Genome-wide identification and developmental expression profiling of long noncoding RNAs during Drosophila metamorphosis.
Genome-wide identification and developmental expression profiling of long noncoding RNAs during Drosophila metamorphosis.
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果蝇变态过程中长非编码RNA的全基因组鉴定和发育表达谱分析
DOI：
10.1038/srep23330
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发表时间：
2016-03-21
影响因子：
4.6
通讯作者：
Kang L
中科院分区：
文献类型：
--
作者：
Chen B;Zhang Y;Zhang X;Jia S;Chen S;Kang L
随着RNA测序技术的发展，越来越多的长链非编码RNA（lncRNA）被发现。lncRNA在多种生物过程中发挥关键作用，并参与发育调控。然而，关于lncRNA的全基因组表达如何在发育中调节的知识仍然有限。我们在这里进行了一个全基因组的lncRNA鉴定，然后在果蝇的发展过程中，这些lncRNA的全球表达谱。我们将lncRNA的生物信息学预测与蛋白质编码转录本的严格过滤和实验验证相结合，以定义一组高置信度的果蝇lncRNA。我们在含有43，967个转录本的给定转录组中鉴定了1，077个lncRNA;其中，646个lncRNA是新的。这些lncRNA在27个发育过程中的体内表达谱显示，lncRNA的表达相对于蛋白质编码基因的表达在时间上受到高度限制。值得注意的是，21%和42%的lncRNA在胚胎晚期和幼虫期显著上调，这是发育转变的关键时期。结果突出了lncRNA表达的发育特异性，并反映了一个大的lncRNA亚类的变态发病的调节意义。对果蝇发育过程中lncRNA的系统注释和表达分析为今后的功能研究奠定了基础。
An increasing number of long noncoding RNAs (lncRNAs) have been discovered with the recent advances in RNA-sequencing technologies. lncRNAs play key roles across diverse biological processes, and are involved in developmental regulation. However, knowledge about how the genome-wide expression of lncRNAs is developmentally regulated is still limited. We here performed a whole-genome identification of lncRNAs followed by a global expression profiling of these lncRNAs during development in Drosophila melanogaster. We combined bioinformatic prediction of lncRNAs with stringent filtering of protein-coding transcripts and experimental validation to define a high-confidence set of Drosophila lncRNAs. We identified 1,077 lncRNAs in the given transcriptomes that contain 43,967 transcripts; among these, 646 lncRNAs are novel. In vivo expression profiling of these lncRNAs in 27 developmental processes revealed that the expression of lncRNAs is highly temporally restricted relative to that of protein-coding genes. Remarkably, 21% and 42% lncRNAs were significantly upregulated at late embryonic and larval stage, the critical time for developmental transition. The results highlight the developmental specificity of lncRNA expression, and reflect the regulatory significance of a large subclass of lncRNAs for the onset of metamorphosis. The systematic annotation and expression analysis of lncRNAs during Drosophila development form the foundation for future functional exploration.