3个时期牛肌肉组织中长链非编码RNA表达谱的生物信息学分析

doi:10.16431/j.cnki.1671-7236.2019.01.001

摘要/Abstract

摘要：

试验旨在分析不同时期牛肌肉组织中长链非编码RNA（long non-coding RNA，lncRNAs）的表达谱，并筛选出可能参与肌肉发育过程的相关的lncRNAs。采集3月龄胚胎、6月龄胚胎和9月龄出生个体的肌肉组织RNA样品进行高通量测序，通过生物信息学方法对鉴定到的lncRNAs进行分析筛选，对lncRNAs靶基因和3个时期差异mRNAs进行Veen分析，并对Veen结果进行GO和KEGG富集分析，筛选与肌肉发育相关的lncRNAs及靶标mRNA。结果显示，高通量测序共鉴定到212 851条新的未注释的lncRNAs，其中在不同时期差异表达的有9 913条，分属于基因间型、正义链型、反义链型和双向型4种类型，在各染色体上均有分布，其中正义链型lncRNAs在各个染色体上分布数量最多，分布范围最广。分析其结构发现这些lncRNAs具有开放阅读框短、表达水平低、编码能力弱、分布广、数量大等特征。通过GO和KEGG富集分析，最终筛选出3月龄胚胎、6月龄胚胎和9月龄出生个体肌肉中差异表达并与肌生成有密切关系的55条lncRNAs和38条候选靶标mRNA。本研究不仅提供了3个时期牛肌肉组织中lncRNAs的表达模式，而且通过预测lncRNAs与mRNA的相互作用关系极大地缩小了与牛肌肉发育相关的lncRNAs的研究范围，为揭示牛肌肉发育的功能提供了重要的靶点。

关键词: 牛肌肉组织; RNA测序; 生物信息学分析; lncRNAs

Abstract:

This study was aimed to analyze the expression profiles of long non-coding RNA (lncRNAs) in bovine muscle tissue from different periods and screen out lncRNAs which might involve in muscle development.The bovine muscle tissue RNA samples from 3-month-old embryos,6-month-old embryos and 9-month-old calf were collected for high-throughput sequencing.The identified lncRNAs were analyzed and filtered with bioinformatics methods,Veen analysis was performed on lncRNAs target gene and three periods differential mRNAs,Go and KEGG enrichment analysis were performed on Veen results to select lncRNAs and target mRNAs which related to muscle development.The results showed that 212 851 novel unannotated lncRNAs were identified by high-throughput sequencing,of which 9 913 were differentially expressed in different periods.These lncRNAs distributed on each chromosome and belonged to four types,which included intergenic,sense strand,antisense strand and bidirectional,and the sense strand lncRNAs had the largest number and the widest distribution range on each chromosome.The structural features analysis revealed that these lncRNAs had the characteristics of short open reading frame,low expression level,weak coding ability,wide distribution and the huge numbers.55 muscle myogenesis related differentially expressed lncRNAs among 3-month-old embryos,6-month-old embryos and 9-month-old calf were screened out by GO and KEGG enrichment analysis,and 38 candidate target mRNAs were also filtered.This study presented the expression pattern of lncRNAs in bovine muscle tissue from three periods by predicting the interaction between lncRNAs and mRNA,and greatly reduced the research range of bovine muscle development related lncRNAs.The study also provided a critical target for revealing the function of bovine muscle development.

Key words: bovine muscle tissue; RNA sequencing; bioinformatics analysis; lncRNAs

中图分类号:

张晓娟, 陈明明, 辛向博, 刘新峰, 张林林, 丁向彬, 郭宏, 李新. 3个时期牛肌肉组织中长链非编码RNA表达谱的生物信息学分析[J]. 《中国畜牧兽医》, 2019, 46(1): 1-9.

ZHANG Xiaojuan, CHEN Mingming, XIN Xiangbo, LIU Xinfeng, ZHANG Linlin, DING Xiangbin, GUO Hong, LI Xin. Bioinformatics Analysis of Long Non-coding RNA Expression Profiles in Bovine Muscle Tissues from Three Periods[J]. , 2019, 46(1): 1-9.

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