scholarly journals Brassica napus Infected with Leptosphaeria maculans

Genes ◽  
2019 ◽  
Vol 10 (4) ◽  
pp. 296 ◽  
Author(s):  
Ma ◽  
Wei ◽  
Lin ◽  
Zhang ◽  
Sun ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Stress Responses ◽  
Intron Retention ◽  
Leptosphaeria Maculans ◽  
Rna Seq ◽  
Hub Genes ◽  
Transcriptional Regulatory ◽  
Genes Encoding ◽  
Alternatively Spliced ◽  
Transcriptome Diversity

Alternative splicing (AS) is a post-transcriptional regulatory process that enhances transcriptome diversity, thereby affecting plant growth, development, and stress responses. To identify the new transcripts and changes in the isoform-level AS landscape of rapeseed (Brassica napus) infected with the fungal pathogen Leptosphaeria maculans, we compared eight RNA-seq libraries prepared from mock-inoculated and inoculated B. napus cotyledons and stems. The AS events that occurred in stems were almost the same as those in cotyledons, with intron retention representing the most common AS pattern. We identified 1892 differentially spliced genes between inoculated and uninoculated plants. We performed a weighted gene co-expression network analysis (WGCNA) to identify eight co-expression modules and their Hub genes, which are the genes most connected with other genes within each module. There are nine Hub genes, encoding nine transcription factors, which represent key regulators of each module, including members of the NAC, WRKY, TRAF, AP2/ERF-ERF, C2H2, C2C2-GATA, HMG, bHLH, and C2C2-CO-like families. Finally, 52 and 117 alternatively spliced genes in cotyledons and stems were also differentially expressed between mock-infected and infected materials, such as HMG and C2C2-Dof; which have dual regulatory mechanisms in response to L. maculans. The splicing of the candidate genes identified in this study could be exploited to improve resistance to L. maculans.

Oxidant stress responses in influenza virus pneumonia: gene expression and transcription factor activation

1996 ◽  
Vol 271 (3) ◽  
pp. L383-L391 ◽  
Author(s):  
A. M. Choi ◽  
K. Knobil ◽  
S. L. Otterbein ◽  
D. A. Eastman ◽  
D. B. Jacoby
Keyword(s):  
Influenza Virus ◽  
Viral Infection ◽  
Heme Oxygenase ◽  
Stress Responses ◽  
Oxidant Stress ◽  
Regulatory Proteins ◽  
Heme Oxygenase 1 ◽  
Nf Kappa B ◽  
Transcriptional Regulatory ◽  
Genes Encoding

The pathogenesis of influenza virus infections of the lungs is in part mediated by oxidative stress. Such infections might therefore be expected to induce expression of stress-response genes and genes encoding antioxidant enzymes and to activate transcriptional regulatory proteins. Mice (C57B1/6 and C3H/HeJ) were infected intranasally with influenza virus A/PR/8/34 (H1N1). Expression of the genes encoding the antioxidant enzymes manganese superoxide dismutase (Mn- SOD), indoleamine-2, 3-dioxygenase (IDO), heme oxygenase-1, and glutathione peroxidase were increased in the lungs of virus-infected animals. Cu/ZnSOD and catalase mRNA were not induced by viral infection. Activation of the transcriptional regulatory proteins AP-1, C/EBP, and NF-kappa B (which are known to be affected by oxidant stress) was demonstrated by electrophoretic mobility shift assay after viral infection. In the case of MnSOD, despite increased gene expression enzyme activity was not increased. In contrast, for heme oxygenase-1 both mRNA and activity were increased. C3H/ HeJ and C57B1/6 mice, which are known to have different responses to other types of oxidant stress, also differed in their responses to viral infection. Induction of heme oxygenase-1 expression was greater in C57B1/6 mice than in C3H/ HeJ mice, although inhibiting this enzyme did not alter virus-induced mortality. In contrast, IDO was more strongly induced in C3H/HeJ mice. Activation of NF-kappa B was much more marked in C57B1/6 mice than in C3H/HeJ mice. Although virus replication and inflammatory responses were equivalent in the two strains, lung injury (as measured by wet-to-dry wt ratios) and mortality were greater in C3H/HeJ mice than in C57B1/6 mice, a difference that may be related to differing oxidant stress responses. Thus influenza pneumonia causes an oxidant stress response in the lungs, the nature of which is determined in part by the genetic background of the host.

