ArticlePlant physiology2021
Full-length annotation with multistrategy RNA-seq uncovers transcriptional regulation of lncRNAs in cotton.
Article in Plant physiology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 35 citations in OpenAlex.
- The Landscape of Long Non-Coding RNAs Provides Insights Into the Domestication and Improvement of Pear Fruit.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Integrative multi-omics analysis widens annotation and functional insights into long non-coding RNAs of Arabidopsis thaliana.Biology direct · 2026Article
- Global atlas of enhancer-promoter interactome in cotton genome revealed by profiling RNA-RNA spatial interactions.Genome biology · 2026Article
- A comprehensive landscape of theFrontiers in plant science · 2026Article
- Transcriptome-Wide Association Uncovers LncRNAs Controlling Seed Weight in Soybean.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- pseudo-GhFAD2-1 Is a lncRNA Involved in Regulating Cottonseed Oleic and Linoleic Acid Ratios and Seed Size in Gossypium hirsutum.Plant biotechnology journal · 2025Article
- Genome level identification of transcription start sites by nanoCAGE sequence in soybean.Scientific data · 2025Article
- InfoScan: A New Transcript Identification Tool Based on scRNA-Seq and Its Application in Glioblastoma.International journal of molecular sciences · 2025Article
- Integrative Multi-Omics Approaches for Identifying and Characterizing Biological Elements in Crop Traits: Current Progress and Future Prospects.International journal of molecular sciences · 2025Review
- GhATL68b regulates cotton fiber cell development by ubiquitinating the enzyme required for β-oxidation of polyunsaturated fatty acids.Plant communications · 2024Article
- Comparative Transcriptomic Analysis ofPlants (Basel, Switzerland) · 2024Article
- An analysis of lncRNAs related to fiber quality and the discovery of their target genes in a Gossypium hirsutum line with Gossypium mustelinum introgression.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Review
- An urgent call on revisions to current genome annotation strategies.Science China. Life sciences · 2023Article
- Assembly and annotation of the Gossypium barbadense L. 'Pima-S6' genome raise questions about the chromosome structure and gene content of Gossypium barbadense genomes.BMC genomics · 2023Article
- Epigenetic modifications: Allusive clues of lncRNA functions in plants.Computational and structural biotechnology journal · 2023Review
- Long non-coding RNA and microRNA landscape of two major domesticated cotton species.Computational and structural biotechnology journal · 2023Article
- Plant long non-coding RNAs: identification and analysis to unveil their physiological functions.Frontiers in plant science · 2023Review
- The Conservation of Long Intergenic Non-Coding RNAs and Their Response toInternational journal of molecular sciences · 2022Article
- lncRNA7 and lncRNA2 modulate cell wall defense genes to regulate cotton resistance to Verticillium wilt.Plant physiology · 2022Article
Corrections and comments
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Authors and funding
9 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Long noncoding RNAs (lncRNAs) are crucial factors during plant development and environmental responses. To build an accurate atlas of lncRNAs in the diploid cotton Gossypium arboreum, we combined Isoform-sequencing, strand-specific RNA-seq (ssRNA-seq), and cap analysis gene expression (CAGE-seq) with PolyA-seq and compiled a pipeline named plant full-length lncRNA to integrate multi-strategy RNA-seq data. In total, 9,240 lncRNAs from 21 tissue samples were identified. 4,405 and 4,805 lncRNA transcripts were supported by CAGE-seq and PolyA-seq, respectively, among which 6.7% and 7.2% had multiple transcription start sites (TSSs) and transcription termination sites (TTSs). We revealed that alternative usage of TSS and TTS of lncRNAs occurs pervasively during plant growth. Besides, we uncovered that many lncRNAs act in cis to regulate adjacent protein-coding genes (PCGs). It was especially interesting to observe 64 cases wherein the lncRNAs were involved in the TSS alternative usage of PCGs. We identified lncRNAs that are coexpressed with ovule- and fiber development-associated PCGs, or linked to GWAS single-nucleotide polymorphisms. We mapped the genome-wide binding sites of two lncRNAs with chromatin isolation by RNA purification sequencing. We also validated the transcriptional regulatory role of lnc-Ga13g0352 via virus-induced gene suppression assay, indicating that this lncRNA might act as a dual-functional regulator that either activates or inhibits the transcription of target genes.
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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.