Cilia and flagella play important roles in many physiological processes, including cell and fluid movement, sensory perception, and development. The biogenesis and maintenance of cilia depend on intraflagellar transport (IFT), a motility process that operates bidirectionally along the ciliary axoneme. Disruption in IFT and cilia function causes several human disorders, including polycystic kidneys, retinal dystrophy, neurosensory impairment, and Bardet-Biedl syndrome (BBS). To uncover new ciliary components, including IFT proteins, we compared C. elegans ciliated neuronal and nonciliated cells through serial analysis of gene expression (SAGE) and screened for genes potentially regulated by the ciliogenic transcription factor, DAF-19. Using these complementary approaches, we identified numerous candidate ciliary genes and confirmed the ciliated-cell-specific expression of 14 novel genes. One of these, C27H5.7a, encodes a ciliary protein that undergoes IFT. As with other IFT proteins, its ciliary localization and transport is disrupted by mutations in IFT and bbs genes. Furthermore, we demonstrate that the ciliary structural defect of C. elegans dyf-13(mn396) mutants is caused by a mutation in C27H5.7a. Together, our findings help define a ciliary transcriptome and suggest that DYF-13, an evolutionarily conserved protein, is a novel core IFT component required for cilia function.
Completion of the DNA sequences of the human genome and that of the nematode Caenorhabditis elegans allows the large-scale identification and analysis of orthologs of human genes in an organism amenable to detailed genetic and molecular analyses. We are determining gene expression profiles in specific cells, tissues, and developmental stages in C. elegans. Our ultimate goal is not only to describe detailed gene expression profiles, but also to gain a greater understanding of the organization of gene regulatory networks and to determine how they control cell function during development and differentiation. The use of C. elegans as a platform to investigate the details of gene regulatory networks has several major advantages. Two key advantages are that it is the simplest multicellular organism for which there is a complete sequence (C. elegans Sequencing Consortium 1998), and it is the only multicellular organism for which there is a completely documented cell lineage (Sulston and Horvitz 1977; Sulston et al. 1983). C. elegans is amenable to both forward and reverse genetics (for review, see Riddle et al. 1997). A 2-week life span and generation time of just 3 days for C. elegans allows experimental procedures to be much shorter, more flexible, and more cost-effective compared to the use of mouse or zebrafish models for genomic analyses. Finally, the small size, transparency, and limited cell number of the worm make it possible to observe many complex cellular and developmental processes that cannot easily be observed in more complex organisms. Morphogenesis of organs and tissues can be observed at the level of a single cell (White et al. 1986). As events have shown, investigating the details of C. elegans biology can lead to fundamental observations about human health and biology (Sulston 1976; Hedgecock et al. 1983; Ellis and Horvitz 1986). We are using complementary approaches to examine gene expression in C. elegans. We are constructing transgenic animals containing promoter green fluorescent protein (GFP) fusions of nematode orthologs of human genes. These transgenic animals are examined to determine the time and tissue expression pattern of the promoter::GFP constructs. Concurrently, we are undertaking serial analysis of gene expression (SAGE) on all developmental stages of intact animals and on selected purified cells. Tissues and selected cells are isolated using a fluorescence activated cell sorter (FACS) to sort promoter::GFP marked cell populations. To date we have purified to near homogeneity cell populations for embryonic muscle, gut, and a subset of neurons. The SAGE and promoter::GFP expression data are publicly available at http://elegans.bcgsc.bc.ca.
Starting with SAGE-libraries prepared from C. elegans FAC-sorted embryonic intestine cells (8E-16E cell stage), from total embryos and from purified oocytes, and taking advantage of the NextDB in situ hybridization data base, we define sets of genes highly expressed from the zygotic genome, and expressed either exclusively or preferentially in the embryonic intestine or in the intestine of newly hatched larvae; we had previously defined a similarly expressed set of genes from the adult intestine. We show that an extended TGATAA-like sequence is essentially the only candidate for a cis-acting regulatory motif common to intestine genes expressed at all stages. This sequence is a strong ELT-2 binding site and matches the sequence of GATA-like sites found to be important for the expression of every intestinal gene so far analyzed experimentally. We show that the majority of these three sets of highly expressed intestinal-specific/intestinal-enriched genes respond strongly to ectopic expression of ELT-2 within the embryo. By flow-sorting elt-2(null) larvae from elt-2(+) larvae and then preparing Solexa/Illumina-SAGE libraries, we show that the majority of these genes also respond strongly to loss-of-function of ELT-2. To test the consequences of loss of other transcription factors identified in the embryonic intestine, we develop a strain of worms that is RNAi-sensitive only in the intestine; however, we are unable (with one possible exception) to identify any other transcription factor whose intestinal loss-of-function causes a phenotype of comparable severity to the phenotype caused by loss of ELT-2. Overall, our results support a model in which ELT-2 is the predominant transcription factor in the post-specification C. elegans intestine and participates directly in the transcriptional regulation of the majority (> 80%) of intestinal genes. We present evidence that ELT-2 plays a central role in most aspects of C. elegans intestinal physiology: establishing the structure of the enterocyte, regulating enzymes and transporters involved in digestion and nutrition, responding to environmental toxins and pathogenic infections, and regulating the downstream intestinal components of the daf-2/daf-16 pathway influencing aging and longevity.
A crucial step in the development of muscle cells in all metazoan animals is the assembly and anchorage of the sarcomere, the essential repeat unit responsible for muscle contraction. In Caenorhabditis elegans, many of the critical proteins involved in this process have been uncovered through mutational screens focusing on uncoordinated movement and embryonic arrest phenotypes. We propose that additional sarcomeric proteins exist for which there is a less severe, or entirely different, mutant phenotype produced in their absence. We have used Serial Analysis of Gene Expression (SAGE) to generate a comprehensive profile of late embryonic muscle gene expression. We generated two replicate long SAGE libraries for sorted embryonic muscle cells, identifying 7,974 protein-coding genes. A refined list of 3,577 genes expressed in muscle cells was compiled from the overlap between our SAGE data and available microarray data. Using the genes in our refined list, we have performed two separate RNA interference (RNAi) screens to identify novel genes that play a role in sarcomere assembly and/or maintenance in either embryonic or adult muscle. To identify muscle defects in embryos, we screened specifically for the Pat embryonic arrest phenotype. To visualize muscle defects in adult animals, we fed dsRNA to worms producing a GFP-tagged myosin protein, thus allowing us to analyze their myofilament organization under gene knockdown conditions using fluorescence microscopy. By eliminating or severely reducing the expression of 3,300 genes using RNAi, we identified 122 genes necessary for proper myofilament organization, 108 of which are genes without a previously characterized role in muscle. Many of the genes affecting sarcomere integrity have human homologs for which little or nothing is known.
A new integrin-associated protein, CPNA-1, which is essential for embryonic muscle development, is characterized. CPNA-1 contains a C-terminal copine domain. PAT-6 (actopaxin, parvin) recruits CPNA-1, and CPNA-1 recruits M-line proteins, including UNC-89 (obscurin).
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