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 RNA-binding protein syncrip regulates starvation-induced hyperactivity in adult Drosophila

PLoS Genetics ◽  
2021 ◽  
Vol 17 (2) ◽  
pp. e1009396
Author(s):  
Wanhao Chi ◽  
Wei Liu ◽  
Wenqin Fu ◽  
Shengqian Xia ◽  
Ellie S. Heckscher ◽  
...  
Keyword(s):  
Rna Binding ◽  
Association Studies ◽  
Target System ◽  
Genome Wide Association Studies ◽  
Rna Seq ◽  
Behavioral Trait ◽  
Genes Encoding ◽  
Alternatively Spliced ◽  
Mrna Binding

How to respond to starvation determines fitness. One prominent behavioral response is increased locomotor activities upon starvation, also known as Starvation-Induced Hyperactivity (SIH). SIH is paradoxical as it promotes food seeking but also increases energy expenditure. Despite its importance in fitness, the genetic contributions to SIH as a behavioral trait remains unexplored. Here, we examined SIH in the Drosophila melanogaster Genetic Reference Panel (DGRP) and performed genome-wide association studies. We identified 23 significant loci, corresponding to 14 genes, significantly associated with SIH in adult Drosophila. Gene enrichment analyses indicated that genes encoding ion channels and mRNA binding proteins (RBPs) were most enriched in SIH. We are especially interested in RBPs because they provide a potential mechanism to quickly change protein expression in response to environmental challenges. Using RNA interference, we validated the role of syp in regulating SIH. syp encodes Syncrip (Syp), an RBP. While ubiquitous knockdown of syp led to semi-lethality in adult flies, adult flies with neuron-specific syp knockdown were viable and exhibited decreased SIH. Using the Temporal and Regional Gene Expression Targeting (TARGET) system, we further confirmed the role of Syp in adult neurons in regulating SIH. To determine how syp is regulated by starvation, we performed RNA-seq using the heads of flies maintained under either food or starvation conditions. RNA-seq analyses revealed that syp was alternatively spliced under starvation while its expression level was unchanged. We further generated an alternatively-spliced-exon-specific knockout (KO) line and found that KO flies showed reduced SIH. Together, this study demonstrates a significant genetic contribution to SIH as a behavioral trait, identifies syp as a SIH gene, and highlights the significance of RBPs and post-transcriptional processes in the brain in regulating behavioral responses to starvation.

scholarly journals Nitrogen Assimilation Related Genes in Brassica napus: Systematic Characterization and Expression Analysis Identified Hub Genes in Multiple Nutrient Stress Responses

Plants ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2160
Author(s):  
Xuyou He ◽  
Hao Zhang ◽  
Xiangsheng Ye ◽  
Juan Hong ◽  
Guangda Ding
Keyword(s):  
Brassica Napus ◽  
Stress Responses ◽  
Gene Evolution ◽  
Hub Genes ◽  
Ammonium Toxicity ◽  
Oil Crops ◽  
Genome Wide ◽  
N Assimilation ◽  
Expansion Pattern ◽  
Phosphorus And Potassium

