Functional transcriptomics of a migrating cell in Caenorhabditis elegans
Abstract
In both metazoan development and metastatic cancer, migrating cells must carry out a detailed, complex program of sensing cues, binding substrates, and moving their cytoskeletons. The linker cell in Caenorhabditis elegans males undergoes a stereotyped migration that guides gonad organogenesis, occurs with precise timing, and requires the nuclear hormone receptor NHR-67. To better understand how this occurs, we performed RNA-seq of individually staged and dissected linker cells, comparing transcriptomes from linker cells of third-stage (L3) larvae, fourth-stage (L4) larvae, and nhr-67-RNAi–treated L4 larvae. We observed expression of 8,000– 10,000 genes in the linker cell, 22–25% of which were up- or downregulated 20-fold during development by NHR-67. Of genes that we tested by RNAi, 22% (45 of 204) were required for normal shape and migration, suggesting that many NHR-67–dependent, linker cell-enriched genes play roles in this migration. One unexpected class of genes up-regulated by NHR-67 was tandem pore potassium channels, which are required for normal linker-cell migration. We also found phenotypes for genes with human orthologs but no previously described migratory function. Our results provide an extensive catalog of genes that act in a migrating cell, identify unique molecular functions involved in nematode cell migration, and suggest similar functions in humans.
Additional Information
© 2012 by the National Academy of Sciences. Edited by Ruth Lehmann, New York University Medical Center, New York, NY, and approved August 24, 2012 (received for review February 22, 2012). Published online before print September 18, 2012. We thank M. Goodman, M. Chalfie, and A. Mortazavi for early support in developing single-cell RT-PCR; B. Williams for providing control spike poly(A)+ RNAs; L. Schaeffer, D. Trout, and I. Antoshechkin of the Jacobs Genome Center for Illumina sequencing; A. Narayan for help setting up the dissection rig; J. Downes for scoring linker cell migration phenotypes; J. Thomas for his list of transcription factors; WormBase for gene annotations; and T. Brown, Y.-P. Hsueh, A. Roeder, K. Yook, and A. Zaslaver for comments. This work was supported by National Institutes of Health Grant GM084389 and by the Howard Hughes Medical Institute, with which P.W.S. is an Investigator. Author contributions: E.M.S. and M.K. designed research; E.M.S. and M.K. performed research; E.M.S., M.K., and P.W.S. analyzed data; and E.M.S., M.K., and P.W.S. wrote the paper. The authors declare no conflict of interest.Attached Files
Published - PNAS-2012-Schwarz-16246-51.pdf
Supplemental Material - sapp.doc
Supplemental Material - sd01.xlsx
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Additional details
- PMCID
- PMC3479585
- Eprint ID
- 34313
- Resolver ID
- CaltechAUTHORS:20120924-131548711
- NIH
- GM084389
- Howard Hughes Medical Institute (HHMI)
- Created
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2012-09-24Created from EPrint's datestamp field
- Updated
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2021-11-09Created from EPrint's last_modified field