Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species

An RFX-binding site is shown to be conserved in the promoters of a subset of ciliary genes and a subsequent screen for this site in two Drosophila species identified novel RFX target genes that are involved in sensory ciliogenesis

A Genome-Wide Collection of Mos1 Transposon Insertion Mutants for the C. elegans Research Community

Methods that use homologous recombination to engineer the genome of C. elegans commonly use strains carrying specific insertions of the heterologous transposon Mos1. A large collection of known Mos1 insertion alleles would therefore be of general interest to the C. elegans research community. We describe here the optimization of a semi-automated methodology for the construction of a substantial collection of Mos1 insertion mutant strains. At peak production, more than 5,000 strains were generated per month. These strains were then subject to molecular analysis, and more than 13,300 Mos1 insertions characterized. In addition to targeting directly more than 4,700 genes, these alleles represent the potential starting point for the engineered deletion of essentially all C. elegans genes and the modification of more than 40% of them. This collection of mutants, generated under the auspices of the European NEMAGENETAG consortium, is publicly available and represents an important research resource

The coiled-coil domain containing protein CCDC151 is required for the function of IFT-dependent motile cilia in animals

International audienceCilia are evolutionarily conserved organelles endowed with essential physiological and developmental functions. In humans, disruption of cilia motility or signaling leads to complex pleiotropic genetic disorders called ciliopathies. Cilia motility requires the assembly of multi-subunit motile components such as dynein arms, but mechanisms underlying their assembly pathway and transport into the axoneme are still largely unknown. We identified a previously uncharacterized coiled-coil domain containing protein CCDC151, which is evolutionarily conserved in motile ciliated species and shares ancient features with the outer dynein arm-docking complex 2 of Chlamydomonas. In Drosophila, we show that CG14127/CCDC151 is associated with motile intraflagellar transport (IFT)-dependent cilia and required for geotaxis behavior of adult flies. In zebrafish, Ccdc151 is expressed in tissues with motile cilia, and morpholino-induced depletion of Ccdc151 leads to left-right asymmetry defects and kidney cysts. We demonstrate that Ccdc151 is required for proper motile function of cilia in the Kupffer's vesicle and in the pronephros by controlling dynein arm assembly, showing that Ccdc151 is a novel player in the control of IFT-dependent dynein arm assembly in animals. However, we observed that CCDC151 is also implicated in other cellular functions in vertebrates. In zebrafish, ccdc151 is involved in proper orientation of cell divisions in the pronephros and genetically interacts with prickle1 in this process. Furthermore, knockdown experiments in mammalian cells demonstrate that CCDC151 is implicated in the regulation of primary cilium length. Hence, CCDC151 is required for motile cilia function in animals but has acquired additional non-motile functions in vertebrates

hemingway is required for sperm flagella assembly and ciliary motility in Drosophila

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Dzip1 and Fam92 form a ciliary transition zone complex with cell type specific roles in Drosophila

International audienceCilia and flagella are conserved eukaryotic organelles essential for cellular signaling and motility. Cilia dysfunctions cause life-threatening ciliopathies, many of which are due to defects in the transition zone (TZ), a complex structure of the ciliary base. Therefore, understanding TZ assembly, which relies on ordered interactions of multiprotein modules, is of critical importance. Here, we show that Drosophila Dzip1 and Fam92 form a functional module which constrains the conserved core TZ protein, Cep290, to the ciliary base. We identify cell type specific roles of this functional module in two different tissues. While it is required for TZ assembly in all Drosophila ciliated cells, it also regulates basal-body growth and docking to the plasma membrane during spermatogenesis. We therefore demonstrate a novel regulatory role for Dzip1 and Fam92 in mediating membrane/basal-body interactions and show that these interactions exhibit cell type specific functions in basal-body maturation and TZ organization

Comparison of the DCBB set of genes with the Ciliary proteome and Ciliome databases

Venn diagram presenting the overlaps between the three datasets: the cilia proteome [46,48]; the ciliome [47,49], and the DCBB (Additional data file 2). Asterisks indicate this study. Note that only 412 common genes are found in the three datasets. The number of genes also found in the 1,462, 412 or 83 X-box gene lists (Table 4), respectively, are noted in parentheses. The numbers of genes selected in the different studies to construct each dataset are given in Additional data file 3.<p><b>Copyright information:</b></p><p>Taken from "Identification of novel regulatory factor X (RFX) target genes by comparative genomics in species"</p><p>http://genomebiology.com/2007/8/9/R195</p><p>Genome Biology 2007;8(9):R195-R195.</p><p>Published online 17 Sep 2007</p><p>PMCID:PMC2375033.</p><p></p

Finding <i>Mos1</i> alleles with MosLocator.

<p>(A) MosLocator (<a href="http://www.ciml.univ-mrs.fr/applications/MosLocator" target="_blank">www.ciml.univ-mrs.fr/applications/MosLocator</a>) finds <i>Mos1</i> alleles using gene sequence or transcript names. For large lists of genetic gene names, the gene sequence or transcript names can be obtained using WormMart, or here, using WormBase Converter (<a href="http://www.ciml.univ-mrs.fr/applications/WB_converter" target="_blank">www.ciml.univ-mrs.fr/applications/WB_converter</a>) <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030482#pone.0030482-Engelmann1" target="_blank">[15]</a>. In the example shown, the 23 <i>ptr</i> genes were used as input. (B) Screen grabs were captured to illustrate the use of MosLocator. Left panel: a list of sequence names was entered, and the search parameters were defined. Upper right panel: a display of the output for this search. Clicking on a non-zero number displayed in either of the last two columns, for example the “2” associated with the gene T21H3.2 (<i>ptr-16</i>), generates the display shown in the inset. This is a list of the 2 <i>Mos1</i> mutant alleles that are found within the gene T21H3.2. Each allele name is hyperlinked to Wormbase. (C) A partial view of the Variation report for the <i>Mos1</i> allele <i>ttTi21065</i> found on chromosome V at Wormbase (version WS225). (D) The genomic environment of the <i>ttTi21065</i> allele is displayed. The figure is a screen-grab from Wormbase.</p

Genomic coverage of <i>Mos1</i>.

<p>Graphical representation of each <i>C. elegans</i> chromosome showing the regions of the genome that are potentially amenable to genome engineering using the publicly-available <i>Mos1</i> alleles; it is assumed that any point up to 1.5 kb away from a transposon-insertion site can be targeted. The bottom line is a magnified view of the boxed region on chromosome X.</p

Distribution of <i>Mos1</i> alleles.

<p>(A) Graph showing the relationship between chromosome length (as a percentage of the whole nuclear genome) and the proportion of <i>Mos1</i> alleles per chromosome reported in a previous study <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0030482#pone.0030482-Granger1" target="_blank">[5]</a>, and the 10,858 alleles obtained in the current project (black and red circles, respectively). The outliers, concerning chromosomes I and V, from the previous study are highlighted with lines. (B) Distribution of distances from one <i>Mos1</i> allele to the next, in a 5′ to 3′ direction along each chromosome. The graph shows the cumulative percentage of alleles that are separated by less than the indicated distance. (C) Concentration of <i>Mos1</i> alleles at the extreme right end of chromosome I (length 15,072,423 bp). The separation of the allele numbers indicates that almost all the alleles were generated independently, except in two cases (ttTi2276 and ttTi2284; ttTi13453 and ttTi13460), highlighted by an asterisk. This region was also preferentially targeted during the previous study as reflected by the presence of several cxTi alleles.</p