Cataloging transcription factor and major signaling molecule genes for functional genomic studies in Ciona intestinalis
Cataloging transcription factor and major signaling molecule genes for functional genomic studies in Ciona intestinalis
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DOI：
10.1007/s00427-005-0016-9
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发表时间：
2005-11-01
影响因子：
2.4
通讯作者：
Satoh, N
中科院分区：
文献类型：
--
作者：
Satou, Y;Satoh, N
海鞘为功能基因组研究提供了一个很好的实验系统，因为（1）其基因组已被测序，（2）转录因子基因和主要信号转导分子的基因已被广泛筛选和注释，在全基因组范围内使用分子遗传学方法，（3）其胚胎表达谱已几乎完全确定。然而，在这些先前的研究中使用的大多数基因模型的整个遗传结构，包括5'和3'非翻译区和蛋白质编码区，并不总是由cDNA证据支持，因此，这些基因模型是潜在的不精确的。为了便于基于精确基因结构的功能基因组学研究，本研究确定了357个转录因子基因的406个cDNA序列和107个信号转导分子基因的112个cDNA序列，大大改进了以前的基因模型，并揭示了44个基因的转录变体。考虑到这些数据以及那些先前在日本DNA数据库/欧洲分子生物学实验室/GENBANK数据库中保存的特征基因，95.6%的编目转录因子基因（373/390）和98.3%的编目信号转导分子基因（117/119）现在已经通过cDNA序列验证。因此，本研究极大地提高了可用于功能基因组研究的资源。好吧
The ascidian Ciona intestinalis provides an excellent experimental system for functional genomic studies because (1) its genome has been sequenced, (2) the transcription factor genes and genes for major signal transduction molecules have been extensively screened and annotated on a genome-wide scale using the molecular phylogenetical method, and (3) their embryonic expression profiles have been almost completely determined. However, the entire genetic structure, including the 5' and 3' untranslated regions and the protein-coding regions, of most gene models used in these prior studies is not always supported by cDNA evidence, and thus, these gene models are potentially imprecise. To facilitate functional genomic studies based on precise gene structures, our present study determined 406 cDNA sequences for 357 transcription factor genes and 112 cDNA sequences for 107 signal transduction molecule genes, greatly improving the previous gene models and revealing transcript variants for 44 genes. Considering these data alongside those of previously characterized genes deposited in the DNA Data Bank of Japan/European Molecular Biology Laboratory/GENBANK databases, 95.6% of the catalogued transcription factor genes (373/390) and 98.3% of the catalogued signal transduction molecule genes (117/119) have now been verified by cDNA sequences. Thus, the present study greatly improves the resources available for functional genomic studies in C. intestinalis.