Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data
Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data
复制标题
基于深度测序数据 isomiR 的 miRNA 基因簇和家族的全局表达分析
DOI：
10.1016/j.compbiolchem.2010.06.001
复制
发表时间：
2010-06-01
影响因子：
3.1
通讯作者：
Lu, Zuhong
中科院分区：
文献类型：
--
作者：
Guo, Li;Lu, Zuhong
在本研究中，我们基于深度测序数据中不同的异构体（isomiRs）选择方案，对人类微小RNA（miRNA）基因簇和家族中的miRNAs进行了全局相对表达分析。分别基于最丰富的异构体的序列计数和所有异构体序列计数之和的表达分布之间观察到了一些差异。但这种差异对miRNA基因簇和家族中的表达模式影响较小。由于测序技术的高灵敏度以及常见异构体在多拷贝miRNA前体和同源基因之间的模糊分布，大多数基因簇和家族表现出不一致的表达水平。不一致的表达模式暗示了体内的表达多样化，尽管它们在转录和/或基因调控过程中可能表现出密切的关系。一些基因簇和家族从相同的臂产生成熟的miRNAs，甚至长度相同，特别是在基因家族中。这种有趣的表达和长度分布可能暗示了在由Dicer和Drosha切割的前体miRNA加工过程中的严格调控。研究表明，最丰富的异构体可能是一个更好的标记，并且miRNA基因簇和家族的全局表达分析为分析相对表达水平以及理解miRNAs在调控网络中的功能关系和表达调控机制提供了线索。（C）2010爱思唯尔有限公司。保留所有权利。
In this study, we present a global relative expression analysis of miRNAs in human miRNA gene cluster and family based on different selection schemes of isomiRs from deep sequencing data. Some divergence was observed between expression distributions based on sequence count of the most abundant isomiR and sum of all isomiR sequence counts, respectively. But the divergence showed less effect on expression patterns in miRNA gene cluster and family. Because of high sensitivity of sequencing technology and ambiguous distribution of common isomiRs among multicopy miRNA precursors and homologous genes, most gene clusters and families showed inconsistent expression levels. Inconsistent expression pattern implied expression diversification in vivo although they maybe showed close relationship during transcription and/or gene regulation. Some gene clusters and families generated mature miRNAs from the same arms and even with the same lengths, especially in gene family. The interesting expression and length distribution maybe implied strict regulation during pre-miRNA processing through cleavage of Dicer and Drosha. The study showed that the most abundant isomiR may be a better marker, and global expression analysis of miRNA gene cluster and family provide clues for analyzing relative expression levels and understanding the function relationship and mechanism for expression regulation of miRNAs in regulation network. (C) 2010 Elsevier Ltd. All rights reserved.