scholarly journals Genome-wide identification of ubiquitin proteasome subunits as superior reference genes for transcript normalization during receptacle development in strawberry cultivars

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Jianqing Chen ◽  
Jinyu Zhou ◽  
Yanhong Hong ◽  
Zekun Li ◽  
Xiangyu Cheng ◽  
...  
Keyword(s):  
Gene Expression ◽  
Reference Genes ◽  
Housekeeping Genes ◽  
Ubiquitin Proteasome System ◽  
Genome Wide ◽  
A Genome ◽  
Proteasome Subunits ◽  
Ubiquitin Proteasome ◽  
Gene Transcripts ◽  
Strawberry Cultivars

Abstract Background Gene transcripts that show invariant abundance during development are ideal as reference genes (RGs) for accurate gene expression analyses, such as RNA blot analysis and reverse transcription–quantitative real time PCR (RT-qPCR) analyses. In a genome-wide analysis, we selected three “Commonly used” housekeeping genes (HKGs), fifteen “Traditional” HKGs, and nine novel genes as candidate RGs based on 80 publicly available transcriptome libraries that include data for receptacle development in eight strawberry cultivars. Results The results of the multifaceted assessment consistently revealed that expression of the novel RGs showed greater stability compared with that of the “Commonly used” and “Traditional” HKGs in transcriptome and RT-qPCR analyses. Notably, the majority of stably expressed genes were associated with the ubiquitin proteasome system. Among these, two 26 s proteasome subunits, RPT6A and RPN5A, showed superior expression stability and abundance, and are recommended as the optimal RGs combination for normalization of gene expression during strawberry receptacle development. Conclusion These findings provide additional useful and reliable RGs as resources for the accurate study of gene expression during receptacle development in strawberry cultivars.

scholarly journals Identification and evaluation of suitable reference genes for gene expression analysis in rubber tree leaf

2019 ◽  
Author(s):  
xiangyu long ◽  
Jilai Lu ◽  
Nat N. V. Kav ◽  
Yunxia Qin ◽  
Yongjun Fang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Reference Genes ◽  
Rubber Tree ◽  
Ubiquitin Proteasome System ◽  
New Genes ◽  
Ubiquitin Proteasome ◽  
Suitable Reference ◽  
Tree Leaf

Abstract Backgroud Gene expression profiling is increasingly applied to investigate molecular mechanisms for which, normalization with suitable reference genes is critical. Previously we have reported several suitable reference genes for laticifer samples from rubber, however, little is known about reference genes in leaf. Results The main objective of this current study was to identify some reference genes with stable expression patterns in leaf at various developmental stages, as well as during abiotic (temperature extremes) and biotic stresses. Gene expression profiling experiments in rubber tree leaf identified the ubiquitin-proteasome system as having excellent potential as reference genes. Among a total of 30 tested genes investigated, 24 new (including 11 genes involved in the ubiquitin-proteasome system), 4 previously identified and 2 specific genes, were further evaluated using quantitative real-time PCR. Our results indicated that the new genes had better stability of expression when compared with others. For instance, an ubiquitin conjugating enzyme (RG0099) and three ubiquitin-protein ligases (RG0928, RG2190 and RG0118) expressed stably in all samples, and were confirmed to be suitable reference genes in rubber tree leaf in four different conditions. Finally, we suggest that using more than one reference gene may be appropriate in gene expression studies when employing different software to normalize gene expression data. Conclusion Our findings have significant implications for the reliability of data obtained from genomics studies in rubber tree and perhaps in other species.

scholarly journals Fitness costs and benefits of gene expression plasticity in rice under drought

2021 ◽  
Author(s):  
Simon C Groen ◽  
Elena Hamann ◽  
Irina Calic ◽  
Colleen Cochran ◽  
Rachel Konshok ◽  
...  
Keyword(s):  
Gene Expression ◽  
Environmental Variability ◽  
Housekeeping Genes ◽  
Costs And Benefits ◽  
Compensatory Evolution ◽  
Architectural Features ◽  
Genome Wide ◽  
A Genome ◽  
Gene Modules ◽  
Genome Wide Gene Expression

Genome-wide gene expression changes in response to environmental variability have been widely documented, but we lack detailed and comprehensive understanding of the interplay between this form of phenotypic plasticity and natural selection. Selection on expression plasticity may be limited by environment-specific costs, and plasticity may in turn affect selection on baseline expression levels. Here, we address this fundamental issue by measuring selection on drought-induced plasticity of leaf transcripts in field-grown rice populations. Selection disfavored switching off housekeeping genes under drought. This stress-induced dysregulation did not constrain selection on baseline transcript levels, suggesting compensatory evolution may be possible. Selection rarely acted strongly on individual transcripts but worked polygenically on gradual (continuous) plasticity of co-expressed gene modules regulating photosynthesis via known drought-responsive transcription factors. Finally, selection was tied to inefficient gene architectural features and metabolic costs of expression. Our study provides a genome-wide view of costs and benefits of gene expression plasticity.

