broad spectrum of human acute myeloid leukemias (AML). To understand the role of YTHDF2 in AML, we generated m6A meRIP-seq libraries form Ythdf2fl/fl; Vav-iCre (Ythdf2CKO) pre-leukemic cells.
2019-04-05 | E-MTAB-7783 | biostudies-arrayexpress
Project description:Viruses have evolved numerous strategies to impair immunity so that they can replicate more efficiently, such as the immunosuppressive effects of Morbillivirus infection. In the present work we hypothesized that the highly contagious morbillivirus Peste des Petits Ruminants virus (PPRV) could target monocytes and dendritic cells (DC) to contribute to the immunosuppressive effects produced by the infection. Monocytes isolated from healthy sheep donor, a natural host of the disease, could be infected by PPRV and this impaired the differentiation and phagocytic ability of immature monocyte-derived DC (MoDC). Ovine MoDC could be productively infected by PPRV, and this drastically reduced MoDC capacity to activate allogeneic T cell responses. Transcriptomic analysis of infected MoDC indicated that several tolerogenic DC signature genes were upregulated upon PPRV infection.
2022-09-06 | GSE203515 | GEO
Project description:To find the m6A methylation targets of ABRO1, we performed m6A methylated RNA immunoprecipitation sequencing (MeRIP-seq) in ABRO1 Knockout or Wild type (WT) mice heart. The analysis of the distribution of m6A peak density in mRNA transcripts showed that m6A peaks are mainly found in coding sequences (CDS) and a considerable amount of m6A peaks enriched around start codon and stop codon regions in mRNA transcripts from ABRO1 KO and WT hearts. Among the total RNA transcripts with m6A sites, more than half (59.4%) of mRNA transcripts contain ≤ 2 m6A peaks, 27.4% mRNA transcripts comprise 3 to 5 m6A peaks and more than 5 m6A peaks exist in 13.2% of mRNA transcripts. MeRIP-seq analysis results from ABRO1 deleted hearts showed that a total of 3444 m6A peaks were upregulated and 4631 m6A were downregulated compared to WT hearts.
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Project description:Peste des Petits Ruminants (PPR) is a highly infectious disease caused by a virus of the genus Morbillivirus (PPRV), infecting mainly sheep and goat. Susceptibility of host can vary widely with host breed and virus strain. The mechanisms underlying this variability are not well understood. Here, we carried out the first comparative in vitro study on goat peripheral blood mononuclear cells (PBMCs) infected with PPRV strains of different virulence, vaccine strain (N75/1), low- (IC89), and high-virulent strain (MA08). Goat PBMCs were infected by the different strains and stimulated with Concanavalin A (Con A), and proteome changes of these cells were evaluated during the infection. The level of PPRV replication was assessed first by RT-qPCR quantification of viral N mRNA and by labelling the viral N protein inside the cells with specific antibodies and analysed by flow cytometry. The dynamics of PBMC sub-populations were also evaluated by flow cytometry. Our results showed that viral replication is critical for PPRV inhibitory effect on PBMCs proliferation. Highly virulent MA08 strain reached a higher level of replication in ConA-stimulated PBMCs and induced higher mortality compared to other strains. Low-virulent IC89 strain showed the lower replication level and cell proliferative inhibitory capacities. Differences in immune genes expression levels were assessed using RNAseq analysis and protein expression was compared using mass spectrometry. Analysis of these data provided the transcriptional and proteome landscape of PBMCs infected with these strains. The possible association between the transcriptional and proteome landscape and changes in immune cell subpopulations dynamics was explored.
2021-11-03 | PXD024890 | Pride
Project description:Peste des petits ruminants virus (PPRV) is a negative-stranded RNA virus belonging to the Paramyxoviridae family and causes acute, highly contagious disease in small ruminants. Lysine acetylation plays central role in regulating gene expression. However, the extent and function of lysine acetylation in host cells during PPRV infection remains unknown. In this study, intensive proteomic quantification analysis of the proteome and acetylome of PPRV-infected Vero cells was performed using dimethylation labeling-based quantitative proteomics. As results, we identified 4729 proteins and 1068 acetylated proteins with 2641 quantified modification sites detected by mass spectrometry, of which 304 acetylated proteins with 410 acetylation sites were significantly acetylated in response to PPRV infection. Bioinformatics analyses revealed that the differentially acetylated proteins participated in carbohydrate catabolic and DNA metabolic process, and were associated with multifarious functions, suggesting that intracellular activities were extensively changed after PPRV infection. Protein-protein interaction network of the identified proteins further indicated that a variety of chaperone and ribosome processes were modulated by acetylation. To our knowledge, this is the first study on acetylome in host cell infected with PPRV. It provides an important point for future studies on the acetylated proteins involved in the host response to PPRV replication.
2023-10-24 | PXD025081 | Pride
Project description:We report the application of MeRIP sequencing technology for high-throughput profiling of m6A methylome in breast cancer cells. Comparison of m6A methylome between control and BETi-treated cells revealed the following findings: 1) Significant global alteration of methylation sites due to BETi-treatment (herein defined as BETi-m6A signature). 2) Gene Ontology (GO) analysis of the differential meRIP-seq candidates enriched pathways involved in chromatin modification, RNA splicing and pathways regulating cell fate , reflecting a critical role of m6A in diverse biological processes.
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Project description:To investigate the role of m6A modification,MeRIP-seq was used to identify differential m6A modifications in lung adenocarcinoma .
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Project description:Our study demonstrated that the expression of Igf2bp1 in activated microglia was significantly up-regulated, implying a role of Igf2bp1 in LPS-induced m6A modifications in microglia. To understand the roles of Igf2bp1 on LPS-induced m6A modification in microglia, we performed Igf2bp1 loss-of-function (LOF) approach. Microglia stimulated by LPS were transfected with either scrambled siRNA control or Igf2bp1 siRNA for 48 hours. To m6A modification profiles in control and Igf2bp1 LOF microglia were determined by MeRIP-seq analysis.
2022-12-31 | E-MTAB-11411 | biostudies-arrayexpress