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

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.

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

Translational Psychiatry ◽

10.1038/s41398-021-01270-5 ◽

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.

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Modular genome-wide gene expression architecture shared by early traits of osteoporosis and atherosclerosis in the Young Finns Study

Scientific Reports ◽

10.1038/s41598-021-86536-0 ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Binisha H. Mishra ◽

Pashupati P. Mishra ◽

Emma Raitoharju ◽

Saara Marttila ◽

Nina Mononen ◽

...

Keyword(s):

Gene Expression ◽

Smoking Habit ◽

Intima Media Thickness ◽

Mineral Density ◽

Genome Wide ◽

Study Support ◽

Gene Modules ◽

Study Participants ◽

Genome Wide Gene Expression ◽

Young Finns Study

AbstractWe analysed whole blood genome-wide expression data to identify gene co-expression modules shared by early traits of osteoporosis and atherosclerosis. Gene expression was profiled for the Young Finns Study participants. Bone mineral density and content were measured as early traits of osteoporosis. Carotid and bulbus intima media thickness were measured as early traits of atherosclerosis. Joint association of the modules, identified with weighted co-expression analysis, with early traits of the diseases was tested with multivariate analysis. Among the six modules significantly correlated with early traits of both the diseases, two had significant (adjusted p-values (p.adj) < 0.05) and another two had suggestively significant (p.adj < 0.25) joint association with the two diseases after adjusting for age, sex, body mass index, smoking habit, alcohol consumption, and physical activity. The three most significant member genes from the significant modules were NOSIP, GXYLT2, and TRIM63 (p.adj ≤ 0.18). Genes in the modules were enriched with biological processes that have separately been found to be involved in either bone metabolism or atherosclerosis. The gene modules and their most significant member genes identified in this study support the osteoporosis-atherosclerosis comorbidity hypothesis and can provide new joint biomarkers for both diseases and their dual prevention.

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Angiogenesis and Lymphangiogenesis in IBC: Insights from a Genome-Wide Gene Expression Profiling Study

Inflammatory Breast Cancer: An Update ◽

10.1007/978-94-007-3907-9_18 ◽

2012 ◽

pp. 225-242

Author(s):

Peter B. Vermeulen ◽

Gert Van den Eynden ◽

Pascal Finetti ◽

Daniel Birnbaum ◽

Naoto T. Ueno ◽

...

Keyword(s):

Gene Expression ◽

Gene Expression Profiling ◽

Expression Profiling ◽

Genome Wide ◽

A Genome ◽

Genome Wide Gene Expression

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A Transcription Factor Map as Revealed by a Genome-Wide Gene Expression Analysis of Whole-Blood mRNA Transcriptome in Multiple Sclerosis

PLoS ONE ◽

10.1371/journal.pone.0014176 ◽

2010 ◽

Vol 5 (12) ◽

pp. e14176 ◽

Cited By ~ 35

Author(s):

Carlos Riveros ◽

Drew Mellor ◽

Kaushal S. Gandhi ◽

Fiona C. McKay ◽

Mathew B. Cox ◽

...

Keyword(s):

Gene Expression ◽

Multiple Sclerosis ◽

Transcription Factor ◽

Whole Blood ◽

Gene Expression Analysis ◽

Genome Wide ◽

A Genome ◽

Factor Map ◽

Genome Wide Gene Expression ◽

Mrna Transcriptome

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

BMC Genomics ◽

10.1186/s12864-021-07393-9 ◽

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.

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