The zebrafish transcriptome during early development.
The zebrafish transcriptome during early development.
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DOI：
10.1186/1471-213x-11-30
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发表时间：
2011-05-24
影响因子：
--
通讯作者：
Kere J
中科院分区：
文献类型：
--
作者：
Vesterlund L;Jiao H;Unneberg P;Hovatta O;Kere J
从受精卵到胚胎的转变伴随着基因表达的大量变化，这些过程的转录事件尚未完全表征。在这项研究中，RNA-Seq被用来比较全球范围内斑马鱼（Danio rerio）四个早期发育阶段的转录谱。从不同阶段检测到平均79 M总读段。在读段总数中，65% - 73%的读段被成功映射，其中36% - 44%被唯一映射。检测到的独特基因转录本的总数为11187个，其中10096个存在于1-细胞阶段。在1-细胞期和16-细胞期观察到最多的共同转录本。随着发育的进行，具有DNA结合、蛋白质折叠和加工以及金属离子结合等分子功能的基因转录本越来越丰富。序列数据（登录号ERP 000635）可在欧洲核苷酸档案馆获得。聚类的表达谱显示，大多数检测到的基因转录本是存在于稳定的水平，因此少数的基因转录本集群的增加或减少在四个研究的发展阶段的表达。当比较高表达基因时，最早的三个发育阶段是相似的，而50%表生阶段在高表达基因的身份、独特表达基因的数量和GO分子功能的富集方面与其他三个阶段不同。两者合计，这些观察结果表明，在基因调控和转录活性之间发生的512细胞和50% epiboly阶段，根据以前的研究的主要转变。
The transition from fertilized egg to embryo is accompanied by a multitude of changes in gene expression, and the transcriptional events that underlie these processes have not yet been fully characterized. In this study RNA-Seq is used to compare the transcription profiles of four early developmental stages in zebrafish (Danio rerio) on a global scale. An average of 79 M total reads were detected from the different stages. Out of the total number of reads 65% - 73% reads were successfully mapped and 36% - 44% out of those were uniquely mapped. The total number of detected unique gene transcripts was 11187, of which 10096 were present at 1-cell stage. The largest number of common transcripts was observed between 1-cell stage and 16-cell stage. An enrichment of gene transcripts with molecular functions of DNA binding, protein folding and processing as well as metal ion binding was observed with progression of development. The sequence data (accession number ERP000635) is available at the European Nucleotide Archive. Clustering of expression profiles shows that a majority of the detected gene transcripts are present at steady levels, and thus a minority of the gene transcripts clusters as increasing or decreasing in expression over the four investigated developmental stages. The three earliest developmental stages were similar when comparing highly expressed genes, whereas the 50% epiboly stage differed from the other three stages in the identity of highly expressed genes, number of uniquely expressed genes and enrichment of GO molecular functions. Taken together, these observations indicate a major transition in gene regulation and transcriptional activity taking place between the 512-cell and 50% epiboly stages, in accordance with previous studies.