Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data.
Comparison of D. melanogaster and C. elegans developmental stages, tissues, and cells by modENCODE RNA-seq data.
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DOI：
10.1101/gr.170100.113
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发表时间：
2014-07
期刊：
影响因子：
7
通讯作者：
Brenner SE
中科院分区：
文献类型：
--
作者：
Li JJ;Huang H;Bickel PJ;Brenner SE
我们报告了一项统计研究，该研究利用modENCODE RNA - seq数据来发现黑腹果蝇（D. melanogaster）和秀丽隐杆线虫（C. elegans）发育阶段的转录组相似性。我们关注“阶段相关基因”，这些基因捕捉每个阶段特定的转录活性，并利用它们通过超几何检验绘制两个物种内部以及之间的成对阶段。在每个物种内，正如预期的那样，时间上相邻的阶段表现出高度的转录组相似性。此外，由于母体基因表达，果蝇雌性成虫和线虫成虫分别与果蝇和线虫的胚胎相对应。在果蝇和线虫之间，从早期胚胎到晚期幼虫的时间进程中观察到一种意想不到的强共线性。此外，在果蝇的预蛹期到成虫期以及线虫的晚期胚胎到成虫期之间发现了第二种平行模式，这与果蝇生命周期中第二次大规模的细胞增殖和分化浪潮相一致。这些结果表明果蝇的发育程序存在部分重复。我们的研究结果构成了黑腹果蝇和秀丽隐杆线虫发育时间进程之间的首次全面比较，并为它们发育过程中的相似性提供了新的见解。我们使用一种类似的方法来比较果蝇和线虫的组织和细胞。研究结果包括果蝇细胞系的转录组高度相似性，果蝇成虫组织按来源聚类（不论性别和年龄），以及线虫组织和解剖细胞按发育阶段聚类。基因本体分析支持我们的结果，并对不同阶段、组织和细胞给出了详细的功能注释。最后，我们表明标准的相关性分析无法有效地检测出我们的方法所发现的对应关系。
We report a statistical study to discover transcriptome similarity of developmental stages from D. melanogaster and C. elegans using modENCODE RNA-seq data. We focus on “stage-associated genes” that capture specific transcriptional activities in each stage and use them to map pairwise stages within and between the two species by a hypergeometric test. Within each species, temporally adjacent stages exhibit high transcriptome similarity, as expected. Additionally, fly female adults and worm adults are mapped with fly and worm embryos, respectively, due to maternal gene expression. Between fly and worm, an unexpected strong collinearity is observed in the time course from early embryos to late larvae. Moreover, a second parallel pattern is found between fly prepupae through adults and worm late embryos through adults, consistent with the second large wave of cell proliferation and differentiation in the fly life cycle. The results indicate a partially duplicated developmental program in fly. Our results constitute the first comprehensive comparison between D. melanogaster and C. elegans developmental time courses and provide new insights into similarities in their development . We use an analogous approach to compare tissues and cells from fly and worm. Findings include strong transcriptome similarity of fly cell lines, clustering of fly adult tissues by origin regardless of sex and age, and clustering of worm tissues and dissected cells by developmental stage. Gene ontology analysis supports our results and gives a detailed functional annotation of different stages, tissues and cells. Finally, we show that standard correlation analyses could not effectively detect the mappings found by our method.
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