Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing
Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing
复制标题
使用下一代测序鉴定鸡骨骼肌中的长非蛋白质编码 RNA
DOI：
10.1016/j.ygeno.2012.02.003
复制
发表时间：
2012-05-01
期刊：
影响因子：
4.4
通讯作者：
Zhang, Yong
中科院分区：
文献类型：
--
作者：
Li, Tingting;Wang, Suya;Zhang, Yong
脊椎动物基因组编码数千种非编码RNA，包括短链非编码RNA（如微小RNA）和长链非编码RNA（lncRNAs）。鸡（原鸡）是发育生物学的一种重要模式生物，近期组装的鸡基因组序列将有助于理解非编码RNA基因在发育过程中的功能作用。本研究首次利用RNA - Seq对鸡肌肉发育过程中的转录组进行取样，从而系统地鉴定lncRNAs。采用一种计算方法在鸡基因组中鉴定出281种新的基因间lncRNAs。一般来说，新的lncRNAs比蛋白质编码基因保守性低，比随机非编码序列保守性略高。本研究提供了一个初步的鸡lncRNA目录，并极大地增加了非蛋白质编码RNA数据库中鸡的非编码RNA数量。此外，当前研究中提出的计算流程将有助于对从深度测序数据中获得的lncRNAs进行特征分析。（C）2012爱思唯尔公司。保留所有权利。
Vertebrate genomes encode thousands of non-coding RNAs including short non-coding RNAs (such as microRNAs) and long non-coding RNAs (IncRNAs). Chicken (Gallus gallus) is an important model organism for developmental biology, and the recently assembled genome sequences for chicken will facilitate the understanding of the functional roles of non-coding RNA genes during development. The present study concerns the first systematic identification of IncRNAs using RNA-Seq to sample the transcriptome during chicken muscle development. A computational approach was used to identify 281 new intergenic IncRNAs in the chicken genome. Novel IncRNAs in general are less conserved than protein-coding genes and slightly more conserved than random non-coding sequences. The present study has provided an initial chicken IncRNA catalog and greatly increased the number of chicken ncRNAs in the non-protein coding RNA database. Furthermore, the computational pipeline presented in the current work will be useful for characterizing IncRNAs obtained from deep sequencing data. (C) 2012 Elsevier Inc. All rights reserved.