ArticleBMC genomics2020
Integrative expression network analysis of microRNA and gene isoforms in sacred lotus.
Article in BMC genomics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
9 citing papers in PubMed, 11 citations in OpenAlex.
- Integrated RNA-seq and small RNA-seq profiling reveals tissue-associated transcriptional programs and candidate miRNA-mRNA relationships across tea floral tissues.Frontiers in plant science · 2026Article
- Divergence in MiRNA targeting of AchAco and its role in citrate accumulation in kiwifruit.BMC plant biology · 2024Article
- Genome-Wide Identification and Co-Expression Networks ofPlants (Basel, Switzerland) · 2024Article
- Evolution of isoform-level gene expression patterns across tissues during lotus species divergence.The Plant journal : for cell and molecular biology · 2022Article
- Evaluation of the Possible Contribution of Various Regulatory Genes to Determination of Carpel Number as a Potential Mechanism for Optimal Agricultural Yield.International journal of molecular sciences · 2022Review
- Genome-wide association study of traits in sacred lotus uncovers MITE-associated variants underlying stamen petaloid and petal number variations.Frontiers in plant science · 2022Article
- Expression rewiring and methylation of non-coding RNAs involved in rhizome phenotypic variations of lotus ecotypes.Computational and structural biotechnology journal · 2022Article
- Review
- Nelumbo genome database, an integrative resource for gene expression and variants of Nelumbo nucifera.Scientific data · 2021Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 2 countries.
Funding
Abstract
backgroundGene expression is complex and regulated by multiple molecular mechanisms, such as miRNA-mediated gene inhibition and alternative-splicing of pre-mRNAs. However, the coordination of interaction between miRNAs with different splicing isoforms, and the change of splicing isoform in response to different cellular environments are largely unexplored in plants. In this study, we analyzed the miRNA and mRNA transcriptome from lotus (Nelumbo nucifera), an economically important flowering plant.
resultsThrough RNA-seq analyses on miRNAs and their target genes (isoforms) among six lotus tissues, expression of most miRNAs seem to be negatively correlated with their targets and tend to be tissue-specific. Further, our results showed that preferential interactions between miRNAs and hub gene isoforms in one coexpression module which is highly correlated with leaf. Intriguingly, for many genes, their corresponding isoforms were assigned to different co-expressed modules, and they exhibited more divergent mRNA structures including presence and absence of miRNA binding sites, suggesting functional divergence for many isoforms is escalated by both structural and expression divergence. Further detailed functional enrichment analysis of miRNA targets revealed that miRNAs are involved in the regulation of lotus growth and development by regulating plant hormone-related pathway genes.
conclusionsTaken together, our comprehensive analyses of miRNA and mRNA transcriptome elucidate the coordination of interaction between miRNAs and different splicing isoforms, and highlight the functional divergence of many transcript isoforms from the same locus in lotus.
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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.