Systematic analysis of embryonic expression profiles of zinc finger genes in Ciona intestinalis

Abstract

The recent decoding of a number of animal genomes has provided unprecedented information regarding evolution and gene structures, but this information must be supplemented with precise gene annotations and the temporal and spatial expression patterns of individual genes. In the present study, we systematically identified and characterized 566 zinc finger genes in the genome of Ciona intestinalis, an emerging model system for genome-wide studies of development and evolution. Of these genes, 356 genes encoded a potential transcription factor based on putative nucleic acid binding activity or domains of unknown function. We further examined the expression patterns of 225 genes during embryogenesis, and, when considered with a previous study [Imai, K.S., Hino, K., Yagi, K., Satoh, N., Satou, Y., 2004. Gene expression profiles of transcription factors and signaling molecules in the ascidian embryo: towards a comprehensive understanding of gene networks. Development 131, 4047-4058], we have characterized the developmental expression patterns of nearly 85% of the potential zinc finger-containing transcription factors. Overall, zinc finger genes are preferentially maternally expressed with little larval expression during development. The present study provides a valuable reference for genome-wide studies in this species and for future studies wishing to examine zinc finger gene expression patterns in other animals.

Genomic cis-regulatory networks in the early Ciona intestinalis embryo

“…Among 670 potential TF genes in the Ciona genome, at least 607 encode proteins with known TF motifs or proteins with two or more zinc-finger motifs that potentially bind to DNA Miwata et al, 2006). As shown in Table 3, we found a significantly greater number of TF genes among the targets than would be expected from random sampling (>99% confidence in  2 tests).…”

“…To test the action of this feed-forward loop comprising MyoD and Tbx6b in the regulation of musclespecific gene expression, we examined the expression patterns of genes under the control of this circuit. Of the 155 genes under the direct control of MyoD and Tbx6b, 50 (including the above ten) were already known to be expressed in muscle cells (Fujiwara et al, 2002;Imai et al, 2004;Kusakabe et al, 2002;Miwata et al, 2006;Satou et al, 2001). From the remaining 105 genes, we randomly chose 20, and found that 15 are expressed in muscle cells (Fig.…”

“…The fate of most cells is already specified before gastrulation is complete. The Ciona genome contains ~670 TF genes and their expression profiles during embryonic development have almost all been described at singlecell resolution Miwata et al, 2006). Comprehensive functional assays examining regulatory genes expressed in the early embryo have revealed, at single-cell resolution, the molecular pathways that regulate early embryonic specification events (Imai et al, 2006).…”

The ANISEED database: Digital representation, formalization, and elucidation of a chordate developmental program

“…Ascidian early embryology has been extensively studied in its cellular and molecular details (for review, see Lemaire 2009), and the functions of several hundred genes have been analyzed using loss-or gain-of-function approaches (e.g., Yamada et al 2003;Wada et al 2008). Central to the project described here, embryonic expression patterns by in situ hybridization are available for several thousand genes , including most transcription factor genes and signaling ligands (Imai et al 2004;Miwata et al 2006). Several specialized databases cover specific aspects of ascidian biology: genomes and coding genes (Ensembl, Birney et al 2006;Hubbard et al 2007; JGI, Dehal et al 2002), embryonic anatomy (FABA, Hotta et al 2007), gene expression (GHOST, Satou et al 2002;MAGEST, Kawashima et al 2002), or cis-regulatory sequences (DBTGR, Sierro et al 2006).…”

Les embryons d’ascidies

“…Cette approche, couplée à un atlas spatio-temporel extensif des patrons d'expression de plus de 500 gènes de facteurs de transcription ou de signalisation [25,26], permet de dresser, à chaque stade du développement, un schéma précis des gènes exprimés dans chacune des cellules de l'embryon, puis de les relier à leurs régulateurs en amont et à leurs cibles en aval. De telles cascades géniques émergent pour le mésenchyme [6], le muscle [16], le coeur [27], la régionalisation de la plaque neurale [28] ou de l'épiderme de la queue [6,29].…”