Comprehensive gene expression analyses in pluripotent stem cells of a planarian, Dugesia japonica

International Journal of Developmental Biology

Volumn 56, Issue 1-3, 2012, Pages 93-102

  Shibata, Norito ^a   Hayashi, Tetsutaro ^a   Fukumura, Ryutaro ^a   Fujii, Junsuke ^a   Kudome Takamatsu, Tomomi ^a   Nishimura, Osamu ^a   Sano, Syozo ^a   Son, Fuyan ^a   Suzuki, Nobuko ^a   Araki, Ryoko ^a   Abe, Masumi ^a   Agata, Kiyokazu ^a  

^a KYOTO UNIVERSITY   (Japan)

Author keywords

Comprehensive gene expression analysis; HiCEP; Planarian; Pluripotent stem cell

Indexed keywords

TRANSCRIPTOME;

ANIMAL CELL; ANIMAL EXPERIMENT; ANIMAL TISSUE; ARTICLE; CELL TYPE; CELLULAR DISTRIBUTION; CONTROLLED STUDY; DUGESIA JAPONICA; FLUORESCENCE ACTIVATED CELL SORTING; GENE EXPRESSION; GENE IDENTIFICATION; GENE SEQUENCE; GENETIC PROCEDURES; GENOME; HIGH COVERAGE EXPRESSION PROFILING; IN SITU HYBRIDIZATION; NEOBLAST; NONHUMAN; PLURIPOTENT STEM CELL; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PURIFICATION; SAMPLE; SINGLE CELL ANALYSIS; SOMATIC STEM CELL; STEM CELL; TURBELLARIA; X IRRADIATION;

ANIMALS; BIOLOGICAL MARKERS; GENE EXPRESSION PROFILING; GENE EXPRESSION REGULATION, DEVELOPMENTAL; HELMINTH PROTEINS; IN SITU HYBRIDIZATION; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; PLANARIANS; PLURIPOTENT STEM CELLS; REAL-TIME POLYMERASE CHAIN REACTION; REGENERATION; RNA, MESSENGER;

ANIMALIA; DUGESIA JAPONICA; PLANARIA; TURBELLARIA;

EID: 84859128368     PISSN: 02146282     EISSN: None     Source Type: Journal    
DOI: 10.1387/ijdb.113434ns     Document Type: Article

References (32)

