Genomic Features and Regulatory Roles of Intermediate-Sized Non-Coding RNAs in Arabidopsis
Genomic Features and Regulatory Roles of Intermediate-Sized Non-Coding RNAs in Arabidopsis
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拟南芥中中等大小非编码RNA的基因组特征和调控作用
DOI：
10.1093/mp/sst177
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发表时间：
2014-03-01
期刊：
影响因子：
27.5
通讯作者：
Deng, Xing Wang
中科院分区：
文献类型：
--
作者：
Wang, Yuqiu;Wang, Xuncheng;Deng, Xing Wang
全基因组技术的最新进展允许鉴定真核生物中数千种不同大小的非编码rna，其中一些已进一步证明在许多生物过程中起重要作用。然而，在模式植物拟南芥中，新的中等大小的ncRNAs (im-ncRNAs)（50类似于300 nt）的信息非常有限。通过改良的分离策略结合深度测序技术，我们在全球范围内鉴定出838个im-ncRNAs。超过一半（58%）是新的ncRNA物种，主要是进化分歧。有趣的是，带有5'- utr衍生的新型im- ncrna的注释蛋白编码基因倾向于高表达。对于基因间的im-ncRNAs，它们的平均丰度与幼苗中的mrna相当，但亚群在衰老叶片中的表达明显较低。此外，基因间的im- ncrna受到与蛋白质编码基因相似的遗传和表观遗传机制的调控，其中一些表现出发育调控的表达模式。大规模的反向遗传筛选显示，大量im-ncRNAs的下调在体内导致明显的分子变化或异常的发育表型，表明im-ncRNAs在植物生长发育中的功能重要性。总之，我们的研究结果表明，新的拟南芥im- ncrna是发育调控的，并且在转录组中发现了功能成分。
Recent advances in genome-wide techniques allowed the identification of thousands of non-coding RNAs with various sizes in eukaryotes, some of which have further been shown to serve important functions in many biological processes. However, in model plant Arabidopsis, novel intermediate-sized ncRNAs (im-ncRNAs) (50 similar to 300 nt) have very limited information. By using a modified isolation strategy combined with deep-sequencing technology, we identified 838 im-ncRNAs in Arabidopsis globally. More than half (58%) are new ncRNA species, mostly evolutionary divergent. Interestingly, annotated protein-coding genes with 5'-UTR-derived novel im-ncRNAs tend to be highly expressed. For intergenic im-ncRNAs, their average abundances were comparable to mRNAs in seedlings, but subsets exhibited significantly lower expression in senescing leaves. Further, intergenic im-ncRNAs were regulated by similar genetic and epigenetic mechanisms to those of protein-coding genes, and some showed developmentally regulated expression patterns. Large-scale reverse genetic screening showed that the down-regulation of a number of im-ncRNAs resulted in either obvious molecular changes or abnormal developmental phenotypes in vivo, indicating the functional importance of im-ncRNAs in plant growth and development. Together, our results demonstrate that novel Arabidopsis im-ncRNAs are developmentally regulated and functional components discovered in the transcriptome.