Computer Science, University of Central Florida, Orlando, FL-32816, US.
Burnett School of Biomedical Science, University of Central Florida, Orlando, FL-32816, US.
Brief Bioinform. 2021 Jan 18;22(1):380-392. doi: 10.1093/bib/bbz178.
MicroRNAs (miRNAs) are small noncoding RNAs that play important roles in gene regulation and phenotype development. The identification of miRNA transcription start sites (TSSs) is critical to understand the functional roles of miRNA genes and their transcriptional regulation. Unlike protein-coding genes, miRNA TSSs are not directly detectable from conventional RNA-Seq experiments due to miRNA-specific process of biogenesis. In the past decade, large-scale genome-wide TSS-Seq and transcription activation marker profiling data have become available, based on which, many computational methods have been developed. These methods have greatly advanced genome-wide miRNA TSS annotation.
In this study, we summarized recent computational methods and their results on miRNA TSS annotation. We collected and performed a comparative analysis of miRNA TSS annotations from 14 representative studies. We further compiled a robust set of miRNA TSSs (RSmirT) that are supported by multiple studies. Integrative genomic and epigenomic data analysis on RSmirT revealed the genomic and epigenomic features of miRNA TSSs as well as their relations to protein-coding and long non-coding genes.
MicroRNAs (miRNAs) 是在基因调控和表型发育中发挥重要作用的小非编码 RNA。miRNA 转录起始位点 (TSS) 的鉴定对于理解 miRNA 基因的功能作用及其转录调控至关重要。与蛋白质编码基因不同，由于 miRNA 生物发生的特异性过程，miRNA TSS 不能直接从常规的 RNA-Seq 实验中检测到。在过去的十年中，基于大规模全基因组 TSS-Seq 和转录激活标记分析数据，已经开发了许多计算方法。这些方法极大地推动了全基因组 miRNA TSS 注释。
在本研究中，我们总结了最近用于 miRNA TSS 注释的计算方法及其结果。我们收集并对来自 14 项代表性研究的 miRNA TSS 注释进行了比较分析。我们进一步编译了一个由多个研究支持的稳健 miRNA TSS 集 (RSmirT)。对 RSmirT 的综合基因组和表观基因组数据分析揭示了 miRNA TSS 的基因组和表观基因组特征及其与蛋白质编码基因和长非编码基因的关系。