1. AGATA, K., NAKAJIMA, E., FUNAYAMA, N., SHIBATA, N., SAITO, Y. and UMESONO, Y. (2006). Two different evolutionary origins of stem cell systems and their molecular basis. Semin Cell Dev Biol 17: 503-509.
2. ALLARD, P., YANG, Q., MARZLUFF, W.F. and CLARKE, H.J. (2005). The stem-loop binding protein regulates translation of histone mRNA during mammalian oogenesis. Dev Biol 286: 195-206.
3. ARAKI, R., FUKUMURA, R., SASAKI, N., KASAMA, Y., SUZUKI, N., TAKAHASHI, H., TABATA, Y., SAITO, T. and ABE, M. (2006). More than 40,000 transcripts, including novel and noncoding transcripts, in mouse embryonic stem cells. Stem Cells 24: 2522-2528.
4. BAGUÑÀ, J., SALÒ, E. and AULADELL, C. (1989). Regeneration and pattern formation in planarians. III. Evidence that neoblasts are totipotent stem cells and the source of blastema cells. Development 107: 77-86.
5. CHAMBERS, I., SILVA, J., COLBY, D., NICHOLS, J., NIJMEIJER, B., ROBERTSON, M., VRANA, J., JONES, K., GROTEWOLD, L. and SMITH, A. (2007). Nanog safeguards pluripotency and mediates germline development. Nature 450: 1230-1234.
6. EISENHOFFER, G.T., KANG, H. and SÁNCHEZ ALVARADO, A. (2008). Molecular analysis of stem cells and their descendants during cell turnover and regeneration in the planarian Schmidtea mediterranea. Cell Stem Cell 3: 327-339.
7. FUKUMURA, R., TAKAHASHI, H., SAITO, T., TSUTSUMI, Y., FUJIMORI, A., SATO, S., TATSUMI, K., ARAKI, R. and ABE, M. (2003). A sensitive transcriptome analysis method that can detect unknown transcripts. Nucleic Acids Res 31: e94.
8. HAYASHI, T., ASAMI, M., HIGUCHI, S., SHIBATA, N. and AGATA, K. (2006). Isolation of planarian X-ray-sensitive stem cells by fluorescence-activated cell sorting. Dev Growth Differ 48: 371-380.
9. HAYASHI, T., SHIBATA, N., OKUMURA, R., KUDOME, T., NISHIMURA, O., TARUI, H. and AGATA, K. (2010). Single-cell gene profiling of planarian stem cells using fluorescent activated cell sorting and its "index sorting" function for stem cell research. Dev Growth Differ 52: 131-144.
10. ISSHIKI, T., PEARSON, B., HOLBROOK, S. and DOE, C.Q. (2001). Drosophila neuroblasts sequentially express transcription factors which specify the temporal identity of their neuronal progeny. Cell 106: 511-521.
11. JUNG, S.O., LEE, J.Y. and KIM, J. (2001). Yeast ribosomal protein S3 has an endonuclease activity on AP DNA. Mol Cells 12: 84-90.
12. LEE, C.H., KIM, S.H., CHOI, J.I., CHOI, J.Y., LEE, C.E. and KIM, J. (2002). Electron paramagnetic resonance study reveals a putative iron-sulfur cluster in human rpS3 protein. Mol Cells 13: 154-156.
13. NEWMARK, P.A. and SÁNCHEZ ALVARADO, A. (2000). Bromodeoxyuridine specifically labels the regenerative stem cells of planarians. Dev Biol 220: 142-153.
14. ORII, H., SAKURAI, T. and WATANABE, K. (2005). Distribution of the stem cells (neoblasts) in the planarian Dugesia japonica. Dev Genes Evol 215: 143-157.
15. PEARSON, B.J. and SÁNCHEZ ALVARADO, A. (2010). A planarian p53 homolog regulates proliferation and self-renewal in adult stem cell lineages. Development 137: 213-221.
16. PELLETTIERI, J., FITZGERALD, P., WATANABE, S., MANCUSO, J., GREEN, D.R. and SÁNCHEZ ALVARADO, A. (2009). Cell death and tissue remodeling in planarian regeneration. Dev Biol 338: 76-85.
17. POLAKIEWICZ, R.D., MUNROE, D.J., SAIT, S.N., TYCOWSKI, K.T., NOWAK, N.J., SHOWS, T.B., HOUSMAN, D.E. and PAGE, D.C. (1995). Mapping of ribosomal protein S3 and internally nested snoRNA U15A gene to human chromosome 11q13.3-q13.5. Genomics 25: 577-580.
18. ROSSI, L., SALVETTI, A., LENA, A., BATISTONI, R., DERI, P., PUGLIESI, C., LORETI, E. and GREMIGNI, V. (2006). DjPiwi-1, a member of the PAZ-Piwi gene family, defines a subpopulation of planarian stem cells. Dev Genes Evol 216: 335-346.
19. ROSSI, L., SALVETTI, A., MARINCOLA, F.M., LENA, A., DERI, P., MANNINI, L., BATISTONI, R., WANG, E. and GREMIGNI, V. (2007). Deciphering the molecular machinery of stem cells: a look at the neoblast gene expression profile. Genome Biol 8: R62.
20. ROUHANA, L., SHIBATA, N., NISHIMURA, O. and AGATA, K. (2010). Different requirements for conserved post-transcriptional regulators in planarian regeneration and stem cell maintenance. Dev Biol 341: 429-443.
21. SAKURAI, T., LEE, H., KASHIMA, M., SAITO, Y., HAYASHI, T., KUDOME-TAKAMATSU, T., NISHIMURA, O., AGATA, K. and SHIBATA, N. (2012). The planarian P2X homolog in the regulation of asexual reproduction. Int. J. Dev. Biol. 56: 173-182. (doi: 10.1387/ijdb.113439ts).
22. SALVETTI, A., ROSSI, L., DERI, P. and BATISTONI, R. (2000). An MCM2-related gene is expressed in proliferating cells of intact and regenerating planarians. Dev Dyn 218: 603-614.
23. SALVETTI, A., ROSSI, L., LENA, A., BATISTONI, R., DERI, P., RAINALDI, G., LOCCI, M.T., EVANGELISTA, M. and GREMIGNI, V. (2005). DjPum, a homologue of Drosophila Pumilio, is essential to planarian stem cell maintenance. Development 132: 1863-1874.
24. SÁNCHEZ ALVARADO, A. and NEWMARK, P.A. (1999). Double-stranded RNA specifically disrupts gene expression during planarian regeneration. Proc Natl Acad Sci USA 96: 5049-5054.
25. SATO, K., SHIBATA, N., ORII, H., AMIKURA, R., SAKURAI, T., AGATA, K., KOBAYASHI, S. and WATANABE, K. (2006). Identification and origin of the germline stem cells as revealed by the expression of nanos-related gene in planarians. Dev Growth Differ 48: 615-628.
26. SHIBATA, N., ROUHANA, L. and AGATA, K. (2010). Cellular and molecular dissection of pluripotent adult somatic stem cells in planarians. Dev Growth Differ 52: 27-41.
27. SHIBATA, N., UMESONO, Y., ORII, H., SAKURAI, T., WATANABE, K. and AGATA, K. (1999). Expression of vasa(vas)-related genes in germline cells and totipotent somatic stem cells of planarians. Dev Biol 206: 73-87.
28. TASAKI, J., SHIBATA, N., NISHIMURA, O., ITOMI, K., TABATA, Y., SON, F., SUZUKI, N., ARAKI, R., ABE, M., ATAGA, K. and UMESONO, Y. (2011) ERK signaling controls blastema cell differentiation during planarian regeneration. Development 138: 2417-2427
29. UMESONO, Y., WATANABE, K. and AGATA, K. (1997). A planarian orthopedia homolog is specifically expressed in the branch region of both the mature and regenerating brain. Dev Growth Differ 39: 723-727.
30. WILSON, A., OSER, G.M., JAWORSKI, M., BLANCO-BOSE, W.E., LAURENTI, E., ADOLPHE, C., ESSERS, M.A., MACDONALD, H.R. and TRUMPP, A. (2007). Dormant and self-renewing hematopoietic stem cells and their niches. Ann N Y Acad Sci 1106: 64-75.
31. YADAVILLI, S., MAYO, L.D., HIGGINS, M., LAIN, S., HEGDE, V. and DEUTSCH, W.A. (2009). Ribosomal protein S3: A multi-functional protein that interacts with both p53 and MDM2 through its KH domain. DNA Repair (Amst) 8: 1215-1224.
32. YOSHIDA-KASHIKAWA, M., SHIBATA, N., TAKECHI, K. and AGATA, K. (2007). DjCBC-1, a conserved DEAD box RNA helicase of the RCK/p54/Me31B family, is a component of RNA-protein complexes in planarian stem cells and neurons. Dev Dyn 236: 3436-3450.