Project description:Transcriptional profiling of chicken embryonic fibroblasts (DF-1 cells) comparing the effects of chicken cells transfected with duck RIG-I compared to empty-vector transfected cells following with low or highly pathogenic avian influenza. Goal was to determine the effects of duck RIG-I on influenza-induced immune gene expression.
Project description:We infected DF-1 cells with avian reovirus, and then used high-throughput sequencing to detect changes in miRNA expression profiles. This research provides a more comprehensive understanding of the interaction between viruses and host cells
Project description:Chicken brain and lung gene expression profiles following infection with two recombinant H5N3 avian influenza viruses - rH5N3 Ori (P0) and rH5N3 P6
Project description:We report the genome-wide DNA methylation mapping of chicken by methylated DNA immunoprecipitation following by highthroughput sequencing, and the gene expression profile of chicken by RNA-seq. For meDIP-seq, about 17,202,074 to 27,501,760 reads were generated for the tissue and liver tissues of the red jungle fowl and the avian broiler each. We found that compared with the red jungle fowl, DNA methylation in muscle tissue of the avian broiler, showed dramatically decline on a genome-wide scale. Furthermore, the length of the highly methylated regions (HMRs) has become shorter in the avian broiler, which has suffered intense artificial selection. In addition to the global changes in DNA methylation, transcriptome-wide analysis of the two breeds of chicken revealed that the patterns of gene expression in the domestic chicken have undergone a specific bias towards a pattern that is more suited to human-made environments with variable expression in certain gene functions, such as immune response and fatty acid metabolism. Our results demonstrated a potential role of epigenetic modification in animal domestication besides the genetic variations. Examination of whole genome DNA methylation status in liver and muscle of two chicken breeds.
Project description:While infection of chickens with highly pathogenic avian influenza (HPAI) H5N1 subtypes often leads to complete mortality within 24 to 48 h, infection of ducks in contrast causes mild or no clinical signs. Rapid onsets of fatal disease in chickens, but with no evidence of severe clinical symptoms in ducks, suggest underlying differences in their innate immune mechanisms. To understand the molecular basis for such difference, chicken and duck primary lung cells, infected with a low-pathogenicity avian influenza (LPAI) and two HPAI H5N1 viruses, were subjected to RNA expression profiling using Affymetrix Chicken GeneChip arrays. We used microarrays to analyze the gene expression profiles of primary chicken and duck lung cells infected with H2N3 LPAI and two H5N1 influenza virus subtypes to understand the molecular basis of host susceptibility and resistance. We have identified a set of key genes and pathways that could play an important role in mediating innate host resistance to avian influenza in chickens and ducks. 24 hours following infection, total RNA from cells was extracted. Replicate RNA samples from each of the virus-infected (H2N3, H5N1 50-92, or H5N1 ty-Ty) or mock-infected chicken and duck cells (4 treatment groups for each species) were used for microarray analysis. Each of the RNA samples was hybridized to one GeneChipM-BM-. Chicken Genome Array (Affymetrix), and a total of 16 array chips were used.
Project description:Temporal regulation of gene expression is essential for early embryonic development. With the development of next-generation sequencing technologies, transcriptional profiling of early developmental processes in various vertebrates are already revealed. However, overall transcriptome analysis of early embryonic development in avian have never been investigated. In this study, to our knowledge, we provide comprehensive profiling of pre-oviposited embryos in chicken by whole-transcriptome RNA-seq for the first time. We demonstrated the presence of avian-specific mechanism of first- and second-wave of zygotic genome activation (ZGA). Chicken early embryo have distinct developmental programs between cleavage and area pellucida formation period. Additional speculation of epigenetic dynamics indicate that maternal-to-zygotic transition (MZT) in chicken is promoted after second-wave of ZGA, through EGK.VI to EGK.X stages. These extensive results contribute to understanding avian early embryogenesis and comparative studies with other species with many developmental aspects.
