Global expression analysis of miRNA gene cluster and family based on isomiRs from deep sequencing data

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.