scholarly journals Genome-wide mapping of alternative splicing in the elite wheat cultivar Xiaoyan 6

2020 ◽  
Author(s):  
Hude Mao ◽  
Jin Zhang ◽  
Lijian Guo ◽  
Qing Chi ◽  
Fangming Mei ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Seed Development ◽  
Developmental Stages ◽  
Wheat Cultivar ◽  
Intron Retention ◽  
Draft Genome ◽  
Gc Content ◽  
Grain Filling ◽  
Transcriptional Level ◽  
Regulation Mechanism

Abstract Background: Triticum aestivum, or common wheat, is a globally important cereal crop. Alternative splicing (AS) is an important post-transcriptional regulation mechanism in higher eukaryotes, but the knowledge of AS in wheat is limited at present. Results: In this study, we performed AS mapping from the elite, high-yielding wheat cultivar Xiaoyan 6. We identified 18,960 and 25,133 novel protein-coding genes and transcript models that were not annotated in the draft genome of wheat cultivar Chinese Spring. We also found that 18,868 genes were alternatively spliced, and classified four major AS types, including alternative acceptor sites (AA), intron retention (IR), alternative donor sites (AD), and exon skipping (ES). Further analysis determined that differences in the AS frequency and AS types displayed a positive correlation with exon number and intron length and were negatively correlated with the GC content, but were not correlated with gene transcriptional level. Furthermore, we identified 2,737 seed-specific AS genes in wheat cultivar Xiaoyan 6, and demonstrated that the number of AS genes in the grain decreased with seed development, suggesting that the earlier developmental stages are more important and complex than are the later stages. In addition, the grain-specific AS genes that were ubiquitously significantly up-regulated during seed development were associated with metabolism-related pathways, indicating that AS of metabolism-related genes is crucial for grain filling in wheat. Conclusions: Through transcriptome analysis, over ten thousand AS genes were identified and characterized in wheat cultivar Xiaoyan 6. Our study provides a comprehensive view of AS in the wheat cultivar Xiaoyan 6 and provides new insights into the complexity of AS in wheat. The data generated in this study provides a foundation for further studies of seed development in wheat.

scholarly journals Alternative Splicing in the Obligate Biotrophic Oomycete Pathogen Pseudoperonospora cubensis

2015 ◽  
Vol 28 (3) ◽  
pp. 298-309 ◽  
Author(s):  
Alyssa Burkhardt ◽  
Alex Buchanan ◽  
Jason S. Cumbie ◽  
Elizabeth A. Savory ◽  
Jeff H. Chang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Intron Retention ◽  
Draft Genome ◽  
Pseudoperonospora Cubensis ◽  
Rna Seq ◽  
Transcriptome Regulation ◽  
Oomycete Pathogen ◽  
Alternatively Spliced ◽  
Genome Annotations ◽  
Obligate Pathogen

Pseudoperonospora cubensis is an obligate pathogen and causative agent of cucurbit downy mildew. To help advance our understanding of the pathogenicity of P. cubensis, we used RNA-Seq to improve the quality of its reference genome sequence. We also characterized the RNA-Seq dataset to inventory transcript isoforms and infer alternative splicing during different stages of its development. Almost half of the original gene annotations were improved and nearly 4,000 previously unannotated genes were identified. We also demonstrated that approximately 24% of the expressed genome and nearly 55% of the intron-containing genes from P. cubensis had evidence for alternative splicing. Our analyses revealed that intron retention is the predominant alternative splicing type in P. cubensis, with alternative 5′- and alternative 3′-splice sites occurring at lower frequencies. Representatives of the newly identified genes and predicted alternatively spliced transcripts were experimentally validated. The results presented herein highlight the utility of RNA-Seq for improving draft genome annotations and, through this approach, we demonstrate that alternative splicing occurs more frequently than previously predicted. In total, the current study provides evidence that alternative splicing plays a key role in transcriptome regulation and proteome diversification in plant-pathogenic oomycetes.

