Functional transcriptomic analysis of the role of MAB-5/Hox in Q neuroblast migration in Caenorhabditis elegans

Joel V Tamayo,Erik A Lundquist,Mahekta Gujar,Stuart J Macdonald

doi:10.1186/1471-2164-14-304

Abstract

BackgroundDirected cell migration is a fundamental process in normal development and in tumor metastasis. In C. elegans the MAB-5/Hox transcription factor is a determinant of posterior migration of the Q neuroblast descendants. In this work, mab-5 transcriptional targets that control Q descendant migration are identified by comparing RNA-seq profiles in wild type and mab-5 mutant backgrounds.ResultsTranscriptome profiling is a widely-used and potent tool to identify genes involved in developmental and pathological processes, and is most informative when RNA can be isolated from individual cell or tissue types. Cell-specific RNA samples can be difficult to obtain from invertebrate model organisms such as Drosophila and C. elegans. Here we test the utility of combining a whole organism RNA-seq approach with mab-5 loss and gain-of-function mutants and functional validation using RNAi to identify genes regulated by MAB-5 to control Q descendant migration. We identified 22 genes whose expression was controlled by mab-5 and that controlled Q descendant migration. Genes regulated by mab-5 were enriched for secreted and transmembrane molecules involved in basement membrane interaction and modification, and some affected Q descendant migration.ConclusionsOur results indicate that a whole-organism RNA-seq approach, when combined with mutant analysis and functional validation, can be a powerful method to identify genes involved in a specific developmental process, in this case Q descendant posterior migration. These genes could act either autonomously in the Q cells, or non-autonomously in other cells that express MAB-5. The identities of the genes regulated by MAB-5 indicate that MAB-5 acts by modifying interactions with the basement membrane, resulting in posterior versus anterior migration.

Highlights

Directed cell migration is a fundamental process in normal development and in tumor metastasis
Total RNA was isolated from each genotype at the early L1 larval stage approximately 4.5-5 h after hatching, after the Q cells had undergone their initial migrations and divisions, and when mab-5 is activated by egl-20/ Wnt signaling in QL and QL descendants
Ceh-20 and unc-62 are epistatic to mab-5(gof) in posterior AQR migration As proof of principle of using posterior AQR migration in mab-5(e1751)gof as a background to define mab-5 targets that affect Q cell descendant migrations, we studied genetic interactions of mab-5(e1751)gof with two genes previously shown to interact with the Hox gene lin-39 in Q descendant migration, ceh-20 and unc-62 [32]. ceh-20 encodes a homeodomain transcription factor of the Extradenticle/Pbx family, and unc-62 encodes a homeodomain transcription factor of the Homothorax/Meis1 family [33], vertebrate counterparts of which can act as cofactors with other Hox factors to regulate gene expression [34]

Summary

Introduction

Directed cell migration is a fundamental process in normal development and in tumor metastasis. Mab-5 transcriptional targets that control Q descendant migration are identified by comparing RNA-seq profiles in wild type and mab-5 mutant backgrounds. Single migrating linker cells of the C. elegans male gonad were dissected from living animals and transcriptionally profiled using RNA-seq [3]. Despite these advances, isolation of cell-specific transcripts from model organisms using these techniques is not trivial, and not feasible for every cell type at this time. By comparing transcript levels in wild type and various mab-5 mutant backgrounds defective in Q cell migration, we test if genes with effects on Q migration can be identified by RNA-seq of whole animal lysates

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