Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening.
Genome-wide profiling of long non-coding RNAs from tomato and a comparison with mRNAs associated with the regulation of fruit ripening.
复制标题
番茄长非编码 RNA 的全基因组分析以及与果实成熟调节相关 mRNA 的比较
DOI：
10.1186/s12870-018-1300-y
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发表时间：
2018-05-04
影响因子：
5.3
通讯作者：
Zhao L
中科院分区：
文献类型：
--
作者：
Wang M;Zhao W;Gao L;Zhao L
长非编码 RNA (lncRNA) 参与哺乳动物和植物的多种生物过程。越来越多的证据表明它们与发育有关。但它们在模型植物番茄（Solanum lycopersicum）果实成熟过程中的表达和调节尚未得到描述。在整合 134 个 RNA-seq 数据集后，我们鉴定了 79,322 个假定的 lncRNA，其中包括 70,635 个 lincRNA、8085 个反义非编码 RNA (ancRNA) 和 602 个正义 lncRNA (slncRNA)。 lncRNA 具有与 mRNA 不同的特定特征，包括组织特异性以及更短和更少的外显子。值得注意的是，超过 5000 个新型 lincRNA 被发现在成熟绿色 (MG)、破坏者 (BR) 和破坏者加 7 天 (BR + 7) 发育阶段表达。不同表达的 lincRNA 具有与 mRNA 不同的 DNA 甲基化谱。整合转录组数据集和全基因组筛选能够鉴定出一套全面的番茄 lncRNA。在这里，我们发现 lncRNA DNA 甲基化谱与 mRNA 不同。这将有助于未来lncRNA功能的研究，特别是对果实发育调控分子机制的剖析。本文的在线版本 (10.1186/s12870-018-1300-y) 包含补充材料，可供授权用户使用。
Long non-coding RNAs (lncRNAs) are involved in multiple biological processes in both mammals and plants. There is growing evidence that they are associated with development; but their expression and regulation during fruit ripening in the model plant tomato (Solanum lycopersicum) has yet to be described. Following integration of 134 RNA-seq data sets, we identified 79,322 putative lncRNAs, consisting of 70,635 lincRNAs, 8085 antisense non-coding RNAs (ancRNAs) and 602 sense lncRNAs (slncRNAs). lncRNAs had specific features that are distinct from mRNAs, including tissue-specificity, and shorter and fewer exons. Notably, more than 5000 of the novel lincRNAs were found to be expressed across the mature green (MG), breaker (BR) and breaker plus 7 days (BR + 7) developmental stages. The differently expressed lincRNAs had different DNA methylation profiles from the mRNAs. Integrating transcriptome datasets and genome-wide screening enabled the identification of a comprehensive set of tomato lncRNAs. Here, we found that the lncRNAs DNA methylation profiles were different from those of mRNAs. This will help future investigation of lncRNA function, especially for the dissection of the molecular mechanisms involved in the regulation of fruit development. The online version of this article (10.1186/s12870-018-1300-y) contains supplementary material, which is available to authorized users.
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影响因子：
19
作者：
Böhmdorfer G;Wierzbicki AT
通讯作者：
Wierzbicki AT
影响因子：
48
作者：
Langmead, Ben;Salzberg, Steven L.
通讯作者：
Salzberg, Steven L.
影响因子：
12.3
作者：
Li L;Eichten SR;Shimizu R;Petsch K;Yeh CT;Wu W;Chettoor AM;Givan SA;Cole RA;Fowler JE;Evans MM;Scanlon MJ;Yu J;Schnable PS;Timmermans MC;Springer NM;Muehlbauer GJ
通讯作者：
Muehlbauer GJ
DOI：
10.1016/j.gpb.2015.02.003
发表时间：
2015-06
期刊：
Genomics, proteomics & bioinformatics
影响因子：
--
作者：
Liu X;Hao L;Li D;Zhu L;Hu S
通讯作者：
Hu S
影响因子：
7.4
作者：
Barry, Cornelius S.;McQuinn, Ryan P.;Giovannoni, James J.
通讯作者：
Giovannoni, James J.