scholarly journals Genome-wide profiling of alternative splicing genes in hybrid poplar (P.alba×P.glandulosa cv.84K) leaves

PLoS ONE ◽  
2020 ◽  
Vol 15 (11) ◽  
pp. e0241914
Author(s):  
Ruixue Wang ◽  
Peng Yin ◽  
Yang Ruixia ◽  
Xiao Liu ◽  
Lie Luo ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Inositol Phosphate ◽  
Intron Retention ◽  
Rna Extraction ◽  
Hybrid Poplar ◽  
Gc Content ◽  
Plant Production ◽  
Splice Sites ◽  
Illumina Hiseq ◽  
Poplar Leaves

Alternative splicing (AS) is a post-transcriptional process common in plants and essential for regulation of environmental fitness of plants. In the present study, we focus on the AS events in poplar leaves to understand their effects on plant growth and development. The hybrid poplar (P.alba×P.glandulosa cv.84K) leaves were collected for RNA extraction. The extracted RNA was sequenced using on an Illumina HiSeq™ 2000 platform. Using the Populus trichocarpa genome as the reference, a total of 3810 AS genes were identified (9225 AS events), which accounted for 13.51% of all the expressed genes. Intron retention was the most common AS event, accounting for 43.86% of all the AS events, followed by alternative 3′ splice sites (23.75%), alternative 5′ splice sites (23.71%), and exon skipping (8.68%). Chromosomes 10 had the most condensed AS events (33.67 events/Mb) and chromosome 19 had the least (12.42 events/Mb). Association analysis showed that AS in the poplar leaves was positively correlated with intron length, exon number, exon length, and gene expression level, and was negatively correlated with GC content. AS genes in the poplar leaves were associated mainly with inositol phosphate metabolism and phosphatidylinositol signaling system pathways that would be significant on wooden plant production.

scholarly journals Differences in Alternative Splicing between Yellow and Black-Seeded Rapeseed

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 977
Author(s):  
Ai Lin ◽  
Jinqi Ma ◽  
Fei Xu ◽  
Wen Xu ◽  
Huanhuan Jiang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Seed Coat ◽  
Rna Binding ◽  
Developmental Stages ◽  
Coat Color ◽  
Intron Retention ◽  
Seed Color ◽  
Seed Coat Color ◽  
Flavonoid Pathway ◽  
Transcriptional Regulatory

Yellow seed coat color is a desirable characteristic in rapeseed (Brassica napus), as it is associated with higher oil content and higher quality of meal. Alternative splicing (AS) is a vital post-transcriptional regulatory process contributing to plant cell differentiation and organ development. To identify novel transcripts and differences at the isoform level that are associated with seed color in B. napus, we compared 31 RNA-seq libraries of yellow- and black-seeded B. napus at five different developmental stages. AS events in the different samples were highly similar, and intron retention accounted for a large proportion of the observed AS pattern. AS mainly occurred in the early and middle stage of seed development. Weighted gene co-expression network analysis (WGCNA) identified 23 co-expression modules composed of differentially spliced genes, and we picked out two of the modules whose functions were highly associated with seed color. In the two modules, we found candidate DAS (differentially alternative splicing) genes related to the flavonoid pathway, such as TT8 (BnaC09g24870D), TT5 (BnaA09g34840D and BnaC08g26020D), TT12 (BnaC06g17050D and BnaA07g18120D), AHA10 (BnaA08g23220D and BnaC08g17280D), CHI (BnaC09g50050D), BAN (BnaA03g60670D) and DFR (BnaC09g17150D). Gene BnaC03g23650D, encoding RNA-binding family protein, was also identified. The splicing of the candidate genes identified in this study might be used to develop stable, yellow-seeded B. napus. This study provides insight into the formation of seed coat color in B. napus.

scholarly journals Differential Alternative Splicing Genes and Isoform Regulation Networks of Rapeseed (Brassica napus L.) Infected with Sclerotinia sclerotiorum

