The Importance of Stiff Change of U(T) Content Around Splicing Sites in Efficient Plant Intron Splicing -- A Case Study in Rice DOI Creative Commons
Fangyu Zhang, Zhengfeng Zhang, Enci Wang

et al.

Computational Biology and Bioinformatics, Journal Year: 2023, Volume and Issue: unknown

Published: June 5, 2023

Pre-mRNAs splicing is one of the fundamental process which generates multiple transcripts from a single gene, contributing to transcriptome and proteome diversity. AS regulated by cooperation trans-factors cis-elements. In plants, extensive alternative occurs not only in tissue-specific manner but also response stress conditions. Intron retention most predominant type. However, cis-elements regulating intron are still ambiguous especially under environmental stresses. This study aimed elucidate underlying plants adverse enrironments. Using RNA-seq data rice cultivars IRAT109 ZS97 drought environments, we compared sequence characteristics between constitutive retained introns. The results show that main types include (IR), acceptor sites (AA), donor (AD) cassette exon (exon skipping, ES). Among them, IR was prevelent pattern with frequencies 30.8-31.2%. Motif analysis 5' 3' 200bp sequences found rich U(T) motifs for both By further base composition flanking splice sites, detected notable difference content introns their neighboring exons introns, this suggested lack significant changes might be potential cis feature retention.

Language: Английский

The CONSTANS-LIKE gene PeCOL13 regulates flowering through intron-retained alternative splicing in Phyllostachys edulis DOI

Hongjia Ma,

Jialong Pei,

Juan Zhuo

et al.

International Journal of Biological Macromolecules, Journal Year: 2024, Volume and Issue: 274, P. 133393 - 133393

Published: June 24, 2024

Language: Английский

Citations

5
Alternative splicing in a coral during heat stress acclimation and recovery DOI
Nitin S. Baliga, Kathryn H. Stankiewicz, Jacob J. Valenzuela

et al.

Research Square (Research Square), Journal Year: 2025, Volume and Issue: unknown

Published: April 2, 2025

Climate change has caused drastic declines in corals. As sessile organisms, corals acclimate to environmental shifts through genome-wide changes gene expression, epigenetic modifications, and alterations microbiome composition. However, alternative splicing (AS), a conserved mechanism of stress response many been under-explored Using short-term acute thermal assays, we investigated patterns AS the scleractinian coral Acropora cervicornis during low (33°C), medium (35°C), high (37°C) heat subsequent overnight recovery. Our findings demonstrate reproducible dynamic at least 40 percent all genes treatment recovery phase. The relative proportion increased was primarily dominated by intron retention specific classes transcripts, including those related regulation itself. While returned baseline levels post-exposure heat, persisted even after reprieve from higher stress, which associated with irreversible loss photosynthetic efficiency symbiont. that, although animals, are more plant-like their likely usage for regulating

Language: Английский

Citations

0
RNA-Binding Protein-Mediated Alternative Splicing Regulates Abiotic Stress Responses in Plants DOI Open Access
Ying Guo, Xudong Shang, Ligeng Ma

et al.

International Journal of Molecular Sciences, Journal Year: 2024, Volume and Issue: 25(19), P. 10548 - 10548

Published: Sept. 30, 2024

The alternative splicing of pre-mRNA generates distinct mRNA variants from a pre-mRNA, thereby modulating gene’s function. depends on splice sites and regulatory elements in as well the snRNA proteins that recognize these sequences. Among these, RNA-binding (RBPs) are primary regulators play critical role regulation by recognizing pre-mRNA. However, little is known about function RBPs stress response plants. Here, we summarized involved their recent advance RBP-mediated to abiotic stresses This review proposes an important way for plants adapt stresses, promising direction crop breeding.

Language: Английский

Citations

3
Meta-analysis of Arabidopsis thaliana microarray data in relation to heat stress response DOI Creative Commons
Zohra Chaddad, Kaoutar Kaddouri, Abdelaziz Smouni

et al.

