Using RNA-seq to identify transcriptional targets of MAB-5 in C. elegans

In C. elegans, the bilateral Q neuroblasts and their neuronal descendants undergo long-range migrations. QR (on the right) polarizes and migrates anteriorly, whereas QL (on the left) polarizes and migrates posteriorly. The Hox transcription factor MAB-5 is a determinant of this posterior migration of QL, and likely regulates target genes that determine posterior versus anterior migration. We sought to identify these downstream networks of genes via RNA-seq, and identify transcripts that are differentially expressed between wildtype and mab-5 mutant genotypes. We sequenced RNA extracted from early L1 staged animals from four C. elegans genotypes: wildtype worms, mab-5(e1239) and mab-5(gk670) loss-of-function mutants, and the mab-5(e1751) gain-of-function mutant. Tests revealed a number of differentially expressed genes, many of which were validated by subsequent RNAi.

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