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 784
Author(s):  
Jin-Qi Ma ◽  
Wen Xu ◽  
Fei Xu ◽  
Ai Lin ◽  
Wei Sun ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Brassica Napus ◽  
Sclerotinia Sclerotiorum ◽  
Defense Response ◽  
Gene Expression Regulation ◽  
Intron Retention ◽  
Transcriptional Response ◽  
Enrichment Analysis ◽  
Transcriptional Level ◽  
Brassica Napus L

Alternative splicing (AS) is a post-transcriptional level of gene expression regulation that increases transcriptome and proteome diversity. How the AS landscape of rapeseed (Brassica napus L.) changes in response to the fungal pathogen Sclerotinia sclerotiorum is unknown. Here, we analyzed 18 RNA-seq libraries of mock-inoculated and S. sclerotiorum-inoculated susceptible and tolerant B. napus plants. We found that infection increased AS, with intron retention being the main AS event. To determine the key genes functioning in the AS response, we performed a differential AS (DAS) analysis. We identified 79 DAS genes, including those encoding splicing factors, defense response proteins, crucial transcription factors and enzymes. We generated coexpression networks based on the splicing isoforms, rather than the genes, to explore the genes’ diverse functions. Using this weighted gene coexpression network analysis alongside a gene ontology enrichment analysis, we identified 11 modules putatively involved in the pathogen defense response. Within these regulatory modules, six DAS genes (ascorbate peroxidase 1, ser/arg-rich protein 34a, unknown function 1138, nitrilase 2, v-atpase f, and amino acid transporter 1) were considered to encode key isoforms involved in the defense response. This study provides insight into the post-transcriptional response of B. napus to S. sclerotiorum infection.

scholarly journals Mature Neurons sensitivity to oxidative stress is epigenetically programmed by alternative splicing and mRNA stability

2021 ◽  
Author(s):  
Zhou Yuan ◽  
Sherif Rashad ◽  
Teiji Tominaga ◽  
Kuniyasu Niizuma
Keyword(s):  
Oxidative Stress ◽  
Alternative Splicing ◽  
Neuronal Differentiation ◽  
Mrna Stability ◽  
Intron Retention ◽  
Transcriptional Level ◽  
Epigenetic Changes ◽  
Mrna Isoforms ◽  
Functional Changes ◽  
Mature Neurons

Neuronal differentiation is a complex process that entails extensive morphological, transcriptional, metabolic, and functional changes that dictate neuronal lineage commitment. Much less understood is the role that epigenetic and epi-transcriptional reprogramming plays in the process of neuronal differentiation and maturation. To depict the whole landscape of transcriptomics and epigenetic changes during neuronal differentiation and maturation, we differentiated SH-SY5Y cells and performed RNA sequencing on differentiated and undifferentiated cells. 728 differentially expressed genes (DEGs) enriched in synaptic signaling and cell morphogenesis pathways were observed. Moreover, transcriptome-wide mRNA stability profiling revealed that genes with altered stability were exceptionally enriched for redox homeostasis pathways. Mature neurons are known to be highly sensitive to oxidative stress, which is crucial in the pathophysiology of neurodegenerative disease. Our results suggest that this heightened sensitivity is regulated at the mRNA stability level (i.e., epigenetic) rather than at the transcriptional level. Alternative splicing analysis revealed the exon skipping and alternative mRNA isoforms enriched for morphogenesis related pathway. Alternatively, alternative 5 and 3 prime splicing site, intron retention and mutually exclusive exon events exclusively clustered in the translation and translation initiation pathways, suggesting the potential effect of alternative splicing on translation following neuronal maturation. Splice motif analysis revealed enriched motifs for RBPs that regulate various splice types and can be further correlated to distinct phenotypical changes during neuronal differentiation and maturation. Here we present an extensive exploration of the transcriptional and epigenetic changes and their potential association with the process of neuronal differentiation, providing a new insight into understanding the molecular mechanism of neuronal function and behavior.

