Localization is the key to action: regulatory peculiarities of lncRNAs DOI Creative Commons
Joice de Faria Poloni, Fábio Soares de Oliveira, Bruno César Feltes

et al.

Frontiers in Genetics, Journal Year: 2024, Volume and Issue: 15

Published: Dec. 16, 2024

To understand the transcriptomic profile of an individual cell in a multicellular organism, we must comprehend its surrounding environment and cellular space where distinct molecular stimuli responses are located. Contradicting initial perception that RNAs were nonfunctional only few could act chromatin remodeling, over last decades, research has revealed they multifaceted, versatile regulators most processes. Among various RNAs, long non-coding (LncRNAs) regulate multiple biological processes can even impact fate. In this sense, subcellular localization lncRNAs is primary determinant their functions. It affects behavior by limiting potential partner which process it affect. The fine-tuned activity also tissue-specific modulated

Language: Английский

Artificial miRNAs and target-mimics as potential tools for crop improvement DOI
Tilahun Rabuma, Neeti Sanan‐Mishra

Physiology and Molecular Biology of Plants, Journal Year: 2025, Volume and Issue: 31(1), P. 67 - 91

Published: Jan. 1, 2025

Language: Английский

Citations

3
Long Noncoding RNA–Messenger RNA (lncRNA–mRNA) Network in Resistance to Gummy Stem Blight (Stagonosporopsis cucurbitacearum) of Melon Plant Introduction (PI) 420145 DOI Creative Commons
Rui Zhang, Jing Chen, Yongbing Zhang

et al.

Horticulturae, Journal Year: 2025, Volume and Issue: 11(1), P. 31 - 31

Published: Jan. 2, 2025

Gummy stem blight (GSB), caused by Stagonosporopsis cucurbitacearum (Didymella bryoniae), poses a growing threat to greenhouse melon production. Despite this, the defense mechanism of against S. remains poorly understood. In this study, employing electron microscopy and transcriptome sequencing, we investigated cellular ultrastructure differences gene expression dynamics two accessions, PI 420145 (resistant GSB) ‘Baipicui’ (susceptible), pre- post- inoculation. Our results revealed that exhibits thicker waxy layer on leaf surface limited conidial germination without obvious signs cell damage compared ‘Baipicui’. The transcriptomic analysis identified total 23,078 differentially expressed genes (DEGs) 974 long noncoding RNAs (DELs). Specifically, phenylpropanoid biosynthesis, cyanoamino acid metabolism, MAPK signaling–plant plant–pathogen interactions were enriched in 420145, while displayed enrichment metabolism autophagy. Additionally, through lncRNA–mRNA network construction, 38 targeted regulatory relationships four most significant KEGG pathways for disease resistance.

Language: Английский

Citations

1
Transcriptional junk: Waste or a key regulator in diverse biological processes? DOI

Anwesha Anyatama,

Tapasya Datta,

Shambhavi Dwivedi

et al.

Current Opinion in Plant Biology, Journal Year: 2024, Volume and Issue: 82, P. 102639 - 102639

Published: Sept. 26, 2024

Language: Английский

Citations

3
LTR retrotransposon-derived novel lncRNA2 enhances cold tolerance in Moso bamboo by modulating antioxidant activity and photosynthetic efficiency DOI Creative Commons
Jiamin Zhao, Yiqian Ding, Muthusamy Ramakrishnan

et al.

PeerJ, Journal Year: 2025, Volume and Issue: 13, P. e19056 - e19056

Published: Feb. 26, 2025

In Moso bamboo, the mechanism of long terminal repeat (LTR) retrotransposon-derived non-coding RNA (TElncRNA) in response to cold stress remains unclear. this study, several Pe-TElncRNAs were identified from bamboo transcriptome data. qRT-PCR analysis showed that expression a novel Pe-TElncRNA2 seedlings reached its highest level at 8 hours treatment 4 °C and was significantly higher stems compared leaves, roots, buds. Furthermore, cellular localization revealed cytoplasm than nucleus. overexpression protoplasts positively regulated FZR2 , NOT3 ABCG44 AGD6 genes. Further validation lncRNA Arabidopsis thaliana enhanced antioxidant activities, as evidenced by increased superoxide dismutase (SOD) activity proline content, well maximum photochemical efficiency PS II dark-adapted leaves ( F v / m ), transgenic plants wild-type controls. Conversely, malondialdehyde (MDA) lipid peroxidation marker (a oxidative stress), reduced plants. Notably, levels both genes upregulated after two days treatment. These findings elucidate critical role LTR lncRNAs mediating responses bamboo.

Language: Английский

Citations

0
A translocation between chromosome 6 and 8 influences lncRNA_MYB114 and PpRPP13 expression and underpins red leaf trait and powdery mildew resistance in peach DOI Open Access
Shihang Sun, Junren Meng, Wenjun Zhang

et al.

New Phytologist, Journal Year: 2025, Volume and Issue: unknown

Published: March 4, 2025

Summary Red leaf peach has important ornamental value owing to its characteristic coloration. However, this species is highly susceptible powdery mildew, and the mechanisms of red formation, resistance their relationship remain unclear. We performed population genetic analyses peach, revealing that translocation chromosomes 6 8 genetically linked both trait mildew resistance. Bulk segregant analysis‐sequencing, genome resequencing, expression analysis indicated PpMYB114 gene PpRPP13 are responsible for phenotype resistance, respectively. The chromosomal causes a promoter fragment on chromosome integrate into antisense chain 6, thereby enhancing inhibiting . Further, lncRNA‐seq identified new lncRNA, lncRNA_MYB114 , which generated by can activate synthesize anthocyanin. Moreover, overexpression resulted in enhanced mildew. In summary, these results revealed molecular mechanism altering form susceptibility.

