ArticleBMC genomics2015
Genome-wide identification and functional analysis of lincRNAs acting as miRNA targets or decoys in maize.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 70 papers.
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Who cites it
70 citing papers in PubMed.
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- Transcriptome analysis reveals long noncoding RNAs involved in the tuber anthocyanin synthesis of potato (Solanum tuberosum L.).BMC plant biology · 2026Article
- Integrative Analysis of lncRNA-RBP (RNA-Binding Protein) Regulatory Networks Reveals Molecular Targets for EnhancingInternational journal of molecular sciences · 2026Article
- Profiling of extracellular vesicle-associated microRNAs reveals a regulated response to potato virus Y infection in tomato.Frontiers in genetics · 2026Article
- Molecular mechanisms of bamboo-derived miRNA-mediated gene regulation and dietary adaptation in giant pandas.BMC genomics · 2025Article
- TheProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Multi-omics-Based Construction of ncRNA-Gene-Metabolite Networks Provides New Insights Into Metabolic Regulation Under Salt Stress in Rice.Rice (New York, N.Y.) · 2025Article
- Plant long noncoding RNAs: why do we not know more?Biological research · 2025Review
- Identification and characterization of long non-coding RNA (lncRNA) in wild and semi-wild cucumbers.BMC plant biology · 2025Article
- Identification and Validation of Aging- and Endoplasmic Reticulum Stress-Related Genes in Periodontitis Using a Competing Endogenous RNA Network.Inflammation · 2025Article
- Identification and Network Construction of mRNAs, miRNAs, lncRNAs, and circRNAs in Sweetpotato (International journal of molecular sciences · 2025Article
- Artificial miRNAs and target-mimics as potential tools for crop improvement.Physiology and molecular biology of plants : an international journal of functional plant biology · 2025Review
- Vegetal memory through the lens of transcriptomic changes - recent progress and future practical prospects for exploiting plant transcriptional memory.Plant signaling & behavior · 2024Review
- Long intergenic non-coding RNAs modulate proximal protein-coding gene expression and tolerance to Candidatus Liberibacter spp. in potatoes.Communications biology · 2024Article
- Genome-wide analysis of long non-coding RNAs involved in the fruit development process ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2024Article
- Analyzing the defense response mechanism ofFrontiers in plant science · 2024Article
- Identification of Differentially Expressed lncRNAs in Response to Blue Light and Expression Pattern Analysis ofPlants (Basel, Switzerland) · 2023Article
- Biological function research of Fusarium oxysporum f. sp. cubense inducible banana long noncoding RNA Malnc2310 in Arabidopsis.Plant molecular biology · 2023Article
- LncRNA00638 promotes the osteogenic differentiation of periodontal mesenchymal stem cells from periodontitis patients under static mechanical strain.Stem cell research & therapy · 2023Article
10 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
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Abstract
backgroundLong intergenic noncoding RNAs (lincRNAs) are endogenous non-coding RNAs (ncRNAs) that are transcribed from 'intergenic' regions of the genome and may play critical roles in regulating gene expression through multiple RNA-mediated mechanisms. MicroRNAs (miRNAs) are single-stranded small ncRNAs of approximately 21-24 nucleotide (nt) that are involved in transcriptional and post-transcriptional gene regulation. While miRNAs functioning as mRNA repressors have been studied in detail, the influence of miRNAs on lincRNAs has seldom been investigated in plants.
methodsLincRNAs as miRNA targets or decoys were predicted via GSTAr.pl script with a set of rules, and lincRNAs as miRNA targets were validated by degradome data. Conservation analysis of lincRNAs as miRNA targets or decoys were conducted using BLASTN and MAFFT. The function of lincRNAs as miRNA targets were predicted via a lincRNA-mRNA co-expression network, and the function of lincRNAs as miRNA decoys were predicted according to the competing endogenous RNA (ceRNA) hypothesis.
resultsIn this work, we developed a computational method and systematically predicted 466 lincRNAs as 165 miRNA targets and 86 lincRNAs as 58 miRNA decoys in maize (Zea mays L.). Furthermore, 34 lincRNAs predicted as 33 miRNA targets were validated based on degradome data. We found that lincRNAs acting as miRNA targets or decoys are a common phenomenon, which indicates that the regulated networks of miRNAs also involve lincRNAs. To elucidate the function of lincRNAs, we reconstructed a miRNA-regulated network involving 78 miRNAs, 117 lincRNAs and 8834 mRNAs. Based on the lincRNA-mRNA co-expression network and the competing endogenous RNA hypothesis, we predicted that 34 lincRNAs that function as miRNA targets and 86 lincRNAs that function as miRNA decoys participate in cellular and metabolic processes, and play role in catalytic activity and molecular binding functions.
conclusionsThis work provides a comprehensive view of miRNA-regulated networks and indicates that lincRNAs can participate in a layer of regulatory interactions as miRNA targets or decoys in plants, which will enable in-depth functional analysis of lincRNAs.
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