Using RNA-seq to identify Hox transcriptional targets in neuronal migration

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DESCRIPTION (provided by applicant): Neuronal migration is a key developmental event that shapes the brain and central nervous system. In C. elegans, the bilaterally symmetric Q neuroblasts give rise to descendants that migrate anteriorly (on the right) and posteriorly (on the left) dependent upon Wnt signaling. While canonical Wnt pathways resulting in transcriptional changes are understood, it is less clear how these transcriptional changes induced by Wnt result in specific cell and growth cone guidance decisions. In this proposal we seek to understand the mechanisms of Wnt-induced transcriptional changes in the guidance of neuroblast migration in C. elegans. In the absence of the Wnt signal, the Q neuroblast descendants migrate to the anterior. The Hox transcription factor MAB-5 mediates this posterior guidance in response to Wnt, and might regulate other genes that specify posterior versus anterior migration. We will take advantage of this relatively simple guidance decision to identify genes regulated by MAB-5 that control posterior versus anterior migration. We will analyze the transcriptomes of wild-type and mab-5 loss of function and gain of function mutants using the emerging technology of transcript sequencing (RNA-seq) on the Illumina Genome AnalyzerII instrument to identify genes that are upregulated or downregulated in response to MAB-5 activity. We will then use high throughput RNAi to identify which of these candidate genes control Q descendant migration. This would represent a unique advance and insight into the transcriptional regulation of differentiation by identifying downstream differentiation factors regulated by transcripton factors. These studies will also test the efficacy the emerging technology of RNA-seq to identify transcriptional targets of transcription factors via mutant analysis, a question normally addressed with microarrays. While techniques are available to isolate RNA pools from specific cell populations in model organisms, they might not be feasible for all cells types due to limitations on the availability of cell-specific promoters or the low amount of RNA recovered. In this proposal we will test the sensitivity of RNA-seq to detect changes in gene expression in RNA populations isolated from whole organisms. This proposal is significant in that it will identify MAB-5 Hox targets in guided cell migration, and in that it will test the efficacy and sensitivity of the emerging technology of RNA-seq in the identification of transcriptional targets in model organisms where cell-specific RNA pools often cannot be obtained. PUBLIC HEALTH RELEVANCE: Neuronal migration is a key process in brain and central nervous system development. Deficits in this process can lead to developmental disorders with mental retardation, such as lissencephalies, and also might contribute to schizophrenia and autism spectrum disorders. The goal of this proposal is to use the model organism nematode worm C. elegans to understand the basic molecular mechanisms of neuronal migration, which might provide insight into the underlying molecular mechanisms associated with developmental disorders of the central nervous system. The proposal also will test the efficacy the emerging technology of RNA-seq to identify gene expression differences and transcription factor targets.