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First published online March 24, 2005
doi: 10.1242/10.1242/dev.01775

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Analysis of xbx genes in C. elegans

¹ Karolinska Institute, Department of Biosciences and Södertörn University College, Section of Natural Sciences, S-14189 Huddinge, Sweden
² Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
³ Department of Microbiology, University of Washington, Seattle, WA 98195, USA
⁴ Department of Molecular Biology, Massachusetts General Hospital and Department of Genetics, Harvard Medical School, Boston, MA 02114, USA
⁵ Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A 1S6, Canada

View larger version (27K): [in a new window]   Fig. 1. Computational search for the X-box motif. (A) Schematic of the X-box search algorithm. The algorithm finds all matches for a defined motif consensus and cross-matches them against a list of predicted genes or available ESTs. The search space upstream of predicted genes was set to 1000 bp. (B) The number of matches obtained with different consensus sequences (top to bottom: relaxed, average, refined) searching the C. elegans genome. (C) The `relaxed' X-box consensus (RYYNYY WW RRNRAC), used for initial searches, generates the largest number of matches that spread equally within promoter regions. (D) The `refined' X-box consensus (GTHNYY AT RRNAAC), obtained on the basis of in vivo expression analysis of xbx genes, shows a significant concentration of matches in the region of around 100 bp upstream of the ATG.

View larger version (45K): [in a new window]   Fig. 2. Functional repertoire of xbx genes. Functional repertoire of xbx genes and some representative members from different molecular groups, including possible components of cilium structure and transport machinery, transcription factors and receptors. The diagram represents data from the `average' consensus list of xbx genes/candidates (758 members) (see Table S1 in supplementary material), including experimentally proven genes.

View larger version (82K): [in a new window]   Fig. 3. Newly discovered X-box genes. (A) xbx-2::gfp is expressed in most or all CSN. (B) xbx-3::gfp is expressed in amphid and phasmid (not shown) neurons. (C) xbx-4::gfp is expressed in a subset of amphid neurons. (D) xbx-5::gfp is expressed in a subset of amphid neurons. (E) xbx-6::gfp is expressed in many different types of cells, including the phasmid neurons PHA and PHB. (F) xbx-7::gfp is expressed in a subset of amphid and interlabial neurons. (G) tub-1::gfp is expressed in most or all CSN. (H) Schematic diagram of CSN positioning in the C. elegans hermaphrodite (after Collet et al., 1998).

View larger version (28K): [in a new window]   Fig. 4. An example of retrograde movement for XBX-2::GFP particles in a phasmid cilium (see also Movie 1 in supplementary material). The ciliary transition zone is marked with an asterisk. The arrowhead indicates the initial position of the moving particle at time zero (t=0). The arrow indicates the position of the moving particle at different time points (t=0.5 and 1 seconds). Scale bars: 1 µm.

View larger version (15K): [in a new window]   Fig. 5. Properties of the X-box motif in C. elegans. (A) The X-box consensus sequence obtained from in vivo expression analysis. Nucleotides marked in red are strongly conserved and important for the proper function of the motif. (B) Proposed scheme for the difference in expression patterns observed for xbx genes. Depending on the nucleotide composition of the X-box, DAF-19 can bind to the motif either in homodimer (driving expression in many, most or all CSN) or in heterodimer form, interacting together with some cell-specific factor (driving expression in a subset of CSN).

View larger version (19K): [in a new window]   Fig. 6. Development of a `ciliary module' in C. elegans. DAF-19 regulates the development of the module, which includes genes for the cilium structure and transport machinery, receptors and other factors. The activation of this module leads to the formation of functional ciliated endings during specification of sensory neurons in the worm.