ArticleBMC genomics2018
A systematic approach to RNA-associated motif discovery.
Article in BMC genomics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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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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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
18 citing papers in PubMed.
- FUS Selectively Facilitates circRNAs Packing into Small Extracellular Vesicles within Hypoxia Neuron.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Beyond the Bubble: A Debate on microRNA Sorting Into Extracellular Vesicles.Laboratory investigation; a journal of technical methods and pathology · 2025Review
- Review
- DeepMiRBP: a hybrid model for predicting microRNA-protein interactions based on transfer learning and cosine similarity.BMC bioinformatics · 2024Article
- MicroRNAs in Pancreatic Cancer: Advances in Biomarker Discovery and Therapeutic Implications.International journal of molecular sciences · 2024Review
- Whole-Genome Identification and Characterization of the DKK Gene Family and Its Transcription Profiles: An Analysis of the Chinese Soft-Shell Turtle (Animals : an open access journal from MDPI · 2024Article
- Exosomal microRNAs in regulation of tumor cells resistance to apoptosis.Biochemistry and biophysics reports · 2024Review
- Exosomal miRNAs as a Promising Source of Biomarkers in Colorectal Cancer Progression.International journal of molecular sciences · 2022Review
- Exosome-mediated miR-7-5p delivery enhances the anticancer effect of Everolimus via blocking MNK/eIF4E axis in non-small cell lung cancer.Cell death & disease · 2022Article
- The mScience immunology · 2021Article
- Exosomal microRNAs in colorectal cancer: Overcoming barriers of the metastatic cascade (Review).International journal of molecular medicine · 2021Review
- Regulation of exosome production and cargo sorting.International journal of biological sciences · 2021Review
- Morphine-mediated release of miR-138 in astrocyte-derived extracellular vesicles promotes microglial activation.Journal of extracellular vesicles · 2020Article
- The Messenger Apps of the cell: Extracellular Vesicles as Regulatory Messengers of Microglial Function in the CNS.Journal of neuroimmune pharmacology : the official journal of the Society on NeuroImmune Pharmacology · 2020Review
- Circulating microRNA trafficking and regulation: computational principles and practice.Briefings in bioinformatics · 2020Review
- Exosomal miRNA: Small Molecules, Big Impact in Colorectal Cancer.Journal of oncology · 2019Review
- Astrocyte EV-Induced lincRNA-Cox2 Regulates Microglial Phagocytosis: Implications for Morphine-Mediated Neurodegeneration.Molecular therapy. Nucleic acids · 2018Article
- Exosomal long noncoding RNAs and microRNAs in colorectal cancer.Tzu chi medical journalReview
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
backgroundSequencing-based large screening of RNA-protein and RNA-RNA interactions has enabled the mechanistic study of post-transcriptional RNA processing and sorting, including exosome-mediated RNA secretion. The downstream analysis of RNA binding sites has encouraged the investigation of novel sequence motifs, which resulted in exceptional new challenges for identifying motifs from very short sequences (e.g., small non-coding RNAs or truncated messenger RNAs), where conventional methods tend to be ineffective. To address these challenges, we propose a novel motif-finding method and validate it on a wide range of RNA applications.
resultsWe first perform motif analysis on microRNAs and longer RNA fragments from various cellular and exosomal sources, and then validate our prediction through literature search and experimental test. For example, a 4 bp-long motif, GUUG, was detected to be responsible for microRNA loading in exosomes involved in human colon cancer (SW620). Additional performance comparisons in various case studies have shown that this new approach outperforms several existing state-of-the-art methods in detecting motifs with exceptional high coverage and explicitness.
conclusionsIn this work, we have demonstrated the promising performance of a new motif discovery approach that is particularly effective in current RNA applications. Important discoveries resulting from this work include the identification of possible RNA-loading motifs in a variety of exosomes, as well as novel insights in sequence features of RNA cargos, i.e., short non-coding RNAs and messenger RNAs may share similar loading mechanism into exosomes. This method has been implemented and deployed as a new webserver named MDS
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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.