Frontiers in Plant Science, Journal Year: 2023, Volume and Issue: 14

Published: Dec. 19, 2023

Introduction Increasing global warming has made heat stress a serious threat to crop productivity and food security in recent years. One of the most promising solutions address this issue is developing heat-stress-tolerant plants. Hence, thorough understanding response mechanisms, particularly molecular ones, crucial. Methods Although numerous studies have used microarray expression profiling technology explore area, these experiments often face limitations, leading inconsistent results. To overcome random effects meta-analysis was employed using advanced statistical methods. A 16 datasets related Arabidopsis thaliana conducted. Results The analysis revealed 1,972 significant differentially expressed genes between control heat-stressed plants (826 over-expressed 1,146 down-expressed), including 128 transcription factors from different families. significantly enriched biological processes, functions, KEGG pathways for included response, mRNA splicing via spliceosome pathways, unfolded protein binding, shock binding. Conversely, down-expressed genes, categories cell wall organization or biogenesis, phosphorylation, transmembrane transporter activity, ion transporter, biosynthesis secondary metabolites, metabolic pathways. Discussion Through our comprehensive transcriptomics, we identified pivotal integral offering profound insights into mechanisms by which counteract such stressors. Our findings elucidate that influences gene both at transcriptional phase post-transcriptionally, thereby substantially augmenting comprehension plant adaptive strategies stress.

Language: Английский

Citations

2
Monitoring transcription by nascent RNA sequencing in crop plants DOI Creative Commons
Mingliang Zhu, Min Liu, Zhicheng Dong

et al.

New Crops, Journal Year: 2024, Volume and Issue: 2, P. 100031 - 100031

Published: July 10, 2024

Plants can quickly adapt to changing environments and external stimuli by undergoing a series of transcriptional responses. The process maturing nascent RNA (direct product transcription) into mRNA, which is crucial for the plant's response factors, involves co-transcriptional post-transcriptional processing. Although RNA-seq has greatly facilitated study plant transcriptomes providing snapshots stable molecules, detecting dynamic changes unstable transcripts remains challenging. In recent years, various sequencing methods have been developed identify in eukaryotes, shedding light on dynamics processing uncovering transcripts. At same time, analysis provided valuable insights regulation crops, highlighting differences their features compared model plants potentially influencing breeding strategies. This review aims explore applications different technologies plants, focusing significant findings achieved crops.

Language: Английский

Citations

0
Bioinformatic Analysis of Alternative Splicing DOI
Kshitish K. Acharya,

Raghupathi Medini,

Tanvi Thakur

et al.

Elsevier eBooks, Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 1, 2024

Language: Английский

Citations

0
The Importance of Stiff Change of U(T) Content Around Splicing Sites in Efficient Plant Intron Splicing -- A Case Study in Rice DOI Creative Commons
Fangyu Zhang, Zhengfeng Zhang, Enci Wang

et al.

Computational Biology and Bioinformatics, Journal Year: 2023, Volume and Issue: unknown

Published: June 5, 2023

Pre-mRNAs splicing is one of the fundamental process which generates multiple transcripts from a single gene, contributing to transcriptome and proteome diversity. AS regulated by cooperation trans-factors cis-elements. In plants, extensive alternative occurs not only in tissue-specific manner but also response stress conditions. Intron retention most predominant type. However, cis-elements regulating intron are still ambiguous especially under environmental stresses. This study aimed elucidate underlying plants adverse enrironments. Using RNA-seq data rice cultivars IRAT109 ZS97 drought environments, we compared sequence characteristics between constitutive retained introns. The results show that main types include (IR), acceptor sites (AA), donor (AD) cassette exon (exon skipping, ES). Among them, IR was prevelent pattern with frequencies 30.8-31.2%. Motif analysis 5' 3' 200bp sequences found rich U(T) motifs for both By further base composition flanking splice sites, detected notable difference content introns their neighboring exons introns, this suggested lack significant changes might be potential cis feature retention.

Language: Английский

Citations

0