scholarly journals Aberrantly high activation of a FoxM1–STMN1 axis contributes to progression and tumorigenesis in FoxM1-driven cancers

2021 ◽  
Vol 6 (1) ◽  
Author(s):  
Jun Liu ◽  
Jipeng Li ◽  
Ke Wang ◽  
Haiming Liu ◽  
Jianyong Sun ◽  
...  
Keyword(s):  
Cell Proliferation ◽  
Poor Prognosis ◽  
Soft Agar ◽  
Transcriptional Level ◽  
Regulation Mechanism ◽  
Strong Positive Correlation ◽  
Cell Viability Assay ◽  
High Level

AbstractFork-head box protein M1 (FoxM1) is a transcriptional factor which plays critical roles in cancer development and progression. However, the general regulatory mechanism of FoxM1 is still limited. STMN1 is a microtubule-binding protein which can inhibit the assembly of microtubule dimer or promote depolymerization of microtubules. It was reported as a major responsive factor of paclitaxel resistance for clinical chemotherapy of tumor patients. But the function of abnormally high level of STMN1 and its regulation mechanism in cancer cells remain unclear. In this study, we used public database and tissue microarrays to analyze the expression pattern of FoxM1 and STMN1 and found a strong positive correlation between FoxM1 and STMN1 in multiple types of cancer. Lentivirus-mediated FoxM1/STMN1-knockdown cell lines were established to study the function of FoxM1/STMN1 by performing cell viability assay, plate clone formation assay, soft agar assay in vitro and xenograft mouse model in vivo. Our results showed that FoxM1 promotes cell proliferation by upregulating STMN1. Further ChIP assay showed that FoxM1 upregulates STMN1 in a transcriptional level. Prognostic analysis showed that a high level of FoxM1 and STMN1 is related to poor prognosis in solid tumors. Moreover, a high co-expression of FoxM1 and STMN1 has a more significant correlation with poor prognosis. Our findings suggest that a general FoxM1-STMN1 axis contributes to cell proliferation and tumorigenesis in hepatocellular carcinoma, gastric cancer and colorectal cancer. The combination of FoxM1 and STMN1 can be a more precise biomarker for prognostic prediction.

scholarly journals Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Guiomar Martín ◽  
Yamile Márquez ◽  
Federica Mantica ◽  
Paula Duque ◽  
Manuel Irimia
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Alternative Splicing ◽  
Stress Responses ◽  
Target Genes ◽  
Intron Retention ◽  
Single Gene ◽  
Exon Skipping ◽  
Environmental Response ◽  
Biotic Stresses

Abstract Background Alternative splicing (AS) is a widespread regulatory mechanism in multicellular organisms. Numerous transcriptomic and single-gene studies in plants have investigated AS in response to specific conditions, especially environmental stress, unveiling substantial amounts of intron retention that modulate gene expression. However, a comprehensive study contrasting stress-response and tissue-specific AS patterns and directly comparing them with those of animal models is still missing. Results We generate a massive resource for Arabidopsis thaliana, PastDB, comprising AS and gene expression quantifications across tissues, development and environmental conditions, including abiotic and biotic stresses. Harmonized analysis of these datasets reveals that A. thaliana shows high levels of AS, similar to fruitflies, and that, compared to animals, disproportionately uses AS for stress responses. We identify core sets of genes regulated specifically by either AS or transcription upon stresses or among tissues, a regulatory specialization that is tightly mirrored by the genomic features of these genes. Unexpectedly, non-intron retention events, including exon skipping, are overrepresented across regulated AS sets in A. thaliana, being also largely involved in modulating gene expression through NMD and uORF inclusion. Conclusions Non-intron retention events have likely been functionally underrated in plants. AS constitutes a distinct regulatory layer controlling gene expression upon internal and external stimuli whose target genes and master regulators are hardwired at the genomic level to specifically undergo post-transcriptional regulation. Given the higher relevance of AS in the response to different stresses when compared to animals, this molecular hardwiring is likely required for a proper environmental response in A. thaliana.

