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.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Many sea urchin defense genes are expressed during development.
“Many of the defense genes are expressed during development (10,42)”
From The Genome of the Sea Urchin <i>Strongylocentrotus purpuratus</i> (2006) · cites this paper as [10]
Only limited expression was found for surreal-GPCR genes in the transcriptome map of Samanta et al. (2006).
“In contrast, only limited expression was found for surreal-GPCR genes in the transcriptome map of Samanta et al. (2006).”
From Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome (2006) · cites this paper as Samanta et al., 2006
Many predicted genes are supported by expression data from a whole genome tiling array.
“Many of these predicted genes are supported by expression data from a whole genome tiling array”
From The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome (2006) · cites this paper as Samanta et al., 2006
25 of the 30 sea urchin ABCC genes show significant expression at some developmental stage.
“As one indication of their functional importance, 25 of these 30 genes show significant levels of expression at some stage of development”
From The chemical defensome: Environmental sensing and response genes in the Strongylocentrotus purpuratus genome (2006) · cites this paper as Samanta et al., 2006
Cites
Gene Activity in Early Development
Davidson, E. H. (1968) · Elsevier eBooks · doi:10.1016/c2013-0-12432-4 · Cited by 1,704 · see citing works
Self-citationThe Genome of the Sea Urchin <i>Strongylocentrotus purpuratus</i>
Sodergren, E., Weinstock, G. M., Davidson, E. H., Cameron, R. A., Gibbs, R. A., Angerer, R. C., Angerer, L. M., Arnone, M. I., Burgess, D. R., Burke, R. D., et al. (2006) · Science · doi:10.1126/science.1133609 · Cited by 1,132 · see citing works
Self-citationGlobal Identification of Human Transcribed Sequences with Genome Tiling Arrays
Bertone, P., Štolc, V., Royce, T. E., Rozowsky, J. S., Urban, A. E., Zhu, X., Rinn, J. L., Tongprasit, W., Samanta, M. P., Weissman, S. M., et al. (2004) · Science · doi:10.1126/science.1103388 · Cited by 1,014 · see citing works
Self-citationGene Expression During the Life Cycle of Drosophila melanogaster
Arbeitman, M. N., Furlong, E. E. M., Imam, F. B., Johnson, E. A., Null, B. H., Baker, B. S., Krasnow, M. A., Scott, M. P., Davis, R. W., & White, K. P. (2002) · Science · doi:10.1126/science.1072152 · Cited by 926 · see citing works
Large-Scale Transcriptional Activity in Chromosomes 21 and 22
Kapranov, P., Cawley, S. E., Drenkow, J., Bekiranov, S., Strausberg, R. L., Fodor, S. P. A., & Gingeras, T. (2002) · Science · doi:10.1126/science.1068597 · Cited by 871 · see citing works
The immune gene repertoire encoded in the purple sea urchin genome
Hibino, T., Loza-Coll, M., Messier, C., Majeske, A. J., Cohen, A. H., Terwilliger, D. P., Buckley, K. M., Brockton, V., Nair, S. V., Berney, K., et al. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.08.065 · Cited by 630 · see citing works
Self-citationA Gene Expression Map for the Euchromatic Genome of Drosophila melanogaster
Štolc, V., Gauhar, Z., Mason, C. E., Halasz, G., van Batenburg, M. F., Rifkin, S. A., Hua, S., Herreman, T., Tongprasit, W., Barbano, P. E., et al. (2004) · Science · doi:10.1126/science.1101312 · Cited by 290 · see citing works
Self-citationSpecification of cell fate in the sea urchin embryo: summary and some proposed mechanisms
Davidson, E. H., Cameron, R. A., & Ransick, A. (1998) · Development · doi:10.1242/dev.125.17.3269 · Cited by 277 · see citing works
Self-citationBolouri, H., & Davidson, E. H. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1533293100 · Cited by 212 · see citing works
Self-citationOpsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome
Raible, F., Tessmar-Raible, K., Arboleda, E., Kaller, T., Bork, P., Arendt, D., & Arnone, M. I. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.08.070 · Cited by 170 · see citing works
Set‐aside cells in maximal indirect development: Evolutionary and developmental significance
Peterson, K. J., Cameron, R. A., & Davidson, E. H. (1997) · BioEssays · doi:10.1002/bies.950190713 · Cited by 164 · see citing works
Self-citationRansick, A., Rast, J. P., Minokawa, T., Calestani, C., & Davidson, E. H. (2002) · Developmental Biology · doi:10.1006/dbio.2002.0607 · Cited by 152 · see citing works