Language: Английский

Citations

0
Multidimensional analysis of long noncoding RNAs function in Solanaceae plants DOI
Wenjing Yang, Quanzi Bai, Xuan Zhang

et al.

New Phytologist, Journal Year: 2025, Volume and Issue: unknown

Published: June 1, 2025

Summary Long noncoding RNAs (lncRNAs) have been gradually verified as functional regulators in plants, yet their functions remain underexplored, especially the Solanaceae family. While substantial progress has made identifying lncRNAs different species, systematic annotations are lacking. In this study, we uniformly identified and systematically characterized from seven Solanaceous species using large‐scale strand‐specific RNA‐seq (ssRNA‐seq). About 113 700 lncRNA genes were obtained analyzed for sequence, conservation, expression profile, epigenetic signals, genetic mutants. tomato, 97.4% of annotated with basic characteristics. Also, 25.7% further predicted to be involved stress response, development, metabolism. Comparisons between protein‐coding (PCGs) highlighted unique characteristics tissue expression, responses, sequence composition, signal distribution. We shared our datasets on at http://solanaceae‐lncrna‐source.liu‐lab.com/ . Taking fruit development ripening an example, mined data resources a total 1158 associated process, presenting how curated can utilized discover plant lncRNAs. Overall, study provides comprehensive multidimensional framework research, which serves valuable reference understanding other plants.

Language: Английский

Citations

0
Comparative RNA-seq analysis of tomato (Solanum lycopersicum L.) provides insights into natural and postharvest ripening DOI
Xiuming Zhao, Fujun Li,

Jun Ding

et al.

Postharvest Biology and Technology, Journal Year: 2024, Volume and Issue: 216, P. 113079 - 113079

Published: July 1, 2024

Language: Английский

Citations

2
Metabolomic and Transcriptomic Analysis Revealed the Maturation Mechanism of White-Fleshed Strawberry DOI Creative Commons

Lin-Lin Xu,

Xiaohong Chen, Qinglian Wang

et al.

Agronomy, Journal Year: 2024, Volume and Issue: 14(12), P. 2860 - 2860

Published: Nov. 30, 2024

Strawberry (Fragaria ananassa) is a widely grown horticultural crop, which exists in red, yellow, and white varieties. In recent years, the white-fleshed strawberry variety gaining more attention from consumers for its unique taste appearance, but comprehensive understanding of molecular processes governing ripening remains undisclosed. this study, based on joint analysis physiology, metabolome, transcriptome, we screened identified key metabolites that were highly correlated to maturation (cv. ‘snow white’, SW short) fruits. contrast red-fleshed strawberries, fruits exhibited three main stages during maturation, accompanied by increases total soluble solid sugar declines anthocyanin acid. Metabolomic 832 differential accumulated (DAMs) at secondary level LC-MS/MS, further investigations suggested increase sucrose, citric acid, epicatechin levels potentially play role process Furthermore, abscisic acid methyl jasmonate recognized as primary phytohormones involved production these metabolites. The enrichment RNA-Seq data revealed expressed genes (DEGs) primarily attributed pathways ‘Starch sucrose metabolism’ ‘Plant hormone signal transduction’ undetected ‘Flavonoid biosynthesis’ late stage. Moreover, de novo biosynthesis pathway, WGCNA, Pearson correlation indicated direct relationship between FaSPS1, FaSPP1, FaSPP2 with FaPEPC1, FaV-PPase2, FaV-PPase3 Fa4CL2, Fa4CL3, FaANR1 anthocyanin. Further co-expression MYBs, bHLHs, NACs, WRKYs structural mentioned. Overall, our findings uncovered mechanism regulating strawberry, providing valuable insights enhancing flavor through gene-editing technique.

Language: Английский

Citations

2
Long non-coding RNAs: a promising tool to improve horticultural quality traits DOI Creative Commons
Ahmed Alabd, Junbei Ni, Xuxu Wang

et al.

Current Plant Biology, Journal Year: 2024, Volume and Issue: 40, P. 100413 - 100413

Published: Nov. 6, 2024

Language: Английский

Citations

0
Localization is the key to action: regulatory peculiarities of lncRNAs DOI Creative Commons
Joice de Faria Poloni, Fábio Soares de Oliveira, Bruno César Feltes

et al.

Frontiers in Genetics, Journal Year: 2024, Volume and Issue: 15

Published: Dec. 16, 2024

To understand the transcriptomic profile of an individual cell in a multicellular organism, we must comprehend its surrounding environment and cellular space where distinct molecular stimuli responses are located. Contradicting initial perception that RNAs were nonfunctional only few could act chromatin remodeling, over last decades, research has revealed they multifaceted, versatile regulators most processes. Among various RNAs, long non-coding (LncRNAs) regulate multiple biological processes can even impact fate. In this sense, subcellular localization lncRNAs is primary determinant their functions. It affects behavior by limiting potential partner which process it affect. The fine-tuned activity also tissue-specific modulated

Language: Английский

Citations

0