starBase: a database for exploring microRNA–mRNA interaction maps from Argonaute CLIP-Seq and Degradome-Seq data

TLDR

MicroRNAs regulate gene expression by targeting messenger RNAs, but assigning them to regulatory targets is technically challenging, and high‑throughput CLIP‑Seq and Degradome‑Seq methods now enable identification of Argonaute binding sites and miRNA cleavage sites. The authors introduce starBase, a database designed to facilitate comprehensive exploration of miRNA‑target interaction maps derived from CLIP‑Seq and Degradome‑Seq data. starBase incorporates high‑throughput sequencing data from 21 CLIP‑Seq and 10 Degradome‑Seq experiments across six organisms and provides web servers that support diverse query types, target discovery, and pathway exploration. Analysis of millions of reads identified approximately 1 million Ago‑binding clusters, 2 million cleaved target clusters, and about 400 000 and 66 000 miRNA‑target regulatory relationships, and the database is available at http://starbase.sysu.edu.cn/.

Abstract

MicroRNAs (miRNAs) represent an important class of small non-coding RNAs (sRNAs) that regulate gene expression by targeting messenger RNAs. However, assigning miRNAs to their regulatory target genes remains technically challenging. Recently, high-throughput CLIP-Seq and degradome sequencing (Degradome-Seq) methods have been applied to identify the sites of Argonaute interaction and miRNA cleavage sites, respectively. In this study, we introduce a novel database, starBase (sRNA target Base), which we have developed to facilitate the comprehensive exploration of miRNA-target interaction maps from CLIP-Seq and Degradome-Seq data. The current version includes high-throughput sequencing data generated from 21 CLIP-Seq and 10 Degradome-Seq experiments from six organisms. By analyzing millions of mapped CLIP-Seq and Degradome-Seq reads, we identified ∼1 million Ago-binding clusters and ∼2 million cleaved target clusters in animals and plants, respectively. Analyses of these clusters, and of target sites predicted by 6 miRNA target prediction programs, resulted in our identification of approximately 400,000 and approximately 66,000 miRNA-target regulatory relationships from CLIP-Seq and Degradome-Seq data, respectively. Furthermore, two web servers were provided to discover novel miRNA target sites from CLIP-Seq and Degradome-Seq data. Our web implementation supports diverse query types and exploration of common targets, gene ontologies and pathways. The starBase is available at http://starbase.sysu.edu.cn/.