title: Comprehensive gene expression analyses in pluripotent stem cells of a planarian, Dugesia japonica.
abstract: The neoblasts are the only somatic stem cells in planarians possessing pluripotency, and can give rise to all types of cells, including germline cells. Recently, accumulated knowledge about the transcriptome and expression dynamics of various pluripotent somatic stem cells has provided important opportunities to understand not only fundamental mechanisms of pluripotency, but also stemness across species at the molecular level. The neoblasts can easily be eliminated by radiation. Also, by using fluorescence activated cell sorting (FACS), we can purify and collect many neoblasts, enabling identification of neoblast-related genes by comparison of the gene expression level among intact and X-ray-irradiated animals, and purified neoblasts. In order to find such genes, here we employed the high coverage expression profiling (HiCEP) method, which enables us to observe and compare genome-wide gene expression levels between different samples without advance sequence information, in the planarian D. japonica as a model organism of pluripotent stem cell research. We compared expression levels of ~17,000 peaks corresponding to independent genes among different samples, and obtained 102 peaks as candidates. Expression analysis of genes identified from those peaks by in situ hybridization revealed that at least 42 genes were expressed in the neoblasts and in neoblast-related cells that had a different distribution pattern in the body than neoblasts. Also, single-cell PCR analysis of those genes revealed heterogeneous expression of some genes in the neoblast population. Thus, using multidimensional gene expression analyses, we were able to obtain a valuable data set of neoblast-related genes and their expression patterns.
authors.affiliation: Global COE Program: Evolution and Biodiversity, Graduate School of Science, Kyoto University, Japan. shiba@mdb.biophys.kyoto-u.ac.jp
authors.forename: Norito
authors.initials: N
authors.lastname: Shibata
authors.forename: Tetsutaro
authors.initials: T
authors.lastname: Hayashi
authors.forename: Ryutaro
authors.initials: R
authors.lastname: Fukumura
authors.forename: Junsuke
authors.initials: J
authors.lastname: Fujii
authors.forename: Tomomi
authors.initials: T
authors.lastname: Kudome-Takamatsu
authors.forename: Osamu
authors.initials: O
authors.lastname: Nishimura
authors.forename: Syozo
authors.initials: S
authors.lastname: Sano
authors.forename: Fuyan
authors.initials: F
authors.lastname: Son
authors.forename: Nobuko
authors.initials: N
authors.lastname: Suzuki
authors.forename: Ryoko
authors.initials: R
authors.lastname: Araki
authors.forename: Masumi
authors.initials: M
authors.lastname: Abe
authors.forename: Kiyokazu
authors.initials: K
authors.lastname: Agata
mesh_terms: D000818:Animals; D015415:Biomarkers / Q000378:metabolism*; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D015801:Helminth Proteins / Q000235:genetics* / Q000378:metabolism; D017403:In Situ Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D010932:Planarians / Q000166:cytology / Q000502:physiology*; D039904:Pluripotent Stem Cells / Q000166:cytology / Q000502:physiology*; D012333:RNA, Messenger / Q000235:genetics; D060888:Real-Time Polymerase Chain Reaction; D012038:Regeneration / Q000502:physiology*
chemical_list: D015415:Biomarkers; D015801:Helminth Proteins; D012333:RNA, Messenger