title: Cross-mapping events in miRNAs reveal potential miRNA-mimics and evolutionary implications.
abstract: MicroRNAs (miRNAs) have important roles in various biological processes. miRNA cross-mapping is a prevalent phenomenon where miRNA sequence originating from one genomic region is mapped to another location. To have a better understanding of this phenomenon in the human genome, we performed a detailed analysis in this paper using public miRNA high-throughput sequencing data and all known human miRNAs. We observed widespread cross-mapping events between miRNA precursors (pre-miRNAs), other non-coding RNAs (ncRNAs) and the opposite strands of pre-miRNAs by analyzing the high-throughput sequencing data. Computational analysis on all known human miRNAs also confirmed that many of them could be involved in cross-mapping events. The processing or decay of both ncRNAs and pre-miRNA opposite strand transcripts may contribute to miRNA enrichment, although some might be miRNA-mimics due to miRNA mis-annotation. Comparing to canonical miRNAs, miRNAs involved in cross-mapping events between pre-miRNAs and other ncRNAs normally had shorter lengths (17-19 nt), lower prediction scores and were classified as pseudo miRNA precursors. Notably, 4.9% of all human miRNAs could be accurately mapped to the opposite strands of pre-miRNAs, which showed that both strands of the same genomic region had the potential to produce mature miRNAs and simultaneously implied some potential miRNA precursors. We proposed that the cross-mapping events are more complex than we previously thought. Sequence similarity between other ncRNAs and pre-miRNAs and the specific stem-loop structures of pre-miRNAs may provide evolutionary implications.
authors.affiliation: State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, China.
authors.forename: Li
authors.initials: L
authors.lastname: Guo
authors.forename: Tingming
authors.initials: T
authors.lastname: Liang
authors.forename: Wanjun
authors.initials: W
authors.lastname: Gu
authors.forename: Yuming
authors.initials: Y
authors.lastname: Xu
authors.forename: Yunfei
authors.initials: Y
authors.lastname: Bai
authors.forename: Zuhong
authors.initials: Z
authors.lastname: Lu
mesh_terms: D001483:Base Sequence; D019143:Evolution, Molecular; D014644:Genetic Variation; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D035683:MicroRNAs / Q000235:genetics*; D008969:Molecular Sequence Data; D012322:RNA Precursors / Q000235:genetics; D022661:RNA, Untranslated / Q000235:genetics
chemical_list: D035683:MicroRNAs; D012322:RNA Precursors; D022661:RNA, Untranslated