The transcriptional diversity of 25 Drosophila cell lines
The transcriptional diversity of 25 Drosophila cell lines
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DOI：
10.1101/gr.112961.110
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发表时间：
2011-02-01
期刊：
影响因子：
7
通讯作者：
Cherbas, Peter
中科院分区：
文献类型：
--
作者：
Cherbas, Lucy;Willingham, Aarron;Cherbas, Peter
黑腹果蝇细胞系是细胞生物学家研究的重要资源。在这里，我们编目了25个品系的外显子、基因和未注释的转录信号的表达。未注释的转录是大量的（通常占常染色信号的19%）。保守地说，我们鉴定出1405个新的转录区域；其中684个似乎是邻近基因的新外显子，通常是遥远的基因。64%的基因至少在一个品系中可以被检测到，但只有21%的基因在所有品系中都可以被检测到。每个细胞系平均表达5885个基因，包括一组共有的3109个基因。表达水平相差好几个数量级。主要的信号通路得到了很好的体现：大多数分化通路是“关闭”的，而生存/生长通路是“打开”的。每一个品系所表达的基因中，大约有50%不是共同基因的一部分，这些基因表现出相当大的个性。31%的基因在至少一种细胞系中的表达水平高于任何单一发育阶段，这表明每一种细胞系都富含小组细胞的特征基因。最值得注意的是，在表现的基础上，想象的椎间盘衍生线通常可以被分配到正在发育的椎间盘内的小区域。这些映射揭示了即使是细粒度的空间确定也具有意想不到的稳定性。没有两个细胞系显示完全相同的转录因子表达。我们得出的结论是，每个细胞系都保留了一个共同的“细胞系”基因表达模式上的单个创始细胞的特征。
Drosophila melanogaster cell lines are important resources for cell biologists. Here, we catalog the expression of exons, genes, and unannotated transcriptional signals for 25 lines. Unannotated transcription is substantial (typically 19% of euchromatic signal). Conservatively, we identify 1405 novel transcribed regions; 684 of these appear to be new exons of neighboring, often distant, genes. Sixty-four percent of genes are expressed detectably in at least one line, but only 21% are detected in all lines. Each cell line expresses, on average, 5885 genes, including a common set of 3109. Expression levels vary over several orders of magnitude. Major signaling pathways are well represented: most differentiation pathways are "off" and survival/growth pathways "on." Roughly 50% of the genes expressed by each line are not part of the common set, and these show considerable individuality. Thirty-one percent are expressed at a higher level in at least one cell line than in any single developmental stage, suggesting that each line is enriched for genes characteristic of small sets of cells. Most remarkable is that imaginal disc-derived lines can generally be assigned, on the basis of expression, to small territories within developing discs. These mappings reveal unexpected stability of even fine-grained spatial determination. No two cell lines show identical transcription factor expression. We conclude that each line has retained features of an individual founder cell superimposed on a common "cell line" gene expression pattern.