ArticlePlant communications2024
Single-cell transcriptome analysis dissects lncRNA-associated gene networks in Arabidopsis.
Article in Plant communications, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 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
18 citing papers in PubMed, 23 citations in OpenAlex.
- Advances in single-cell and spatial multi-omics for plant development and stress responses.Plant diversity · 2026Review
- Echoes in the powerhouse: mito-lncRNAs contribution to cardiac function and disease.Acta pharmacologica Sinica · 2026Review
- Advances in the study of the role of epigenetic mechanisms in plant growth and response to stress.Horticulture research · 2026Article
- Quantitative RNA spatial profiling using single-molecule RNA FISH on plant tissue cryosections.Plant communications · 2026Article
- Uncovering Spatiotemporal and Functional Dynamics of Long Non-coding RNAs During Alzheimer's Progression in the Human Brain at Single-Cell Resolution.Molecular neurobiology · 2026Article
- Exploring the CeRNA landscape in plants: advances, methods, and challenges.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Review
- The Regulatory Potential of Long Non-Coding RNAs in Bipolar Disorder.International journal of molecular sciences · 2026Review
- Decoding plant physiology through systems biology: Integrative multi-omics and computational perspectives for next-generation crop design.Plant communications · 2026Review
- Comprehensive insights into the development of arabidopsis trichomes by single-nucleus RNA-seq.BMC plant biology · 2026Article
- Long Noncoding RNAs as Emerging Regulators of Seed Development, Germination, and Senescence.International journal of molecular sciences · 2025Review
- Cell type heterogeneity in gene co-expression networks: implications for toxicological research.Briefings in bioinformatics · 2025Review
- A large-scale gene co-expression network analysis reveals Glutamate Dehydrogenase 2 (GhGDH2_D03) as a hub regulator of salt and salt-alkali tolerance in cotton.Plant molecular biology · 2025Article
- Single-Cell Transcriptomic Approaches for Decoding Non-Coding RNA Mechanisms in Colorectal Cancer.Non-coding RNA · 2025Review
- Protective effect of silencing lncRNA HCP5 against brain injury after intracerebral hemorrhage by targeting miR-195-5p.BMC neuroscience · 2025Article
- Unveiling Long Non-coding RNA Networks from Single-Cell Omics Data Through Artificial Intelligence.Methods in molecular biology (Clifton, N.J.) · 2025Article
- The miR3367-lncRNA67-GhCYP724B module regulates male sterility by modulating brassinosteroid biosynthesis and interacting with Aorf27 in Gossypium hirsutum.Journal of integrative plant biology · 2025Article
- Uncovering functional lncRNAs by scRNA-seq with ELATUS.Nature communications · 2024Article
- Single-Cell Transcriptomics Applied in Plants.Cells · 2024Review
Corrections and comments
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Authors and funding
17 authors at 5 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The plant genome produces an extremely large collection of long noncoding RNAs (lncRNAs) that are generally expressed in a context-specific manner and have pivotal roles in regulation of diverse biological processes. Here, we mapped the transcriptional heterogeneity of lncRNAs and their associated gene regulatory networks at single-cell resolution. We generated a comprehensive cell atlas at the whole-organism level by integrative analysis of 28 published single-cell RNA sequencing (scRNA-seq) datasets from juvenile Arabidopsis seedlings. We then provided an in-depth analysis of cell-type-related lncRNA signatures that show expression patterns consistent with canonical protein-coding gene markers. We further demonstrated that the cell-type-specific expression of lncRNAs largely explains their tissue specificity. In addition, we predicted gene regulatory networks on the basis of motif enrichment and co-expression analysis of lncRNAs and mRNAs, and we identified putative transcription factors orchestrating cell-type-specific expression of lncRNAs. The analysis results are available at the single-cell-based plant lncRNA atlas database (scPLAD; https://biobigdata.nju.edu.cn/scPLAD/). Overall, this work demonstrates the power of integrative single-cell data analysis applied to plant lncRNA biology and provides fundamental insights into lncRNA expression specificity and associated gene regulation.
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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.