Center for Cell Regulation and Pathology and Center for Aging and Regeneration, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, Santiago, 8331150, Chile.
Genome Biol. 2009 Feb 11;10(2):R15. doi: 10.1186/gb-2009-10-2-r15.
Recent evidence from global studies of gene expression indicates that transcriptomes are more complex than expected. Xenopus has been typically used as a model organism to study early embryonic development, particularly dorso-ventral patterning. In order to identify novel transcripts involved in dorso-ventral patterning, we compared dorsal and ventral transcriptomes of Xenopus tropicalis at the gastrula stage using serial analysis of gene expression (SAGE).
Of the experimental tags, 54.5% were confidently mapped to transcripts and 125 showed a significant difference in their frequency of occurrence between dorsal and ventral libraries. We selected 20 differentially expressed tags and assigned them to specific transcripts using bioinformatics and reverse SAGE. Five mapped to transcripts with known dorso-ventral expression and the frequency of appearance for these tags in each library is in agreement with the expression described by other methods. The other 15 tags mapped to transcripts with no previously described asymmetric expression along the dorso-ventral axis. The differential expression of ten of these novel transcripts was validated by in situ hybridization and/or RT-PCR. We can estimate that this SAGE experiment provides a list of at least 86 novel transcripts with differential expression along the dorso-ventral axis. Interestingly, the expression of some novel transcripts was independent of beta-catenin.
Our SAGE analysis provides a list of novel transcripts with differential expression in the dorso-ventral axis and a large number of orphan tags that can be used to identify novel transcripts and to improve the current annotation of the X. tropicalis genome.
最近来自全球基因表达研究的证据表明转录组比预期的更复杂。非洲爪蟾通常被用作研究早期胚胎发育的模式生物，特别是背腹模式形成。为了鉴定参与背腹模式形成的新转录本，我们使用基因表达系列分析（SAGE）比较了非洲爪蟾（Xenopus tropicalis）原肠胚期的背侧和腹侧转录组。
实验标签的 54.5%可以被置信地映射到转录本上，并且 125 个标签在背侧和腹侧文库中的出现频率有显著差异。我们选择了 20 个差异表达的标签，并使用生物信息学和反向 SAGE 将它们分配到特定的转录本上。其中 5 个映射到具有已知背腹表达的转录本上，并且这些标签在每个文库中的出现频率与其他方法描述的表达一致。其他 15 个标签映射到没有以前描述的沿着背腹轴不对称表达的转录本上。这 10 个新转录本的差异表达通过原位杂交和/或 RT-PCR 得到验证。我们可以估计这个 SAGE 实验提供了一个至少有 86 个沿着背腹轴差异表达的新转录本的列表。有趣的是，一些新转录本的表达独立于β-catenin。
我们的 SAGE 分析提供了一个沿着背腹轴差异表达的新转录本列表和大量的孤儿标签，可用于鉴定新的转录本，并改进非洲爪蟾（X. tropicalis）基因组的当前注释。
