Novel genes involved in Ciona intestinalis embryogenesis: Characterization of gene knockdown embryos

Abstract

The sequenced genome of the urochordate ascidian Ciona intestinalis contains nearly 2,500 genes that have vertebrate homologues, but their functions are as yet unknown. To identify novel genes involved in early chordates embryogenesis, we previously screened 200 Ciona genes by knockdown experiments using specific morpholino oligonucleotides and found that suppression of the translation of 40 genes caused embryonic defects (Yamada et al.[2003] Development 130:6485-6495). We have since examined an additional 304 genes, that is, screening 504 genes overall, and a total of 111 genes showed morphological defects when gene function was suppressed. We further examined the role of these genes in the differentiation of six major tissues of the embryo: endoderm, muscle, epidermis, neural tissue, mesenchyme, and notochord. Based on the similarity of phenotypes of gene knockdown embryos, genes were categorized into several groups, with the suggestion that the genes within a given group are involved in similar developmental processes. For example, five were shown to be novel genes that are likely involved in ␤-catenin-mediated endoderm formation. The type of large-scale screening used is, therefore, a powerful approach to identify novel genes with significant developmental functions, the details of which will be determined in future studies.

Single-cell transcriptome profiling of theCionalarval brain

“…Cluster 5 cells clustered closely with dorsolateral brain neurons (Cluster 3) and also expressed Rlbp1, but they showed little expression of differentiated neuronal markers (Supplemental Table 1, sheet 5). Expression of markers like Aquaporin 8 (Hamada et al, 2007), Zeb (also known as Zinc Finger (C2H2)-33 or Ci-ZF266) (Imai et al, 2004), and Gonadotropin-releasing hormone.b (Gnrh.b, previously called GnRH2) Kusakabe et al, 2012) (Fig 2C), indicated that these might be the so-called ependymal cells lining the sensory or brain vesicle, a specialized fluid-filled cavity important for the function of associated sensory organs such as the ocellus and otolith (Tsuda et al, 2003b). In addition to forming the epithelium that lines the brain vesicle and other parts of the neural tube (Katz, 1983;Mackie and Bone, 1976), these cells also function as neural progenitors that give rise to the adult CNS after metamorphosis .…”

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

“…Morphological phenotypes were obtained following loss of function of 221 of these genes. These phenotypes were described textually and with a picture (Yamada et al 2003;Hamada et al 2007). In addition, ANISEED describes the transcriptional consequences of gene loss-or gain-of-function of 94 genes with developmental phenotypes, mostly transcription factors, signaling ligands, or genes with no previously known function.…”

Biocuration: A New Challenge for the Tunicate Community

“… Extracting knowledge from scientific articles. After analyzing the article (for example, the article from Hamada et al , ), the biocurator extracts and converts data thanks to the ontologies. He can also refine the annotation using his expertise and the pictures from the article (e.g., “tailbud stage” becomes “mid‐tailbud” and expression in “endoderm and nervous system” becomes “head endoderm and anterior sensory vesicle”).…”

“…Annotating data: Annotating means connecting an entity to broader concepts by attaching a comment, explanation, or tag, defined by standards. This mark-up of data to add value is the basis of data Hamada et al, 2007), the biocurator extracts and converts data thanks to the ontologies. He can also refine the annotation using his expertise and the pictures from the article (e.g., "tailbud stage" becomes "mid-tailbud" and expression in "endoderm and nervous system" becomes "head endoderm and anterior sensory vesicle").…”