Comprehensive Analysis of Human microRNA-mRNA Interactome

Abstract

MicroRNAs play a key role in the regulation of gene expression. A majority of microRNA-mRNA interactions remain unidentified. Despite extensive research, our ability to predict human microRNA-mRNA interactions using computational algorithms remains limited by a complexity of the models for non-canonical interactions, and an abundance of false-positive results. Here, we present the landscape of human microRNA-mRNA interactions derived from comprehensive analysis of HEK293 and Huh7.5 datasets, along with publicly available microRNA and mRNA expression data. We show that, while only 1-2% of human genes were the most regulated by microRNAs, few cell line-specific RNAs, including EEF1A1 and HSPA1B in HEK293 and AFP, APOB, and MALAT1 genes in Huh7.5, display substantial "sponge-like" properties. We revealed a group of microRNAs that are expressed at a very high level, while interacting with only a few mRNAs, which, indeed, serve as their specific expression regulators. In order to establish reliable microRNA-binding regions, we collected and systematically analyzed the data from 79 CLIP datasets of microRNA-binding sites. We report 46,805 experimentally confirmed mRNA-miRNA duplex regions. Resulting dataset is available at http://score.generesearch.ru/services/mirna/. Our study provides initial insight into the complexity of human microRNA-mRNA interactions.

Keywords: miRNA-target RNA duplexes; microRNA; microRNA-binding sites; microRNA–mRNA interactions; regulation of gene expression; web tool for searching microRNA-binding regions.

Figure 1

Analysis of human microRNA–mRNA interactome. (A) Flowchart describing main steps of human microRNA–mRNA interactome data analysis. (B) Distribution of the summarized lengths of 3’UTR, CDS, or 5’UTR mRNA regions in CLEAR-CLIP, CLASH, and GENCODE, respectively.

Figure 2

Expression analysis of microRNA and mRNA in HEK293 and Huh7.5 cell lines. (A) and (B): Analysis of expressed genes according to amounts of their interactions with microRNAs in HEK293 (A) and Huh7.5 (B) cell lines. (C) and (D): Overview of the microRNA-binding regions locations in sponge-like RNAs expressed in HEK293/CLASH (C) and Huh7.5/CLEAR-CLIP (D) datasets. After segmenting each of the presented RNAs into 50-nt pieces, the segments that interacted with microRNAs were marked blue on the mRNA map. The height represents the number of interactions detected in each of the segment. For each of the sponge-like RNAs, both name and length are placed above the gene schematics. Colored parts of RNAs are labeled as follows: 5’UTR—yellow, coding region—violet, 3’UTR—green, noncoding region—gray. (E) The overlaps between expressed and interacting microRNAs in HEK293 and Huh7.5 cell lines.

Figure 3

Detailed analysis of experimentally confirmed microRNA-binding regions (Exp-MiBRs). (A) Validation of the Exp-MiBR by their independent occurrence in two or more datasets, or in two or more chimeric sequences from one dataset. (B) Exp-MiBRs: distribution of the lengths. On horizontal axis—the length of the Exp-MiBRs subsequence; on vertical axis—amounts of the detected Exp-MiBRs (N). (C). Venn diagram depicting Exp-MiBRs detected in experiments employing three different types of identification techniques. (D) Venn diagram depicting tissue specificity of Exp-MiBRs detected in HEK293, Huh7.5, and all other cell lines.