Nitrogen (N) is an essential macronutrient for plants. However, little is known about the molecular regulation of N assimilation in Brassica napus, one of the most important oil crops worldwide. Here, we carried out a comprehensive genome-wide analysis of the N assimilation related genes (NAGs) in B. napus. A total of 67 NAGs were identified encoding major enzymes involved in N assimilation, including asparagine synthetase (AS), glutamate dehydrogenase (GDH), glutamine oxoglutarate aminotransferase (GOGAT), glutamine synthetase (GS), nitrite reductase (NiR), nitrate reductase (NR). The syntenic analysis revealed that segmental duplication and whole-genome duplication were the main expansion pattern during gene evolution. Each NAG family showed different degrees of differentiation in characterization, gene structure, conserved motifs and cis-elements. Furthermore, diverse responses of NAG to multiple nutrient stresses were observed. Among them, more NAGs were regulated by N deficiency and ammonium toxicity than by phosphorus and potassium deprivations. Moreover, 12 hub genes responding to N starvation were identified, which may play vital roles in N utilization. Taken together, our results provide a basis for further functional research of NAGs in rapeseed N assimilation and also put forward new points in their responses to contrasting nutrient stresses.

scholarly journals High frequency of intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Pinki Dey ◽  
John S. Mattick
Keyword(s):  
Nucleosome Occupancy ◽  
Average Length ◽  
Intron Retention ◽  
K562 Cells ◽  
Protein Coding ◽  
Genes Encoding ◽  
Alternatively Spliced ◽  
Non Coding Rnas ◽  
Genomic Regions ◽  
Retained Introns

Abstract Background It is established that protein-coding exons are preferentially localized in nucleosomes. To examine whether the same is true for non-coding exons, we analysed nucleosome occupancy in and adjacent to internal exons in genes encoding long non-coding RNAs (lncRNAs) in human CD4+ T cells and K562 cells. Results We confirmed that internal exons in lncRNAs are preferentially associated with nucleosomes, but also observed an elevated signal from H3K4me3-marked nucleosomes in the sequences upstream of these exons. Examination of 200 genomic lncRNA loci chosen at random across all chromosomes showed that high-density regions of H3K4me3-marked nucleosomes, which we term ‘slabs’, are associated with genomic regions exhibiting intron retention. These retained introns occur in over 50% of lncRNAs examined and are mostly first introns with an average length of just 354 bp, compared to the average length of all human introns of 6355 and 7987 bp in mRNAs and lncRNAs, respectively. Removal of short introns from the dataset abrogated the high upstream H3K4me3 signal, confirming that the association of slabs and short lncRNA introns with intron retention holds genome-wide. The high upstream H3K4me3 signal is also associated with alternatively spliced exons, known to be prominent in lncRNAs. This phenomenon was not observed with mRNAs. Conclusions There is widespread intron retention and clustered H3K4me3-marked nucleosomes in short first introns of human long non-coding RNAs, which raises intriguing questions about the relationship of IR to lncRNA function and chromatin organization.

scholarly journals Transcriptome Analysis of Seed Weight Plasticity in Brassica napus

2021 ◽  
Vol 22 (9) ◽  
pp. 4449
Author(s):  
Javier Canales ◽  
José Verdejo ◽  
Gabriela Carrasco-Puga ◽  
Francisca M. Castillo ◽  
Anita Arenas-M ◽  
...  
Keyword(s):  
Brassica Napus ◽  
Crop Yield ◽  
Stress Responses ◽  
Seed Weight ◽  
Rna Seq ◽  
Sucrose Transport ◽  
Factors Associated ◽  
Expression Of Genes ◽  
Source Sink ◽  
The Relationship

A critical barrier to improving crop yield is the trade-off between seed weight (SW) and seed number (SN), which has been commonly reported in several crops, including Brassica napus. Despite the agronomic relevance of this issue, the molecular factors involved in the interaction between SW and SN are largely unknown in crops. In this work, we performed a detailed transcriptomic analysis of 48 seed samples obtained from two rapeseed spring genotypes subjected to different source–sink (S–S) ratios in order to examine the relationship between SW and SN under different field conditions. A multifactorial analysis of the RNA-seq data was used to identify a group of 1014 genes exclusively regulated by the S–S ratio. We found that a reduction in the S–S ratio during seed filling induces the expression of genes involved in sucrose transport, seed weight, and stress responses. Moreover, we identified five co-expression modules that are positively correlated with SW and negatively correlated with SN. Interestingly, one of these modules was significantly enriched in transcription factors (TFs). Furthermore, our network analysis predicted several NAC TFs as major hubs underlying SW and SN compensation. Taken together, our study provides novel insights into the molecular factors associated with the SW–SN relationship in rapeseed and identifies TFs as potential targets when improving crop yield.