scholarly journals Leaf-derived ABA regulates rice seed development via a transporter-mediated and temperature-sensitive mechanism

2021 ◽  
Vol 7 (3) ◽  
pp. eabc8873
Author(s):  
Peng Qin ◽  
Guohua Zhang ◽  
Binhua Hu ◽  
Jie Wu ◽  
Weilan Chen ◽  
...  
Keyword(s):  
Seed Development ◽  
Starch Synthesis ◽  
Biological Significance ◽  
Grain Filling ◽  
Temperature Sensitive ◽  
Rice Seed ◽  
Dependent Manner ◽  
Long Distance ◽  
Long Distance Transport ◽  
Mechanistic Basis

Long-distance transport of the phytohormone abscisic acid (ABA) has been studied for ~50 years, yet its mechanistic basis and biological significance remain very poorly understood. Here, we show that leaf-derived ABA controls rice seed development in a temperature-dependent manner and is regulated by defective grain-filling 1 (DG1), a multidrug and toxic compound extrusion transporter that effluxes ABA at nodes and rachilla. Specifically, ABA is biosynthesized in both WT and dg1 leaves, but only WT caryopses accumulate leaf-derived ABA. Our demonstration that leaf-derived ABA activates starch synthesis genes explains the incompletely filled and floury seed phenotypes in dg1. Both the DG1-mediated long-distance ABA transport efficiency and grain-filling phenotypes are temperature sensitive. Moreover, we extended these mechanistic insights to other cereals by observing similar grain-filling defects in a maize DG1 ortholog mutant. Our study demonstrates that rice uses a leaf-to-caryopsis ABA transport–based mechanism to ensure normal seed development in response to variable temperatures.

scholarly journals Comparative Transcriptome Analysis Reveals Sex-Based Differences during the Development of the Adult Parasitic Wasp Cotesia vestalis (Hymenoptera: Braconidae)

Genes ◽  
2021 ◽  
Vol 12 (6) ◽  
pp. 896
Author(s):  
Yuenan Zhou ◽  
Pei Yang ◽  
Shuang Xie ◽  
Min Shi ◽  
Jianhua Huang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Adult Development ◽  
Sexual Development ◽  
Molecular Mechanisms ◽  
Parasitic Wasp ◽  
Differentially Expressed Gene ◽  
Regulation Mechanism ◽  
Rna Seq ◽  
Male And Female ◽  
Cotesia Vestalis

The endoparasitic wasp Cotesia vestalis is an important biological agent for controlling the population of Plutella xylostella, a major pest of cruciferous crops worldwide. Though the genome of C. vestalis has recently been reported, molecular mechanisms associated with sexual development have not been comprehensively studied. Here, we combined PacBio Iso-Seq and Illumina RNA-Seq to perform genome-wide profiling of pharate adult and adult development of male and female C. vestalis. Taking advantage of Iso-Seq full-length reads, we identified 14,466 novel transcripts as well as 8770 lncRNAs, with many lncRNAs showing a sex- and stage-specific expression pattern. The differentially expressed gene (DEG) analyses showed 2125 stage-specific and 326 sex-specific expressed genes. We also found that 4819 genes showed 11,856 alternative splicing events through combining the Iso-Seq and RNA-Seq data. The results of comparative analyses showed that most genes were alternatively spliced across developmental stages, and alternative splicing (AS) events were more prevalent in females than in males. Furthermore, we identified six sex-determining genes in this parasitic wasp and verified their sex-specific alternative splicing profiles. Specifically, the characterization of feminizer and doublesex splicing between male and female implies a conserved regulation mechanism of sexual development in parasitic wasps.

Sign in / Sign up

Export Citation Format

Share Document