ArticleGenome biology2021
Uncovering deeply conserved motif combinations in rapidly evolving noncoding sequences.
Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed, 52 citations in OpenAlex.
- RNA-Lexis: a probabilistic algorithm using a non-parametric segmentation logic to detect meaningful sequences in RNA.Nucleic acids research · 2026Article
- An integrative workflow for lncRNA orthology detection and its application to 13 evolutionarily diverse species.Nucleic acids research · 2026Article
- The history and function of a circular RNA.Nature communications · 2026Review
- Metamorphosis and lncRNAs: A Close Relationship.Genesis (New York, N.Y. : 2000) · 2026Review
- Decoding the lncRNA World: Comprehensive Approaches to lncRNA Structure and Interactome Studies.Cells · 2026Review
- Integrative multi-omics analysis widens annotation and functional insights into long non-coding RNAs of Arabidopsis thaliana.Biology direct · 2026Article
- The lncRNA PACER Regulates Lung Adenocarcinoma Phenotypes via COX-2 Signaling and RNA Structural Dynamics.bioRxiv : the preprint server for biology · 2025Article
- PlantLncBoost: key features for plant lncRNA identification and significant improvement in accuracy and generalization.The New phytologist · 2025Article
- Pre-symptomatic Parkinson's disease blood test quantifying repetitive sequence motifs in transfer RNA fragments.Nature aging · 2025Article
- Improved functions for nonlinear sequence comparison using SEEKR.RNA (New York, N.Y.) · 2024Article
- Quest for Orthologs in the Era of Biodiversity Genomics.Genome biology and evolution · 2024Review
- An RNA-centric view of transcription and genome organization.Molecular cell · 2024Review
- Targeting and engineering long non-coding RNAs for cancer therapy.Nature reviews. Genetics · 2024Review
- Integrative analysis of the lncRNA-miRNA-mRNA interactions in smooth muscle cell phenotypic transitions.Frontiers in genetics · 2024Article
- Regulatory RNAs: role as scaffolds assembling protein complexes and their epigenetic deregulation.Exploration of targeted anti-tumor therapy · 2024Review
- Emerging roles of long non-coding RNAs in osteosarcoma.Frontiers in molecular biosciences · 2024Review
- The lncRNAeLife · 2023Article
- Review
- Functional evolutionary convergence of long noncoding RNAs involved in embryonic development.Communications biology · 2023Article
- Long non-coding RNAs: definitions, functions, challenges and recommendations.Nature reviews. Molecular cell biology · 2023Review
Corrections and comments
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAnimal genomes contain thousands of long noncoding RNA (lncRNA) genes, a growing subset of which are thought to be functionally important. This functionality is often mediated by short sequence elements scattered throughout the RNA sequence that correspond to binding sites for small RNAs and RNA binding proteins. Throughout vertebrate evolution, the sequences of lncRNA genes changed extensively, so that it is often impossible to obtain significant alignments between sequences of lncRNAs from evolutionary distant species, even when synteny is evident. This often prohibits identifying conserved lncRNAs that are likely to be functional or prioritizing constrained regions for experimental interrogation.
resultsWe introduce here LncLOOM, a novel algorithmic framework for the discovery and evaluation of syntenic combinations of short motifs. LncLOOM is based on a graph representation of the input sequences and uses integer linear programming to efficiently compare dozens of sequences that have thousands of bases each and to evaluate the significance of the recovered motifs. We show that LncLOOM is capable of identifying specific, biologically relevant motifs which are conserved throughout vertebrates and beyond in lncRNAs and 3'UTRs, including novel functional RNA elements in the CHASERR lncRNA that are required for regulation of CHD2 expression.
conclusionsWe expect that LncLOOM will become a broadly used approach for the discovery of functionally relevant elements in the noncoding genome.
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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.