ArticleMolecular biology and evolution2020
Comparative Transcriptomics Analyses across Species, Organs, and Developmental Stages Reveal Functionally Constrained lncRNAs.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- Correlation of Long Non-Coding RNAs and Gene Expression in Response to Reverse Development of Turritopsis dohrnii.Marine biotechnology (New York, N.Y.) · 2026Article
- Inter-individual gene expression variability implies stable regulation of brain-biased genes across organs in three ray-finned fishes.bioRxiv : the preprint server for biology · 2026Article
- The landscape and evolutionary dynamics of derived lncRNAs in insects.Communications biology · 2025Article
- TheBiomolecules · 2025Review
- Comprehensive analysis of long non-coding RNA and mRNA expression patterns during seminiferous tubules maturation in Guanzhong dairy goats.BMC genomics · 2025Article
- Long non-coding RNAs in cardiac hypertrophy and heart failure: functions, mechanisms and clinical prospects.Nature reviews. Cardiology · 2024Review
- Uncovering a multitude of stage-specific splice variants and putative protein isoforms generated along mouse spermatogenesis.BMC genomics · 2024Article
- The Complex Landscape of Structural Divergence Between the Drosophila pseudoobscura and D. persimilis Genomes.Genome biology and evolution · 2024Article
- Long non-coding RNAs mediate fish gene expression in response to ocean acidification.Evolutionary applications · 2024Article
- Deep Conservation and Unexpected Evolutionary History of Neighboring lncRNAs MALAT1 and NEAT1.Journal of molecular evolution · 2024Article
- The Conserved LncRNA DIO3OS Restricts Hepatocellular Carcinoma Stemness by Interfering with NONO-Mediated Nuclear Export of ZEB1 mRNA.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2023Article
- GepLiver: an integrative liver expression atlas spanning developmental stages and liver disease phases.Scientific data · 2023Article
- Multidimensional conservation analysis decodes the expression of conserved long noncoding RNAs.Life science alliance · 2023Article
- Diapause-Linked Gene Expression Pattern and Related Candidate Duplicated Genes of the Mountain ButterflyInternational journal of molecular sciences · 2023Article
- Evolution and function of developmentally dynamic pseudogenes in mammals.Genome biology · 2022Article
- The Transcriptional RegulatorBiomedicines · 2022Article
- Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana.Scientific reports · 2022Article
- LncRNAs in domesticated animals: from dog to livestock species.Mammalian genome : official journal of the International Mammalian Genome Society · 2022Review
- Evolution of Gene Expression across Species and Specialized Zooids in Siphonophora.Molecular biology and evolution · 2022Article
- Cross-Species Analysis Reveals Co-Expressed Genes Regulating Antler Development in Cervidae.Frontiers in genetics · 2022Article
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2 authors.
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No grant is acknowledged in the PubMed record.
Abstract
The functionality of long noncoding RNAs (lncRNAs) is disputed. In general, lncRNAs are under weak selective pressures, suggesting that the majority of lncRNAs may be nonfunctional. However, although some surveys showed negligible phenotypic effects upon lncRNA perturbation, key biological roles were demonstrated for individual lncRNAs. Most lncRNAs with proven functions were implicated in gene expression regulation, in pathways related to cellular pluripotency, differentiation, and organ morphogenesis, suggesting that functional lncRNAs may be more abundant in embryonic development, rather than in adult organs. To test this hypothesis, we perform a multidimensional comparative transcriptomics analysis, across five developmental time points (two embryonic stages, newborn, adult, and aged individuals), four organs (brain, kidney, liver, and testes), and three species (mouse, rat, and chicken). We find that, overwhelmingly, lncRNAs are preferentially expressed in adult and aged testes, consistent with the presence of permissive transcription during spermatogenesis. LncRNAs are often differentially expressed among developmental stages and are less abundant in embryos and newborns compared with adult individuals, in agreement with a requirement for tighter expression control and less tolerance for noisy transcription early in development. For differentially expressed lncRNAs, we find that the patterns of expression variation among developmental stages are generally conserved between mouse and rat. Moreover, lncRNAs expressed above noise levels in somatic organs and during development show higher evolutionary conservation, in particular, at their promoter regions. Thus, we show that functionally constrained lncRNA loci are enriched in developing organs, and we suggest that many of these loci may function in an RNA-independent manner.
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