by Manoj P. Samanta, Waraporn Tongprasit, Sorin Istrail, R. Andrew Cameron, Qiang Tu, Eric H. Davidson, Viktor Stolc
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.
Reference:
Manoj P. Samanta, Waraporn Tongprasit, Sorin Istrail, R. Andrew Cameron, Qiang Tu, Eric H. Davidson, Viktor Stolc, "The Transcriptome of the Sea Urchin Embryo", In Science, vol. 314, no. 5801, pp. 960-962, 2006.
Bibtex Entry:
@ARTICLE{Samanta2006,
author = {Samanta, Manoj P. and Tongprasit, Waraporn and Istrail, Sorin and
Cameron, R. Andrew and Tu, Qiang and Davidson, Eric H. and Stolc,
Viktor},
title = {The Transcriptome of the Sea Urchin Embryo},
journal = {Science},
year = {2006},
volume = {314},
pages = {960--962},
number = {5801},
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.},
date = {November 10, 2006},
doi = {10.1126/science.1131898},
owner = {Derek},
timestamp = {2012.05.08},
url = {http://www.brown.edu/Research/Istrail_Lab/papers/transcSeaUrchin.pdf},
category = {Regulatory Genomics}
}