ArticleGenome biology2016
Evolutionary analysis across mammals reveals distinct classes of long non-coding RNAs.
Article in Genome biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 115 papers.
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Who cites it
115 citing papers in PubMed.
- LncRNAEpigenetics · 2026Article
- Exploring the Effect of Whole-Genome Duplication on Salmonid LincRNA Repertoire.International journal of molecular sciences · 2026Article
- Retina-specific long non-coding RNAs associated with inherited retinal disease genes.Cellular and molecular life sciences : CMLS · 2026Article
- Reference-guided genome assembly of long non-coding rna transcripts reveals target genes associated with Crohn's disease.Scientific reports · 2026Article
- Substantial unannotated noncoding transcripts in tumors may transcriptionally regulate cancer-related genes.BMC biology · 2026Article
- Walras modulates sex-dependent endoplasmic reticulum stress in cardiomyopathy.Frontiers in physiology · 2026Article
- Reference-guided Genome Assembly of Long Non-coding RNA Transcripts Reveals Target Genes Associated With Crohn's Disease.bioRxiv : the preprint server for biology · 2025Article
- KIAA1522 isoform switching regulates LTR-RTs activity in distinct pluripotency states of hESCs.Science China. Life sciences · 2025Article
- LncRNA HSCHARME is altered in human cardiomyopathies and promotes stem cell-derived cardiomyogenesis via splicing regulation.Nature communications · 2025Article
- MicroRNA-Mediated Regulation of Vascular Endothelium: From Pro-Inflammation to Atherosclerosis.International journal of molecular sciences · 2025Review
- Genome-wide cataloging and orthology analysis of long noncoding RNA expression in three species of Anopheles mosquito.BMC genomics · 2025Article
- Epigenetic Role of Long Non-coding RNAs in Multiple Myeloma.Current oncology reports · 2025Review
- Computational Resources for lncRNA Functions and Targetome.Methods in molecular biology (Clifton, N.J.) · 2025Review
- Characterization of full-length long noncoding RNAs and identification of virus-responsive lncRNAs inFrontiers in microbiology · 2025Article
- Downregulated TRAF3IP2-AS1 promotes hepatocellular carcinoma progression through the miR-374a-5p/SEL1L1/RPL6 axis to enhance DNA damage repair.American journal of translational research · 2025Article
- Quest for Orthologs in the Era of Biodiversity Genomics.Genome biology and evolution · 2024Review
- CANTATAdb 3.0: An Updated Repository of Plant Long Non-Coding RNAs.Plant & cell physiology · 2024Article
- Exploring the Utility of Long Non-Coding RNAs for Assessing the Health Consequences of Vaping.International journal of molecular sciences · 2024Review
- Targeting and engineering long non-coding RNAs for cancer therapy.Nature reviews. Genetics · 2024Review
- Genome-scale pan-cancer interrogation of lncRNA dependencies using CasRx.Nature methods · 2024Article
55 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
backgroundRecent advances in transcriptome sequencing have enabled the discovery of thousands of long non-coding RNAs (lncRNAs) across many species. Though several lncRNAs have been shown to play important roles in diverse biological processes, the functions and mechanisms of most lncRNAs remain unknown. Two significant obstacles lie between transcriptome sequencing and functional characterization of lncRNAs: identifying truly non-coding genes from de novo reconstructed transcriptomes, and prioritizing the hundreds of resulting putative lncRNAs for downstream experimental interrogation.
resultsWe present slncky, a lncRNA discovery tool that produces a high-quality set of lncRNAs from RNA-sequencing data and further uses evolutionary constraint to prioritize lncRNAs that are likely to be functionally important. Our automated filtering pipeline is comparable to manual curation efforts and more sensitive than previously published computational approaches. Furthermore, we developed a sensitive alignment pipeline for aligning lncRNA loci and propose new evolutionary metrics relevant for analyzing sequence and transcript evolution. Our analysis reveals that evolutionary selection acts in several distinct patterns, and uncovers two notable classes of intergenic lncRNAs: one showing strong purifying selection on RNA sequence and another where constraint is restricted to the regulation but not the sequence of the transcript.
conclusionOur results highlight that lncRNAs are not a homogenous class of molecules but rather a mixture of multiple functional classes with distinct biological mechanism and/or roles. Our novel comparative methods for lncRNAs reveals 233 constrained lncRNAs out of tens of thousands of currently annotated transcripts, which we make available through the slncky Evolution Browser.
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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.