Self-citationYuh, C., Brown, C. T., Livi, C. B., Rowen, L., Clarke, P. J. C., & Davidson, E. H. (2002) · Developmental Biology · doi:10.1006/dbio.2002.0618 · Cited by 102 · see citing works
Self-citationRonshaugen, M., & Levine, M. (2004) · Developmental Cell · doi:10.1016/j.devcel.2004.11.001 · Cited by 67 · see citing works
Ashby, M., Materna, S. C., Brown, C. T., Tu, Q., Oliveri, P., Cameron, R. A., & Davidson, E. H. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.10.016 · Cited by 61 · see citing works
Self-citationBiemar, F., Nix, D. A., Piel, J., Peterson, B., Ronshaugen, M., Sementchenko, V., Bell, I., Manak, J. R., & Levine, M. S. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0604484103 · Cited by 53 · see citing works
Flagged first, then by citations
Cited by
Sorted by citations
The Genome of the Sea Urchin <i>Strongylocentrotus purpuratus</i>
Sodergren, E., Weinstock, G. M., Davidson, E. H., Cameron, R. A., Gibbs, R. A., Angerer, R. C., Angerer, L. M., Arnone, M. I., Burgess, D. R., Burke, R. D., et al. (2006) · Science · doi:10.1126/science.1133609 · Cited by 1,132 · see citing works
Self-citationSequencing and de novo analysis of a coral larval transcriptome using 454 GSFlx
Meyer, E., Aglyamova, G. V., Wang, S., Buchanan-Carter, J., Abrego, D., Colbourne, J. K., Willis, B. L., & Matz, M. V. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-219 · Cited by 479 · see citing works
A genomic view of the sea urchin nervous system
Burke, R. D., Angerer, L. M., Elphick, M. R., Humphrey, G. W., Yaguchi, S., Kiyama, T., Liang, S., Mu, X., Agca, C., Klein, W. H., et al. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.08.007 · Cited by 293 · see citing works
Goldstone, J. V., Hamdoun, A., Cole, B. J., Howard-Ashby, M., Nebert, D. W., Scally, M., Dean, M., Epel, D., Hahn, M. E., & Stegeman, J. J. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.08.066 · Cited by 280 · see citing works
Livingston, B. T., Killian, C. E., Wilt, F., Cameron, A., Landrum, M. J., Ermolaeva, O., Sapojnikov, V., Maglott, D. R., Buchanan, A. M., & Ettensohn, C. A. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.07.047 · Cited by 243 · see citing works
Whittaker, C. A., Bergeron, K.-F., Whittle, J., Brandhorst, B. P., Burke, R. D., & Hynes, R. O. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.07.044 · Cited by 183 · see citing works
Opsins and clusters of sensory G-protein-coupled receptors in the sea urchin genome
Raible, F., Tessmar-Raible, K., Arboleda, E., Kaller, T., Bork, P., Arendt, D., & Arnone, M. I. (2006) · Developmental Biology · doi:10.1016/j.ydbio.2006.08.070 · Cited by 170 · see citing works
PETERSON, K. J., SUMMONS, R. E., & DONOGHUE, P. C. J. (2007) · Palaeontology · doi:10.1111/j.1475-4983.2007.00692.x · Cited by 93 · see citing works
- Authors
- Samanta, M. P., Tongprasit, W., Istrail, S., Cameron, R. A., Tu, Q., Davidson, E. H., & Stolc, V.
- Affiliations
- California Institute of Technology (US)
- Systemix Institute, Los Altos, CA 94024, USA.
- Venue
- Science
- Published
- 2006-11-10
- Volume
- 314
- Issue
- 5801
- Pages
- 960-962
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W2090831186
- Cited by
- 102
- References
- 16
- Citations by year
- 2024: 1 · 2022: 1 · 2020: 1 · 2019: 2 · 2018: 3 · 2017: 1 · 2016: 3 · 2015: 3 · 2014: 7 · 2013: 3 · 2012: 8
- FWCI
- 7.61
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion)
- Funders
- National Institutes of Health (5p01hd037105-20)
- Eunice Kennedy Shriver National Institute of Child Health and Human Development (HD37105)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Developmental Biology and Gene Regulation
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- Strongylocentrotus purpuratus, sea urchin embryo, transcriptome, embryonic development, gene expression, gastrula, tiling arrays, gene models, genome annotation, transcription factors, signaling proteins, intergenic regions
- MeSH terms
- Animals, Embryo, Nonmammalian, Gastrula, Nucleic Acid Hybridization, RNA, Messenger, Transcription Factors, Transcription, Genetic, Molecular Probe Techniques, Signal Transduction, Genome, Gene Expression Regulation, Developmental, Computational Biology, Oligonucleotide Array Sequence Analysis, Gene Expression Profiling, RNA, Untranslated, Blastula, Embryonic Development, Strongylocentrotus purpuratus, Intracellular Signaling Peptides and Proteins
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
