长链非编码RNA的调控机制及其在家畜中的预测方法

doi:10.16431/j.cnki.1671-7236.2017.07.001

摘要/Abstract

摘要：

长链非编码RNA（long noncoding RNA，lncRNA）是一类转录本长度超过200个核苷酸，不参与蛋白编码的功能性RNA分子，直接以RNA形式在表观遗传水平、转录水平、转录后水平、翻译水平和翻译后水平调控基因的表达，在家畜体内的各种生物学过程中起重要作用。作者对长链非编码RNA的来源、分类和结构特征、实现生物学功能的4种分子调控机制（信号分子、诱饵分子、引导分子、支架分子）、调控基因表达的5个层面及采用高通量RNA测序技术分析测序数据和预测家畜lncRNA的方法进行了综述，为合理地研究家畜的lncRNA提供基础。家畜lncRNA预测方法主要包括深度测序、转录组重建、新转录本预测、lncRNA识别4个部分，在lncRNA识别阶段，作者所在研究团队前期采用将蛋白质编码潜能评估工具CPAT（coding potential assessment tool）和在线的序列编码能力预测工具CPC（coding potential calculator）结合取交集的方法，较好地从预测得到的大量的候选转录本中快速排除具蛋白编码能力的转录本，预测获得68 604条内蒙古绒山羊的皮肤组织lncRNA，丰富了NONCODE数据库中羊lncRNA转录本的基础数据。

关键词: 长链非编码RNA; 调控; 预测方法; 编码潜能评估; 编码能力预测

Abstract:

Long noncoding RNA (lncRNA)is a functional RNA segment longer than 200 nucleotides,without protein-coding capacity.lncRNAs can directly regulate gene expression in the form of RNA,at epigenetic, transcription,post-transcription,translation and post-translation level,also plays important roles in various biological processes in the body of livestock.The author reviewed origin,classifications and structural features, four kinds of molecular regulation mechanisms for implement biological functions (signal moleculars,decoy moleculars,guide moleculars,scaffold molecules),five levels of regulation gene expression of lncRNA,and the application of high-throughput RNA-Seq technique to analyze the sequencing data and introduce the methods for forecasting livestock lncRNA,provided a basis for the reasonable study of livestock lncRNA.Predition of the livestock lncRNA includes four sections:Deep sequencing, transcriptome reconstruction,new transcription forecast and lncRNA identification.At the stage of lncRNA identification,the author's laboratory adopt coding potential assessment tool and online sequence coding potential calculator intersection method to remove the coding potential transcript from a large of the predicting candidates rapidly,also got 68 604 lncRNA of the skin tissues of Inner Mongolia cashmere goats,enriched the basic data of goat lncRNA transcript in the NONCODE database.

Key words: long noncoding RNAs (lncRNA); regulatory; forecasting methods; CPAT; CPC

中图分类号:

Q756

贾纯琰, 季小阳, 白雪, 戴豪扬, 王建蒙, 张文广. 长链非编码RNA的调控机制及其在家畜中的预测方法[J]. 《中国畜牧兽医》, 2017, 44(7): 1895-1905.

JIA Chun-yan, JI Xiao-yang, BAI Xue, DAI Hao-yang, WANG Jian-meng, ZHANG Wen-guang. Regulatory Mechanisms of Long Noncoding RNAs and Forecasting Methods in Livestock[J]. , 2017, 44(7): 1895-1905.

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