Songbirds such as zebra finches communicate via learned vocalizations (songs) and studies have shown that experiencing song playback triggers complex genomic responses in the zebra finch auditory forebrain. MicroRNAs (miRNAs or miRs) are important regulators of gene expression which may coordinate complex biological processes through post-transcriptional mechanisms. This dissertation aims to explore the potential roles of miRs in the genomic response to song.This study began with a bioinformatic analysis of published microarray data and qPCR analysis of a specific conserved miR (miR-124) in zebra finch auditory forebrain, elements of which contributed to the primary paper describing the zebra finch genome (Warren et al. 2010). These preliminary studies are described in the Introduction to this thesis. Chapter 2 then presents a full de novo characterization of miRs in the songbird brain and demonstrates that song exposure has effects on several. This has now been published as Gunaratne, Lin et al. 2011 (co-first authors). A significant outcome of Chapter 2 was the identification of a novel sex-linked miR, miR-2954. Chapter 3 describes the tissue, cellular and subcellular distribution of miR-2954 and localizes it to subsets of cells in the brain. An antisense inhibitor of miR-2954 was then applied to a zebra finch cell line followed by RNA-seq analysis to test the hypothesis that changes in miR-2954 levels lead to changes in the network of genes expressed. The results confirm this hypothesis and suggest that the initial song-induced decline in miR-2954 expression described in Chapter 2 may help reprogram gene expression networks to support the metabolic changes associated with song habituation (Dong et al., 2009). This thesis research helps better understand the transcriptome of songbird brain and establishes novel roles for microRNAs in song perception, discrimination and memory.
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