title: The transcriptome of the sea urchin embryo.
abstract: The sea urchin Strongylocentrotus purpuratus is a model organism for study of the genomic control circuitry underlying embryonic development. We examined the complete repertoire of genes expressed in the S. purpuratus embryo, up to late gastrula stage, by means of high-resolution custom tiling arrays covering the whole genome. We detected complete spliced structures even for genes known to be expressed at low levels in only a few cells. At least 11,000 to 12,000 genes are used in embryogenesis. These include most of the genes encoding transcription factors and signaling proteins, as well as some classes of general cytoskeletal and metabolic proteins, but only a minor fraction of genes encoding immune functions and sensory receptors. Thousands of small asymmetric transcripts of unknown function were also detected in intergenic regions throughout the genome. The tiling array data were used to correct and authenticate several thousand gene models during the genome annotation process.
authors.affiliation: Systemix Institute, Los Altos, CA 94024, USA.
authors.forename: Manoj P
authors.initials: MP
authors.lastname: Samanta
authors.forename: Waraporn
authors.initials: W
authors.lastname: Tongprasit
authors.forename: Sorin
authors.initials: S
authors.lastname: Istrail
authors.forename: R Andrew
authors.initials: RA
authors.lastname: Cameron
authors.forename: Qiang
authors.initials: Q
authors.lastname: Tu
authors.forename: Eric H
authors.initials: EH
authors.lastname: Davidson
authors.forename: Viktor
authors.initials: V
authors.lastname: Stolc
mesh_terms: D000818:Animals; D036703:Blastula / Q000378:metabolism; D019295:Computational Biology; D004625:Embryo, Nonmammalian / Q000378:metabolism*; D047108:Embryonic Development / Q000235:genetics*; D005775:Gastrula / Q000378:metabolism; D020869:Gene Expression Profiling; D018507:Gene Expression Regulation, Developmental; D016678:Genome; D047908:Intracellular Signaling Peptides and Proteins / Q000235:genetics / Q000378:metabolism; D015336:Molecular Probe Techniques; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D022661:RNA, Untranslated / Q000235:genetics / Q000378:metabolism; D015398:Signal Transduction / Q000235:genetics; D047270:Strongylocentrotus purpuratus / Q000196:embryology* / Q000235:genetics* / Q000254:growth & development; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D047908:Intracellular Signaling Peptides and Proteins; D012333:RNA, Messenger; D022661:RNA, Untranslated; D014157:Transcription Factors