MicroRNAs (miRNAs) are 22-nt RNAs that pair to the mRNAs of plant and animal cells, primarily in their 3'untranslated regions (3'UTRs), to direct the posttranscriptional repression o these messages. More than 500 miRNA genes have been identified in humans, and because most human genes have been under selective pressure to maintain their pairing to miRNAs, it is no surprise that miRNAs have already been shown to play important roles in mammalian development and human disease, including viral infection and cancer. This proposal focuses on the regulatory targets and repressive effects of miRNAs, with the broad, long-term objective of understanding the roles of RNA in regulating gene expression. With recent advances in miRNA genomics, the ability to place miRNAs into gene regulatory networks is limited less by unknown miRNAs and more by unknown 3'UTRs, particularly the alternative 3'UTR isoforms found in some cells but not others.
The specific aims of this proposal are: 1) to identify 3'UTRs of flies and vertebrates, 2) to identify additional mRNA and cellular features that influence miRNA targeting specificity, and 3) to determine the diversity and temporal sequence of miRNA repressive effects. Experiments of Aim #1 will use a newly developed high-throughput method both to characterize 3'UTRs of flies, zebrafish, and mammalian cell lines and to learn how 3'UTR isoforms change during development and cell-cycle arrest. They will also identify long noncoding RNAs in Caenorhabditis elegans, flies, and vertebrates. Experiments of Aim #2 will determine the degree to which poly(A)-tail length, mRNA stability and cellular features influence the efficacy of miRNA targeting. These results and those of Aim #1 will be used to provide a more precise and comprehensive list of predicted miRNA targets-a resource for all biologists, and of particular value for those concerned with eukaryotic gene regulation, development, and disease. Experiments of Aim #3 will determine the extent to which miRNA-mediated repression can be discerned from reduced transcript levels. They also will determine, on a global scale, the earliest detectable molecular consequences of targeting. Knowing which genes each miRNA represses and the molecular consequences of this repression will be useful for determining additional biological functions of miRNAs and learning how their dysfunction can contribute to disease.

Public Health Relevance

The experiments of this proposal focus on short snippets of RNA called microRNAs, which can collaborate with the proteins of the cell to determine how much protein is produced from individual genes, including many genes implicated in cancer and other diseases. The goals are to learn how best to predict which genes the microRNAs regulate and to determine the series of molecular events that reduces protein output from each regulated gene. Achieving these goals will shed light on why microRNAs are needed for normal growth and development, and how their dysfunction can contribute to human diseases.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Genomics, Computational Biology and Technology Study Section (GCAT)
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Bender, Michael T
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Whitehead Institute for Biomedical Research
United States
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Guo, Junjie U; Agarwal, Vikram; Guo, Huili et al. (2014) Expanded identification and characterization of mammalian circular RNAs. Genome Biol 15:409
Subtelny, Alexander O; Eichhorn, Stephen W; Chen, Grace R et al. (2014) Poly(A)-tail profiling reveals an embryonic switch in translational control. Nature 508:66-71
Denzler, Rémy; Agarwal, Vikram; Stefano, Joanna et al. (2014) Assessing the ceRNA hypothesis with quantitative measurements of miRNA and target abundance. Mol Cell 54:766-76
Kronja, Iva; Yuan, Bingbing; Eichhorn, Stephen W et al. (2014) Widespread changes in the posttranscriptional landscape at the Drosophila oocyte-to-embryo transition. Cell Rep 7:1495-508
Eichhorn, Stephen W; Guo, Huili; McGeary, Sean E et al. (2014) mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues. Mol Cell 56:104-15
Nam, Jin-Wu; Rissland, Olivia S; Koppstein, David et al. (2014) Global analyses of the effect of different cellular contexts on microRNA targeting. Mol Cell 53:1031-43
Auyeung, Vincent C; Ulitsky, Igor; McGeary, Sean E et al. (2013) Beyond secondary structure: primary-sequence determinants license pri-miRNA hairpins for processing. Cell 152:844-58
Ulitsky, Igor; Bartel, David P (2013) lincRNAs: genomics, evolution, and mechanisms. Cell 154:26-46
Spies, Noah; Burge, Christopher B; Bartel, David P (2013) 3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts. Genome Res 23:2078-90
Nodine, Michael D; Bartel, David P (2012) Maternal and paternal genomes contribute equally to the transcriptome of early plant embryos. Nature 482:94-7

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