scholarly journals Inhibition of the ubiquitin-proteasome system by an NQO1-activatable compound

2021 ◽  
Vol 12 (10) ◽  
Author(s):  
Tatiana A. Giovannucci ◽  
Florian A. Salomons ◽  
Martin Haraldsson ◽  
Lotta H. M. Elfman ◽  
Malin Wickström ◽  
...  
Keyword(s):  
Ubiquitin Proteasome System ◽  
Malignant Cells ◽  
Genome Wide ◽  
A Genome ◽  
Ubiquitin Proteasome ◽  
Dependent Cell ◽  
Increased Sensitivity ◽  
The Impact

AbstractMalignant cells display an increased sensitivity towards drugs that reduce the function of the ubiquitin-proteasome system (UPS), which is the primary proteolytic system for destruction of aberrant proteins. Here, we report on the discovery of the bioactivatable compound CBK77, which causes an irreversible collapse of the UPS, accompanied by a general accumulation of ubiquitylated proteins and caspase-dependent cell death. CBK77 caused accumulation of ubiquitin-dependent, but not ubiquitin-independent, reporter substrates of the UPS, suggesting a selective effect on ubiquitin-dependent proteolysis. In a genome-wide CRISPR interference screen, we identified the redox enzyme NAD(P)H:quinone oxidoreductase 1 (NQO1) as a critical mediator of CBK77 activity, and further demonstrated its role as the compound bioactivator. Through affinity-based proteomics, we found that CBK77 covalently interacts with ubiquitin. In vitro experiments showed that CBK77-treated ubiquitin conjugates were less susceptible to disassembly by deubiquitylating enzymes. In vivo efficacy of CBK77 was validated by reduced growth of NQO1-proficient human adenocarcinoma cells in nude mice treated with CBK77. This first-in-class NQO1-activatable UPS inhibitor suggests that it may be possible to exploit the intracellular environment in malignant cells for leveraging the impact of compounds that impair the UPS.

scholarly journals Inhibition of the ubiquitin-proteasome system by a bioactivatable compound

2021 ◽  
Author(s):  
Tatiana A. Giovannucci ◽  
Florian A. Salomons ◽  
Martin Haraldsson ◽  
Lotta H. M. Elfman ◽  
Malin Wickström ◽  
...  
Keyword(s):  
Ubiquitin Proteasome System ◽  
Malignant Cells ◽  
Genome Wide ◽  
A Genome ◽  
Ubiquitin Proteasome ◽  
Dependent Cell ◽  
Increased Sensitivity ◽  
The Impact

SummaryMalignant cells display an increased sensitivity towards drugs that reduce the function of the ubiquitin-proteasome system (UPS), which is the primary proteolytic system for destruction of aberrant proteins. Here, we report on the discovery of the bioactivatable compound CBK77, which causes an irreversible collapse of the UPS, accompanied by a general accumulation of ubiquitylated proteins and caspase-dependent cell death. CBK77 caused accumulation of ubiquitin-dependent, but not ubiquitin-independent, reporter substrates of the UPS, suggesting a selective effect on ubiquitin-dependent proteolysis. In a genome-wide CRISPR interference screen, we identified the redox enzyme NAD(P)H:quinone oxidoreductase 1 (NQO1) as a critical mediator of CBK77 activity, and further demonstrated its role as the compound bioactivator. Through affinity-based proteomics, we found that CBK77 covalently interacts with ubiquitin. In vitro experiments showed that CBK77-treated ubiquitin conjugates were less susceptible to disassembly by deubiquitylating enzymes. In vivo efficacy of CBK77 was validated by reduced growth of NQO1-proficient human adenocarcinoma cells in nude mice treated with CBK77. This first-in-class NQO1-activatable UPS inhibitor suggests that it may be possible to exploit the intracellular environment in malignant cells for leveraging the impact of compounds that impair the UPS.

scholarly journals Genome-wide identification and expression analysis of the Brassica oleracea L. chitin-binding genes and response to pathogens infections

Planta ◽  
2021 ◽  
Vol 253 (4) ◽  
Author(s):  
Mingzhao Zhu ◽  
Shujin Lu ◽  
Mu Zhuang ◽  
Yangyong Zhang ◽  
Honghao Lv ◽  
...  
Keyword(s):  
Powdery Mildew ◽  
Gene Family ◽  
Brassica Oleracea ◽  
Downy Mildew ◽  
Fusarium Wilt ◽  
Black Spot ◽  
Housekeeping Genes ◽  
Chitinase Gene ◽  
Genome Wide ◽  
A Genome

