Project description:Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. Methods: spleen mRNA profiles of 8-weeks-old WT and lncRNA-ISIR, used to be called lnRNA-IRF3, knockout mice were generated by deep sequencing, using BGISEQ-500 system. The sequence reads that passed quality filters were analyzed at the transcriptional level with RSEM (RNA-seq by Expectation Maximization). Conclusions: Our study represents the first detailed analysis of retinal transcriptomes, generated by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. Our results show that NGS offers a comprehensive and more accurate quantitative and qualitative evaluation of mRNA content within a cell or tissue. We conclude that RNA-seq based transcriptome characterization would expedite genetic network analyses and permit the dissection of complex biologic functions.
Project description:Infection of mammalian cells by vesicular stomatitis virus (VSV) triggers the activation of the innate immunity pathway. VSV RNA is recognized by RIG-I, leading to the activation of RIG-I and subsequent activation of the essential effector MAVS. To gain a comprehensive understanding of the molecular events occurring in VSV-infected THP1 cells, we employed data-independent acquisition (DIA) and diaPASEF techniques to profile the dynamic phosphoproteomes and proteomes of wild-type (WT), RIG-I knockout (KO), and MAVS KO THP1 cells. This approach enabled the quantification of approximately 8000 proteins and 11000 localized phosphopeptides. The in-depth proteomic and phosphoproteomic analyses provided insights into the molecular mechanisms underlying VSV-induced ATM-mediated PBX2 degradation. Moreover, the phosphoproteomic data revealed that VSV induces phosphorylation events in THP1 cells independently of RIG-I. Additionally, we identified five phosphosites on VSV-coding proteins and predicted the corresponding kinases in host cells. Overall, our findings offer a comprehensive proteomic and phosphoproteomic map of VSV stimulation, highlighting RIG-I or MAVS-related phosphorylation events. This resource serves as a valuable foundation for future studies aimed at understanding the RNA-sensing innate immunity signaling pathway.
Project description:To investigate the function of lncRNA-BTX in the regulation of viral replication , we constructed lncRNA-BTX knockout mice.We separately took the peritoneal macrophages of lncRNA-BTX-/- and lncRNA-BTX+/+ mice, extracted RNA after VSV virus stimulation, and performed RNA-seq.
Project description:To investigate the function of lncRNA-BTX in the regulation of viral replication , we constructed lncRNA-BTX knockout mice.We separately took the peritoneal macrophages of lncRNA-BTX-/- and lncRNA-BTX+/+ mice, extracted RNA after VSV virus stimulation, and performed RNA-seq.
Project description:To gain an understanding of lncRNA-ACOD activity, we performed transcriptome analysis with microarray using liver tissues from mice with or without VSV for 12 hrs.
Project description:Cellular quiescence is coupled with cellular development, tissue homeostasis, and cancer progression. Both quiescence and cell cycle re-entry are controlled by active and precise regulation of gene expression. However, the roles of long noncoding RNAs (lncRNAs) during these processes remain to be elucidated. By performing a genome-wide transcriptome analyses, we identify thousands of differentially expressed lncRNAs, including ~30 of the less-characterized class of microRNA-host-gene lncRNAs (lnc-MIRHGs), during cellular quiescence and during serum-stimulation in human diploid cells. We observe that the mature MIR222HG display serum-stimulated induction due to enhanced pre-RNA splicing. Serum-stimulated binding of the pre-mRNA splicing factor SRSF1 to a micro-exon, which partially overlaps with the primary miR-222 precursor, facilitates enhanced MIR222HG splicing. In serum-stimulated cells, SRSF1 negatively regulates the Drosha/DGCR8-catalyzed cleavage of pri-miR-222, thereby increasing the cellular pool of the mature MIR222HG. Further, loss-of-function studies indicate that the mature MIR222HG facilitates the serum-stimulated cell cycle re-entry in a microRNA-independent manner. Mechanistically, MIR222HG, along with ILF3/2 complex, forms RNA:RNA duplex with DNM3OS lncRNA, thereby promoting DNM3OS stability. The current study identifies a mechanism in which the interplay between splicing versus microprocessor complex dictates the serum-induced expression of lnc-MIRHG MIR222HG for efficient cell cycle re-entry.