ArticleRNA biology2021
Hairpin sequence and structure is associated with features of isomiR biogenesis.
Article in RNA biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Plasma isomiRs as Candidate Biomarkers for Amyotrophic Lateral Sclerosis.Neurology. Genetics · 2026Article
- Several novel classes of small regulatory RNAs show widespread changes in schizophrenia and bipolar disorder and extensive linkages to critical brain processes.Translational psychiatry · 2026Article
- CD44 knockdown alters miRNA expression and their target genes in colon cancer.Frontiers in immunology · 2025Article
- Exosomal miRNAs and isomiRs: potential biomarkers for type 2 diabetes mellitus.Precision clinical medicine · 2024Review
- Interrogating the Role of miR-125b and Its 3'isomiRs in Protection against Hypoxia.International journal of molecular sciences · 2023Article
- A Review of IsomiRs in Colorectal Cancer.Non-coding RNA · 2023Review
- Differential co-expression network analysis with DCoNA reveals isomiR targeting aberrations in prostate cancer.Bioinformatics (Oxford, England) · 2023Article
- The Role of MicroRNAs in Liver Functioning: from Biogenesis to Therapeutic Approaches (Review).Sovremennye tekhnologii v meditsine · 2023Review
- Recent findings on the role of microRNAs in genetic kidney diseases.Molecular biology reports · 2022Review
- Changes in the Expression of miRNA Isoforms and Their Targets in HT-29 Cells after Hypoxic Exposure.Bulletin of experimental biology and medicine · 2022Article
- Article
- ExhauFS: exhaustive search-based feature selection for classification and survival regression.PeerJ · 2022Article
- ECM-Receptor Regulatory Network and Its Prognostic Role in Colorectal Cancer.Frontiers in genetics · 2021Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
MiRNA isoforms (isomiRs) are single stranded small RNAs originating from the same pri-miRNA hairpin as a result of cleavage by Drosha and Dicer enzymes. Variations at the 5'-end of a miRNA alter the seed region of the molecule, thus affecting the targetome of the miRNA. In this manuscript, we analysed the distribution of miRNA cleavage positions across 31 different cancers using miRNA sequencing data of TCGA project. As a result, we found that the processing positions are not tissue specific and that all miRNAs could be correctly classified as ones exhibiting homogeneous or heterogeneous cleavage at one of the four cleavage sites. In 42% of cases (42 out of 100 miRNAs), we observed imprecise 5'-end Dicer cleavage, while this fraction was only 14% for Drosha (14 out of 99). To the contrary, almost all cleavage sites of 3'-ends (either Drosha or Dicer) were heterogeneous. With the use of only four nucleotides surrounding a 5'-end Dicer cleavage position we built a model which allowed us to distinguish between homogeneous and heterogeneous cleavage with the reliable quality (ROC AUC = 0.68). Finally, we showed the possible applications of the study by the analysis of two 5'-end isoforms originating from the same exogeneous shRNA hairpin. It turned out that the less expressed shRNA variant was functionally active, which led to the increased off-targeting. Thus, the obtained results could be applied to the design of shRNAs whose processing will result in a single 5'-variant.
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