Regulation of microRNA transcription

Gene regulation is now widely accepted to happen both at the transcriptional and the post-transcriptional level, and microRNAs (miRNAs) have emerged as critical modulators of gene expression in plants and animals. How do these transcriptional and post-transcriptional mechanisms interact to define robust regulatory networks? A major barrier to this question has historically been a lack of knowledge about the regulation of miRNAs themselves. In this dissertation we seek to characterize the promoters of miRNAs which are transcribed by RNA polymerase II, and to understand the similarities and differences between miRNA and protein-coding gene regulation. We begin by building a method to identify miRNA promoter elements using known transcription factor binding motifs, and apply this technique to perform a comparative analysis of miRNA and protein-coding gene promoters in Arabidopsis. We find that motifs associated with five transcription factors are reported which show evidence of over-representation in miRNA promoter regions relative to the promoter regions of protein-coding genes. In addition to the core promoter element TATA-box, these factors relate to regulation by plant hormones and plant responsiveness to drought. A similar comparison in animal organisms is impeded by the problem of so few currently known animal miRNA transcription start sites, and we therefore develop methods to address this problem. We create a toolset for the construction an animal miRNA promoter region tiling arrays, and design a transcription start site detection algorithm for non-coding primary transcripts of mammalian miRNAs. Finally, we investigate a special case of gene regulation both by and of intronic miRNAs. Since computational and experimental evidence increasingly supports the idea that intronic miRNAs are transcribed along with their host genes, we investigate whether such miRNAs may regulate the expression of the host genes in which they are located. Through this analysis we identify an intronic miRNA which may be involved in neurodegenerative disease, and provide experimental evidence that this miRNA may suppress protein production of the very gene along with which it is transcribed