ArticleBMC bioinformatics2018
Detection of long non-coding RNA homology, a comparative study on alignment and alignment-free metrics.
Article in BMC bioinformatics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Neuid: A Novel Neuron-Enriched LncRNA that Connects Epigenetic Gene Silencing to Alzheimer's Disease.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Long non-coding RNA in the regulation of cell death in hepatocellular carcinoma.World journal of clinical oncology · 2025Review
- Animal models of lupus nephritis: the past, present and a future outlook.Autoimmunity · 2024Review
- Long Non-Coding RNAs and Their Potential Role as Biomarkers in Inflammatory Bowel Disease.International journal of molecular sciences · 2024Review
- Patterns of transcription factor binding and epigenome at promoters allow interpretable predictability of multiple functions of non-coding and coding genes.Computational and structural biotechnology journal · 2023Article
- LncRNA IL21-AS1 interacts with hnRNPU protein to promote IL21 overexpression and aberrant differentiation of Tfh cells in systemic lupus erythematosus.Clinical and translational medicine · 2022Article
- PVT1 is a stress-responsive lncRNA that drives ovarian cancer metastasis and chemoresistance.Life science alliance · 2022Article
- Melatonin Attenuates HInternational journal of molecular sciences · 2022Article
- Global-run on sequencing identifiesiScience · 2022Article
- LncRNAs in domesticated animals: from dog to livestock species.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- LncRNA-Dependent Mechanisms of Transforming Growth Factor-β: From Tissue Fibrosis to Cancer Progression.Non-coding RNA · 2022Review
- MILNP: Plant lncRNA-miRNA Interaction Prediction Based on Improved Linear Neighborhood Similarity and Label Propagation.Frontiers in plant science · 2022Article
- Organ-on-a-chip technology: a novel approach to investigate cardiovascular diseases.Cardiovascular research · 2021Review
- Ensemble Deep Learning Based on Multi-level Information Enhancement and Greedy Fuzzy Decision for Plant miRNA-lncRNA Interaction Prediction.Interdisciplinary sciences, computational life sciences · 2021Article
- The role of long non-coding RNAs in the regulation of pancreatic beta cell identity.Biochemical Society transactions · 2021Review
- Comparative genomics in the search for conserved long noncoding RNAs.Essays in biochemistry · 2021Article
- Decoding LncRNAs.Cancers · 2021Review
- Humanized Mouse Models of Systemic Lupus Erythematosus: Opportunities and Challenges.Frontiers in immunology · 2021Review
- Long non-coding RNAs in development and disease: conservation to mechanisms.The Journal of pathology · 2020Review
- RNAsamba: neural network-based assessment of the protein-coding potential of RNA sequences.NAR genomics and bioinformatics · 2020Article
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Authors and funding
7 authors.
Funding
Abstract
backgroundLong non-coding RNAs (lncRNAs) represent a novel class of non-coding RNAs having a crucial role in many biological processes. The identification of long non-coding homologs among different species is essential to investigate such roles in model organisms as homologous genes tend to retain similar molecular and biological functions. Alignment-based metrics are able to effectively capture the conservation of transcribed coding sequences and then the homology of protein coding genes. However, unlike protein coding genes the poor sequence conservation of long non-coding genes makes the identification of their homologs a challenging task.
resultsIn this study we compare alignment-based and alignment-free string similarity metrics and look at promoter regions as a possible source of conserved information. We show that promoter regions encode relevant information for the conservation of long non-coding genes across species and that such information is better captured by alignment-free metrics. We perform a genome wide test of this hypothesis in human, mouse, and zebrafish.
conclusionsThe obtained results persuaded us to postulate the new hypothesis that, unlike protein coding genes, long non-coding genes tend to preserve their regulatory machinery rather than their transcribed sequence. All datasets, scripts, and the prediction tools adopted in this study are available at https://github.com/bioinformatics-sannio/lncrna-homologs .
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