Abstract Main conclusion Chitinase family genes were involved in the response of Brassica oleracea to Fusarium wilt, powdery mildew, black spot and downy mildew. Abstract Abstract Chitinase, a category of pathogenesis-related proteins, is believed to play an important role in defending against external stress in plants. However, a comprehensive analysis of the chitin-binding gene family has not been reported to date in cabbage (Brassica oleracea L.), especially regarding the roles that chitinases play in response to various diseases. In this study, a total of 20 chitinase genes were identified using a genome-wide search method. Phylogenetic analysis was employed to classify these genes into two groups. The genes were distributed unevenly across six chromosomes in cabbage, and all of them contained few introns (≤ 2). The results of collinear analysis showed that the cabbage genome contained 1–5 copies of each chitinase gene (excluding Bol035470) identified in Arabidopsis. The heatmap of the chitinase gene family showed that these genes were expressed in various tissues and organs. Two genes (Bol023322 and Bol041024) were relatively highly expressed in all of the investigated tissues under normal conditions, exhibiting the expression characteristics of housekeeping genes. In addition, under four different stresses, namely, Fusarium wilt, powdery mildew, black spot and downy mildew, we detected 9, 5, 8 and 8 genes with different expression levels in different treatments, respectively. Our results may help to elucidate the roles played by chitinases in the responses of host plants to various diseases.

scholarly journals Genome-wide gene expression changes in postpartum depression point towards an altered immune landscape

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Divya Mehta ◽  
Karen Grewen ◽  
Brenda Pearson ◽  
Shivangi Wani ◽  
Leanne Wallace ◽  
...  
Keyword(s):  
Gene Expression ◽  
Depressive Symptoms ◽  
Postpartum Depression ◽  
Expression Profiles ◽  
Depression Scale ◽  
Well Being ◽  
Health Concern ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Gene Expression

AbstractMaternal postpartum depression (PPD) is a significant public health concern due to the severe negative impact on maternal and child health and well-being. In this study, we aimed to identify genes associated with PPD. To do this, we investigated genome-wide gene expression profiles of pregnant women during their third trimester of pregnancy and tested the association of gene expression with perinatal depressive symptoms. A total of 137 women from a cohort from the University of North Carolina, USA were assessed. The main phenotypes analysed were Edinburgh Postnatal Depression Scale (EPDS) scores at 2 months postpartum and PPD (binary yes/no) based on an EPDS cutoff of 10. Illumina NextSeq500/550 transcriptomic sequencing from whole blood was analysed using the edgeR package. We identified 71 genes significantly associated with postpartum depression scores at 2 months, after correction for multiple testing at 5% FDR. These included several interesting candidates including TNFRSF17, previously reported to be significantly upregulated in women with PPD and MMP8, a matrix metalloproteinase gene, associated with depression in a genome-wide association study. Functional annotation of differentially expressed genes revealed an enrichment of immune response-related biological processes. Additional analysis of genes associated with changes in depressive symptoms from recruitment to 2 months postpartum identified 66 genes significant at an FDR of 5%. Of these genes, 33 genes were also associated with depressive symptoms at 2 months postpartum. Comparing the results with previous studies, we observed that 15.4% of genes associated with PPD in this study overlapped with 700 core maternal genes that showed significant gene expression changes across multiple brain regions (P = 7.9e-05) and 29–53% of the genes were also associated with estradiol changes in a pharmacological model of depression (P values range = 1.2e-4–2.1e-14). In conclusion, we identified novel genes and validated genes previously associated with oestrogen sensitivity in PPD. These results point towards the role of an altered immune transcriptomic landscape as a vulnerability factor for PPD.

scholarly journals A genome-wide transcriptomic analysis of embryos fathered by obese males in a murine model of diet-induced obesity

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Laura Bernhardt ◽  
Marcus Dittrich ◽  
Rabih El-Merahbi ◽  
Antoine-Emmanuel Saliba ◽  
Tobias Müller ◽  
...  
Keyword(s):  
Gene Expression ◽  
Negative Impact ◽  
Preimplantation Embryos ◽  
High Fat ◽  
Cell Stage ◽  
Genetic Transmission ◽  
Diet Induced Obesity ◽  
Genome Wide ◽  
A Genome ◽  
Paternal Obesity

AbstractPaternal obesity is known to have a negative impact on the male’s reproductive health as well as the health of his offspring. Although epigenetic mechanisms have been implicated in the non-genetic transmission of acquired traits, the effect of paternal obesity on gene expression in the preimplantation embryo has not been fully studied. To this end, we investigated whether paternal obesity is associated with gene expression changes in eight-cell stage embryos fathered by males on a high-fat diet. We used single embryo RNA-seq to compare the gene expression profile of embryos generated by males on a high fat (HFD) versus control (CD) diet. This analysis revealed significant upregulation of the Samd4b and Gata6 gene in embryos in response to a paternal HFD. Furthermore, we could show a significant increase in expression of both Gata6 and Samd4b during differentiation of stromal vascular cells into mature adipocytes. These findings suggest that paternal obesity may induce changes in the male germ cells which are associated with the gene expression changes in the resulting preimplantation embryos.

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