SPELL - Nematode

Citation	Tamayo JV, Gujar M, Macdonald SJ, Lundquist EA. Functional transcriptomic analysis of the role of MAB-5/Hox in Q neuroblast migration in Caenorhabditis elegans. BMC Genomics, 2013.
PubMed ID	23642123
Short Description	Functional transcriptomic analysis of the role of MAB-5/Hox in Q neuroblast migration in Caenorhabditis elegans. GEO Record: N.A. Platform: N.A. Download gene-centric, log2 transformed data: WBPaper00042361.ce.rs.csv
# of Conditions	26
Full Description	BACKGROUND: Directed 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. RESULTS: Transcriptome 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. CONCLUSIONS: Our 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. Experimental Details: RNASeq.elegans.WBStrain00024162.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212092 RNASeq.elegans.WBStrain00024162.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212095 RNASeq.elegans.WBStrain00024162.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212097 RNASeq.elegans.WBStrain00024162.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212098 RNASeq.elegans.WBStrain00024162.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212099 RNASeq.elegans.WBStrain00024162.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212100 RNASeq.elegans.WBStrain00024162.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212101 RNASeq.elegans.WBStrain00024162.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212102 RNASeq.elegans.WBStrain00024165.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212103 RNASeq.elegans.WBStrain00024165.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212104 RNASeq.elegans.WBStrain00024165.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212105 RNASeq.elegans.WBStrain00024165.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212106 RNASeq.elegans.WBStrain00024165.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212107 RNASeq.elegans.WBStrain00024165.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212109 RNASeq.elegans.WBStrain00024166.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212110 RNASeq.elegans.WBStrain00024166.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212111 RNASeq.elegans.WBStrain00024166.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212112 RNASeq.elegans.WBStrain00024166.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212113 RNASeq.elegans.WBStrain00024166.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212114 RNASeq.elegans.WBStrain00024166.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212115 RNASeq.elegans.WBStrain00024167.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212116 RNASeq.elegans.WBStrain00024167.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212118 RNASeq.elegans.WBStrain00024167.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212119 RNASeq.elegans.WBStrain00024167.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212120 RNASeq.elegans.WBStrain00024167.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212121 RNASeq.elegans.WBStrain00024167.WBls:0000024.Hermaphrodite.WBbt:0007833.SRP017621.SRX212122.
Tags	Method: RNAseq, Species: Caenorhabditis elegans, Topic: WT vs. mutant