ArticleBMC plant biology2015
Positionally-conserved but sequence-diverged: identification of long non-coding RNAs in the Brassicaceae and Cleomaceae.
Article in BMC plant biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 75 citations in OpenAlex.
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- Linking discoveries, mechanisms, and technologies to develop a clearer perspective on plant long noncoding RNAs.The Plant cell · 2023Review
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- Plant long non-coding RNAs: identification and analysis to unveil their physiological functions.Frontiers in plant science · 2023Review
- Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae.The Plant cell · 2022Article
- The Conservation of Long Intergenic Non-Coding RNAs and Their Response toInternational journal of molecular sciences · 2022Article
- Revealing the novel complexity of plant long non-coding RNA by strand-specific and whole transcriptome sequencing for evolutionarily representative plant species.BMC genomics · 2022Article
- Long Noncoding RNAs Hepatocyte Nuclear Factor 4A Antisense RNA 1 and Hepatocyte Nuclear Factor 1A Antisense RNA 1 Are Involved in Ritonavir-Induced Cytotoxicity in Hepatoma Cells.Drug metabolism and disposition: the biological fate of chemicals · 2022Article
- The evolutionary landscape and expression pattern of plant lincRNAs.RNA biology · 2022Article
- Comparative analysis of long noncoding RNAs in angiosperms and characterization of long noncoding RNAs in response to heat stress in Chinese cabbage.Horticulture research · 2021Article
- De Novo Profiling of Long Non-Coding RNAs Involved in MC-LR-Induced Liver Injury in Whitefish: Discovery and Perspectives.International journal of molecular sciences · 2021Article
- Long non-coding RNAs: emerging players regulating plant abiotic stress response and adaptation.BMC plant biology · 2020Review
- Landscape of the Noncoding Transcriptome Response of Two Arabidopsis Ecotypes to Phosphate Starvation.Plant physiology · 2020Article
- Splicing conservation signals in plant long noncoding RNAs.RNA (New York, N.Y.) · 2020Article
- Long noncoding RNA LINC00844-mediated molecular network regulates expression of drug metabolizing enzymes and nuclear receptors in human liver cells.Archives of toxicology · 2020Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundLong non-coding RNAs (LncRNAs) have been identified as gene regulatory elements that influence the transcription of their neighbouring protein-coding genes. The discovery of LncRNAs in animals has stimulated genome-wide scans for these elements across plant genomes. Recently, 6480 LincRNAs were putatively identified in Arabidopsis thaliana (Brassicaceae), however there is limited information on their conservation.
resultsUsing a phylogenomics approach, we assessed the positional and sequence conservation of these LncRNAs by analyzing the genomes of the basal Brassicaceae species Aethionema arabicum and Tarenaya hassleriana of the sister-family Cleomaceae. Furthermore, we generated transcriptomes for another three Aethionema species and one other Cleomaceae species to validate their transcriptional activity. We show that a subset of LncRNAs are highly diverged at the nucleotide level, but conserved by position (syntenic). Positionally conserved LncRNAs that are expressed neighbour important developmental and physiological genes. Interestingly, >65 % of the positionally conserved LncRNAs are located within 2.5 Mb of telomeres in Arabidopsis thaliana chromosomes.
conclusionThese results highlight the importance of analysing not only sequence conservation, but also positional conservation of non-coding genetic elements in plants including LncRNAs.
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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.