ArticleThe Plant cell2023
Population-level annotation of lncRNAs in Arabidopsis reveals extensive expression variation associated with transposable element-like silencing.
Article in The Plant cell, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
19 citing papers in PubMed, 30 citations in OpenAlex.
- DNA methylation either antagonizes or promotes Polycomb recruitment at transposable elements in Arabidopsis.Nature communications · 2026Article
- The Landscape of Long Non-Coding RNAs Provides Insights Into the Domestication and Improvement of Pear Fruit.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Long non-coding RNA landscape and ceRNA networks underlying the drought response of Cannabis sativa L.BMC plant biology · 2026Article
- Integrated Symbiotic Pleiotropy: Long Non-Coding RNAs and Disordered Proteins Interweaving the Functional Layers of the Eukaryotic Cell.International journal of molecular sciences · 2026Review
- Genome-wide reprogramming of sRNA and lncRNA in the epigenetic regulation following interspecific hybridization in the Brassica species.Molecular horticulture · 2026Article
- Integrative multi-omics analysis widens annotation and functional insights into long non-coding RNAs of Arabidopsis thaliana.Biology direct · 2026Article
- Diversity of lncRNAs in the pan-transcriptome of maize inbred lines.BMC genomics · 2026Article
- Major alleles of CDCA7 shape CG methylation in Arabidopsis thaliana.Nature plants · 2025Article
- Transcriptome-Wide Association Uncovers LncRNAs Controlling Seed Weight in Soybean.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- Regulatory Landscapes of Non-Coding RNAs During Drought Stress in Plants.International journal of molecular sciences · 2025Review
- A comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism.Nature genetics · 2025Article
- Understanding the Regulation Activities of Transposons in Driving the Variation and Evolution of Polyploid Plant Genome.Plants (Basel, Switzerland) · 2025Review
- Alternative silencing states of transposable elements in Arabidopsis associated with H3K27me3.Genome biology · 2025Article
- Comprehensive genome annotation of the model ciliate Tetrahymena thermophila by in-depth epigenetic and transcriptomic profiling.Nucleic acids research · 2025Article
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- The long noncoding RNA family gets bigger: thousands of new loci identified in natural Arabidopsis accessions.The Plant cell · 2023Article
- Meeting report: transposable elements at the crossroads of evolution, health and disease 2023.Mobile DNA · 2023Article
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Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Long noncoding RNAs (lncRNAs) are understudied and underannotated in plants. In mammals, lncRNA loci are nearly as ubiquitous as protein-coding genes, and their expression is highly variable between individuals of the same species. Using Arabidopsis thaliana as a model, we aimed to elucidate the true scope of lncRNA transcription across plants from different regions and study its natural variation. We used transcriptome deep sequencing data sets spanning hundreds of natural accessions and several developmental stages to create a population-wide annotation of lncRNAs, revealing thousands of previously unannotated lncRNA loci. While lncRNA transcription is ubiquitous in the genome, most loci appear to be actively silenced and their expression is extremely variable between natural accessions. This high expression variability is largely caused by the high variability of repressive chromatin levels at lncRNA loci. High variability was particularly common for intergenic lncRNAs (lincRNAs), where pieces of transposable elements (TEs) present in 50% of these lincRNA loci are associated with increased silencing and variation, and such lncRNAs tend to be targeted by the TE silencing machinery. We created a population-wide lncRNA annotation in Arabidopsis and improve our understanding of plant lncRNA genome biology, raising fundamental questions about what causes transcription and silencing across the genome.
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Registered trials
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 Socratic graph.