scholarly journals Evolution analysis and expression divergence of the chitinase gene family against Leptosphaeria maculans and Sclerotinia sclerotiorum infection in Brassica napus

2018 ◽  
Author(s):  
Wen Xu ◽  
Tengsheng Zhou ◽  
Bo An ◽  
Baojiang Xu ◽  
Genyi Li
Keyword(s):  
Brassica Napus ◽  
Gene Family ◽  
Sclerotinia Sclerotiorum ◽  
Stress Responses ◽  
Leptosphaeria Maculans ◽  
Chitinase Gene ◽  
Evolutionary Analysis ◽  
Sclerotinia Stem Rot ◽  
A Genome ◽  
Chitinase Genes

Abstract:Blackleg and sclerotinia stem rot caused by Leptosphaeria maculans and Sclerotinia sclerotiorum respectively are two major diseases in rapeseed worldwide, which cause serious yield losses. Chitinases are pathogenesis-related proteins and play important roles in host resistance to various pathogens and abiotic stress responses. However, a systematic investigation of the chitinase gene family and its expression profile against L. maculans and S. sclerotiorum infection in rapeseed remains elusive. The recent release of assembled genome sequence of rapeseed allowed us to perform a genome-wide identification of the chitinase gene family. In this study, 68 chitinase genes were identified in Brassica napus genome. These genes were divided into five different classes and distributed among 15 chromosomes. Evolutionary analysis indicated that the expansion of the chitinase gene family was mainly attributed to segmental and tandem duplication. Moreover, the expression profiling of the chitinase gene family was investigated using RNA sequencing (RNA-Seq) and the results revealed that some chitinase genes were both induced while the other members exhibit distinct expression in response to L. maculans and S. sclerotiorum infection. This study presents a comprehensive survey of the chitinase gene family in B. napus and provides valuable information for further understanding the functions of the chitinase gene family.

scholarly journals Rewired Pathways and Disrupted Pathway Crosstalk in Schizophrenia Transcriptomes by Multiple Differential Coexpression Methods

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 665
Author(s):  
Hui Yu ◽  
Yan Guo ◽  
Jingchun Chen ◽  
Xiangning Chen ◽  
Peilin Jia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Focal Adhesion ◽  
Biological Pathways ◽  
Postmortem Brain ◽  
Rna Seq ◽  
Hub Genes ◽  
Differential Coexpression ◽  
Pathway Crosstalk ◽  
Microarray Datasets ◽  
Transcriptomic Studies

Transcriptomic studies of mental disorders using the human brain tissues have been limited, and gene expression signatures in schizophrenia (SCZ) remain elusive. In this study, we applied three differential co-expression methods to analyze five transcriptomic datasets (three RNA-Seq and two microarray datasets) derived from SCZ and matched normal postmortem brain samples. We aimed to uncover biological pathways where internal correlation structure was rewired or inter-coordination was disrupted in SCZ. In total, we identified 60 rewired pathways, many of which were related to neurotransmitter, synapse, immune, and cell adhesion. We found the hub genes, which were on the center of rewired pathways, were highly mutually consistent among the five datasets. The combinatory list of 92 hub genes was generally multi-functional, suggesting their complex and dynamic roles in SCZ pathophysiology. In our constructed pathway crosstalk network, we found “Clostridium neurotoxicity” and “signaling events mediated by focal adhesion kinase” had the highest interactions. We further identified disconnected gene links underlying the disrupted pathway crosstalk. Among them, four gene pairs (PAK1:SYT1, PAK1:RFC5, DCTN1:STX1A, and GRIA1:MAP2K4) were normally correlated in universal contexts. In summary, we systematically identified rewired pathways, disrupted pathway crosstalk circuits, and critical genes and gene links in schizophrenia transcriptomes.

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