Browsing by Author "Dr. Bob Petters, Committee Member"

Filter results by typing the first few letters
Now showing 1 - 2 of 2
  • No Thumbnail Available
    Identification of Targets and Pathways Controlled by the Chicken MicroRNAs miR-10a and miR-143
    (2009-12-02) Hsia, Hung-Ching; Dr. H. -C. Sunny Liu, Committee Chair; Dr. Bob Petters, Committee Member; Dr. Chad Stahl, Committee Member
    MicroRNAs are small non-coding RNAs that regulate gene expression at the posttranscriptional level. The importance of microRNAs in development, tumorogenesis, immune system function, and infectious diseases has gradually come to light. MicroRNAs are often expressed in a temporal and spatial manner and regulate specific gene sets to achieve phenotypic change. To understand the role of microRNAs in the chicken embryonic spleen, we have profiled microRNA expression at E15 and E20 chicken embryos. The objective of the current project is to identify the targets and pathways controlled by two microRNAs, miR-10a and miR-143. Target prediction was carried out by the algorithm miRanda. Eight predicted targets of each microRNA were subjected to validation using a reporter assay that incorporates synthetic or retroviral transduced microRNA. Validated targets for miR-143 known to have profound functions in apoptosis, T and B cell development and maturation, cancer, or adipocyte differentiation were identified with this approach; for miR-10a, validated targets involved in hematopoiesis, immune cells homing and migration and megakaryocyte differentiation were identified. Microarray analysis revealed that several targets not predicted by the algorithm were upregulated upon treatment with a specific microRNA inhibitor. This result suggests that both microRNAs may regulate genes that contribute to cancer formation. In addition, miR-10a may be involved in regulating the complement system, which is a crucial component of innate immunity; miR-143 may be involved in the PPAR/RXR pathway, which regulates glucose and lipid metabolism in cells. Taken together, our results suggest targets and pathways possibly regulated by miR-10a or miR-143. The inferred functions of the targets and pathways identified in our study are mostly consistent with those from previous studies, thereby providing insights and directions for future research into the mechanisms by which miR-10a and miR-143 exert their function in the developing chick embryo. Furthermore, the RCAS system used in this project also proved the usefulness of engineered retrovirus for transducing microRNA. Further development of this tool may aid microRNA research and further contribute to understanding of the role of microRNAs in vertebrate development.
  • No Thumbnail Available
    MicroRNAs in the Spleen and Liver of the Developing Chick Embryo.
    (2008-05-02) Hicks, Julie Ann; Dr. Bob Petters, Committee Member; Dr. Mattew Koci, Committee Member; Dr. HC Sunny Liu, Committee Chair
    MicroRNAs are small (˜19-24nt) non-coding RNAs that are involved in the regulation of gene expression. They are mainly expressed in development and many are expressed in a temporal as well as, a spatial manner. It is thought they may regulate up to 30% of all genes. Pyrosequencing using 454 Life Science technology is becoming the preferred method for microRNA profiling ad sequencing compared to the previous method of cloning and using traditional sequencing techniques. Use of 454 Life Sciences technology allows for a greater coverage of microRNAs and increases the chances of sequence low abundance microRNAs. In the current project we created four small RNA libraries from embryonic chick tissues, the spleen and liver at developmental time points E15 and E20. These libraries were then sequenced using 454 Life Sciences pyrosequencing. A total of 92,919 sequence reads were obtained, representing a total of 52,001 known chicken microRNAs. Of these 92,919 reads, 52,001 represented miRNAs matching the miRBase G. gallus database, and 3,472 were not found in the G. gallus database but were homologues of miRBase miRNAs from other species. Of these homologous reads 391 represented potential novel miRNAs. Other small RNAs, such as tRNA and rRNA, represented 24,672 of the reads, and 12,383 reads represented other types of sequences, such as degraded mRNA. More than one hundred different known miRNAs were identified in this study, and many were expressed in all four libraries. Common miRNAs that yielded multiple reads from all four libraries included miR-125b and miR-21, which are involved in general processes of cellular proliferation. Overall, the spleen libraries had a larger array of miRNAs than the liver libraries. Much of spleen development occurs during the later stages of embryonic development, so we can reasonably expect that many gene expression changes occur during these stages. As a result of this study, we identified nine potential novel chicken miRNAs. These novel miRNAs appear to be tissue-specific. The potential novel miRNAs appeared to be expressed at lower levels than some of the known miRNAs, which could indicate that most of the highly-expressed chicken miRNAs have already been identified, whereas, for the most part, the miRNAs expressed at low levels remain to be discovered.