Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing

被引：158

作者：

Li, Tingting ^{[1
,2
]}

Wang, Suya ^{[1
]}

Wu, Rimao ^{[1
]}

Zhou, Xueya ^{[3
,4
]}

Zhu, Dahai ^{[1
]}

Zhang, Yong ^{[1
]}

机构：

[1] Chinese Acad Med Sci, Inst Basic Med Sci, Natl Lab Med Mol Biol, Sch Basic Med,Peking Union Med Coll, Beijing 100005, Peoples R China

[2] Peking Univ, Hlth Sci Ctr, Sch Basic Med Sci, Dept Biomed Informat, Beijing 100191, Peoples R China

[3] Tsinghua Univ, MOE Key Lab Bioinformat, TNUST, Dept Automat, Beijing 100084, Peoples R China

[4] Tsinghua Univ, Bioinformat Div, TNUST, Dept Automat, Beijing 100084, Peoples R China

来源：

GENOMICS | 2012年 / 99卷 / 05期

基金：

中国国家自然科学基金;

关键词：

IncRNAs; RNA-seq; Computational pipeline; Chicken skeletal muscle; NONCODING RNAS; GENOME; EXPRESSION; GENES; DIFFERENTIATION; TRANSCRIPTS; ANNOTATION; VERTEBRATE; MICRORNAS; REVEALS;

D O I：

10.1016/j.ygeno.2012.02.003

中图分类号：

Q81 [生物工程学（生物技术）]; Q93 [微生物学];

学科分类号：

071005 ; 0836 ; 090102 ; 100705 ;

摘要：

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.

引用

页码：292 / 298

页数：7

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