The <i>C. elegans</i> genome has been completely sequenced, and the developmental anatomy of this model organism is described at single-cell resolution. Here we utilize strategies that exploit this precisely defined architecture to link gene expression to cell type. We obtained RNAs from specific cells and from each developmental stage using tissue-specific promoters to mark cells for isolation by FACS or for mRNA extraction by the mRNA-tagging method. We then generated gene expression profiles of more than 30 different cells and developmental stages using tiling arrays. Machine-learningbased analysis detected transcripts corresponding to established gene models and revealed novel transcriptionally active regions (TARs) in noncoding domains that comprise at least 10% of the total <i>C. elegans</i> genome. Our results show that about 75% of transcripts with detectable expression are differentially expressed among developmental stages and across cell types. Additionally, we used self-organizing maps to define groups of co-regulated transcripts and applied regulatory element analysis to identify known transcription factor and miRNA-binding sites, as well as novel motifs that likely function to control subsets of these genes. By using cell-specific, whole-genome profiling strategies, we have detected a large number of novel transcripts and produced high-resolution gene expression maps that provide a basis for establishing the roles of individual genes in cellular differentiation.
In a second project, I have identified an immunoglobulin-domain containing cell adhesion molecule that promotes synaptic-connectivity between the AVA command interneuron and A-class motor neurons in the <i>C. elegans</i> motor circuit. Animals carrying a mutation in <i>rig-3</i> show moderate backward locomotion defects. Additionally, <i>rig-3</i> mutants show minor AVA axon guidance defects and most synapses between AVA and A-class motor neurons are lost. These data suggest <i>rig-3</i> plays a critical role in synapse formation. It will be interesting to determine the involvement of <i>rig-3</i> function in connectivity between other neurons in the motor circuit and the entire nervous system.
| Identifer | oai:union.ndltd.org:VANDERBILT/oai:VANDERBILTETD:etd-07162011-123812 |
| Date | 21 July 2011 |
| Creators | Spencer, William Clayton |
| Contributors | James Goldenring, Randy Blakely, Ethan Lee, Guoqiang Gu, David Miller |
| Publisher | VANDERBILT |
| Source Sets | Vanderbilt University Theses |
| Language | English |
| Detected Language | English |
| Type | text |
| Format | application/pdf |
| Source | http://etd.library.vanderbilt.edu/available/etd-07162011-123812/ |
| Rights | unrestricted, I hereby certify that, if appropriate, I have obtained and attached hereto a written permission statement from the owner(s) of each third party copyrighted matter to be included in my thesis, dissertation, or project report, allowing distribution as specified below. I certify that the version I submitted is the same as that approved by my advisory committee. I hereby grant to Vanderbilt University or its agents the non-exclusive license to archive and make accessible, under the conditions specified below, my thesis, dissertation, or project report in whole or in part in all forms of media, now or hereafter known. I retain all other ownership rights to the copyright of the thesis, dissertation or project report. I also retain the right to use in future works (such as articles or books) all or part of this thesis, dissertation, or project report. |
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