ArticleThe Plant cell2022
Identification and functional annotation of long intergenic non-coding RNAs in Brassicaceae.
Article in The Plant cell, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed, 47 citations in OpenAlex.
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- Long non-coding RNAs link DNA methylation to immune regulatory networks in bovine subclinical mastitis.Mammalian genome : official journal of the International Mammalian Genome Society · 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
- Bridging development and disease: the potential of LncRNAs as biomarkers and therapeutics in pediatric neurological disorders.Pediatric research · 2026Review
- Haplotype-resolved telomere-to-telomere assembly and haplotype-aware annotation pipeline enable high-quality reannotation of threeHorticulture research · 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
- The 'non-conventional' peptidome: A new layer in plant regulatory mechanisms.Plant communications · 2025Review
- Translational Regulation of Plant Stress Responses: Mechanisms, Pathways, and Applications in Bioengineering.Annual review of phytopathology · 2025Review
- Review
- Exploring genetic diversity, population structure, and subgenome differences in the allopolyploidHorticulture research · 2024Article
- Long Noncoding RNAs in Response to Hyperosmolarity Stress, but Not Salt Stress, Were Mainly Enriched in the Rice Roots.International journal of molecular sciences · 2024Article
- What, where, and how: Regulation of translation and the translational landscape in plants.The Plant cell · 2024Review
- Genome-wide transcriptome analysis reveals the diversity and function of long non-coding RNAs in dinoflagellates.NAR genomics and bioinformatics · 2024Article
- Population-level annotation of lncRNAs in Arabidopsis reveals extensive expression variation associated with transposable element-like silencing.The Plant cell · 2023Article
- Analysis of lncRNAs inNon-coding RNA · 2023Article
- LncRNA FLAIL affects alternative splicing and represses flowering in Arabidopsis.The EMBO journal · 2023Article
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Authors and funding
13 authors at 5 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Long intergenic noncoding RNAs (lincRNAs) are a large yet enigmatic class of eukaryotic transcripts that can have critical biological functions. The wealth of RNA-sequencing (RNA-seq) data available for plants provides the opportunity to implement a harmonized identification and annotation effort for lincRNAs that enables cross-species functional and genomic comparisons as well as prioritization of functional candidates. In this study, we processed >24 Tera base pairs of RNA-seq data from >16,000 experiments to identify ∼130,000 lincRNAs in four Brassicaceae: Arabidopsis thaliana, Camelina sativa, Brassica rapa, and Eutrema salsugineum. We used nanopore RNA-seq, transcriptome-wide structural information, peptide data, and epigenomic data to characterize these lincRNAs and identify conserved motifs. We then used comparative genomic and transcriptomic approaches to highlight lincRNAs in our data set with sequence or transcriptional conservation. Finally, we used guilt-by-association analyses to assign putative functions to lincRNAs within our data set. We tested this approach on a subset of lincRNAs associated with germination and seed development, observing germination defects for Arabidopsis lines harboring T-DNA insertions at these loci. LincRNAs with Brassicaceae-conserved putative miRNA binding motifs, small open reading frames, or abiotic-stress modulated expression are a few of the annotations that will guide functional analyses into this cryptic portion of the transcriptome.
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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 OpenQuestion graph.