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利用玉米高通量RNA-Seq数据预测长链非编码RNA(LncRNA) 被引量:4

Prediction and characterization of long non-coding RNAs using high throughput RNA-Seq data in maize
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摘要 非编码RNA(noncoding RNA,ncRNA)是指不具备编码蛋白质能力的RNA。其中,一类长度大于200 nt的长链非编码RNA(Long noncoding RNA,LncRNA)因其在多层面对基因表达存在调控作用而逐渐成为研究热点。但是由于缺乏有效、准确的预测手段,植物中LncRNA研究相对滞后。本研究结合植物基因组特点以及高通量RNA测序数据,通过生物信息学手段发展、优化了一套基于RNA-Seq数据的植物LncRNA筛选及鉴定方法。随后,利用玉米B73顶端分生组织RNA-Seq数据,预测了6 122条玉米LncRNA,并对其进行了全基因组物理定位。该方法为LncRNA鉴定和后续的功能分析提供了重要的基础。 Numerous studies have shown that most of the plant genome is transcribed to yield not only protein-coding mRNA but also some of non-coding RNAs( noncoding RNA, ncRNA). Long non-coding RNA (long ncRNAs, LncRNA), a group consisting of ncRNA longer than 200 nucleotides, have been found to play a critical role in gene regulation. Thus, the description of the LncRNA in the plant genome will be beneficial for the understanding of gene expression variation, in turn, the morphological polymorphism. Here, large-scale sequencing data from RNA-Seq were integrated into whole genome annotation to characterize LncRNA in maize using an in-house developed pipeline. More than 6 122 LncRNA were identi- fied and classified. The physical map results exhibited that the LncRNA were scattered on maize 10 chromosomes with pos- sible location preferences. The study provided the methodology for plant LncRNA identification, and the predicted LncRNA would be applied in function analyses.
出处 《江苏农业学报》 CSCD 北大核心 2013年第6期1248-1253,共6页 Jiangsu Journal of Agricultural Sciences
基金 江苏省农业科技自主创新基金项目[CX(12)2032]
关键词 长链非编码RNA (LncRNA) 高通量RNA测序 生物信息学 玉米 long non-coding RNA high throughput RNA-Seq bioinformatics maize
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