ArticleRNA biology2014
Comprehensive analysis of small RNA-seq data reveals that combination of miRNA with its isomiRs increase the accuracy of target prediction in Arabidopsis thaliana.
Article in RNA biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 26 papers.
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Who cites it
26 citing papers in PubMed, 38 citations in OpenAlex.
- The miR319/bHLH094 Module Regulates Creeping Bentgrass Thermotolerance by Modulating Auxin Biosynthesis and Signalling Pathway.Plant biotechnology journal · 2026Article
- athisomiRDB: A comprehensive database of Arabidopsis isomiRs.Database : the journal of biological databases and curation · 2024Article
- The importance of genotyping within the climate-smart plant breeding value chain - integrative tools for genetic enhancement programs.Frontiers in plant science · 2024Review
- One locus, several functional RNAs-emerging roles of the mechanisms responsible for the sequence variability of microRNAs.Biologia futura · 2023Review
- Identification of Small RNAs During High Light Acclimation inFrontiers in plant science · 2021Article
- Article
- Investigating the pathogenic SNPs in BLM helicase and their biological consequences by computational approach.Scientific reports · 2020Article
- Investigation into the miRNA/5' isomiRNAs function and drought-mediated miRNA processing in rice.Functional & integrative genomics · 2020Article
- A conserved sequence signature is essential for robust plant miRNA biogenesis.Nucleic acids research · 2020Article
- Post-transcriptional regulation of several biological processes involved in latex production inPeerJ · 2020Article
- Systematic Analysis of Alkaline/Neutral Invertase Genes Reveals the Involvement of Smi-miR399 in Regulation ofPlants (Basel, Switzerland) · 2019Article
- Identifying High Confidence microRNAs in the Developing Seeds of Jatropha curcas.Scientific reports · 2019Article
- Diff isomiRs: Large-scale detection of differential isomiRs for understanding non-coding regulated stress omics in plants.Scientific reports · 2019Article
- Modulation of miRNA expression in natural populations of A. thaliana along a wide altitudinal gradient of Indian Himalayas.Scientific reports · 2019Article
- Integrated Network Analysis Reveals FOXM1 and MYBL2 as Key Regulators of Cell Proliferation in Non-small Cell Lung Cancer.Frontiers in oncology · 2019Article
- Genome-wide microRNA screening in Nile tilapia reveals pervasive isomiRs' transcription, sex-biased arm switching and increasing complexity of expression throughout development.Scientific reports · 2018Article
- Identification of the miRNAome of early mesoderm progenitor cells and cardiomyocytes derived from human pluripotent stem cells.Scientific reports · 2018Article
- High-throughput sequencing analysis revealed the regulation patterns of small RNAs on the development of A. comosus var. bracteatus leaves.Scientific reports · 2018Article
- A Role for the F-Box Protein HAWAIIAN SKIRT in Plant microRNA Function.Plant physiology · 2018Article
- Plant IsomiR Atlas: Large Scale Detection, Profiling, and Target Repertoire of IsomiRs in Plants.Frontiers in plant science · 2018Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Along with the canonical miRNA, distinct miRNA-like sequences called sibling miRNAs (sib-miRs) are generated from the same pre-miRNA. Among them, isomeric sequences featuring slight variations at the terminals, relative to the canonical miRNA, constitute a pool of isomeric sibling miRNAs (isomiRs). Despite the high prevalence of isomiRs in eukaryotes, their features and relevance remain elusive. In this study, we performed a comprehensive analysis of mature precursor miRNA (pre-miRNA) sequences from Arabidopsis to understand their features and regulatory targets. The influence of isomiR terminal heterogeneity in target binding was examined comprehensively. Our comprehensive analyses suggested a novel computational strategy that utilizes miRNA and its isomiRs to enhance the accuracy of their regulatory target prediction in Arabidopsis. A few targets are shared by several members of isomiRs; however, this phenomenon was not typical. Gene Ontology (GO) enrichment analysis showed that commonly targeted mRNAs were enriched for certain GO terms. Moreover, comparison of these commonly targeted genes with validated targets from published data demonstrated that the validated targets are bound by most isomiRs and not only the canonical miRNA. Furthermore, the biological role of isomiRs in target cleavage was supported by degradome data. Incorporating this finding, we predicted potential target genes of several miRNAs and confirmed them by experimental assays. This study proposes a novel strategy to improve the accuracy of predicting miRNA targets through combined use of miRNA with its isomiRs.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.