scholarly journals Network Analysis Prioritizes DEWAX and ICE1 as the Candidate Genes for Major eQTL Hotspots in Seed Germination of Arabidopsis thaliana

2020 ◽  
Vol 10 (11) ◽  
pp. 4215-4226
Author(s):  
Margi Hartanto ◽  
Ronny V. L. Joosen ◽  
Basten L. Snoek ◽  
Leo A. J. Willems ◽  
Mark G. Sterken ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Network Analysis ◽  
Seed Germination ◽  
Recombinant Inbred Lines ◽  
Genetic Regulation ◽  
Regulation Of Gene Expression ◽  
Regulatory Genes ◽  
Regulation Of Expression ◽  
Trait Locus

Seed germination is characterized by a constant change of gene expression across different time points. These changes are related to specific processes, which eventually determine the onset of seed germination. To get a better understanding on the regulation of gene expression during seed germination, we performed a quantitative trait locus mapping of gene expression (eQTL) at four important seed germination stages (primary dormant, after-ripened, six-hour after imbibition, and radicle protrusion stage) using Arabidopsis thaliana Bay x Sha recombinant inbred lines (RILs). The mapping displayed the distinctness of the eQTL landscape for each stage. We found several eQTL hotspots across stages associated with the regulation of expression of a large number of genes. Interestingly, an eQTL hotspot on chromosome five collocates with hotspots for phenotypic and metabolic QTL in the same population. Finally, we constructed a gene co-expression network to prioritize the regulatory genes for two major eQTL hotspots. The network analysis prioritizes transcription factors DEWAX and ICE1 as the most likely regulatory genes for the hotspot. Together, we have revealed that the genetic regulation of gene expression is dynamic along the course of seed germination.

scholarly journals Network Analysis Prioritizes DEWAX and ICE1 as the Candidate Genes for Major eQTL Hotspots in Seed Germination

2020 ◽  
Author(s):  
Margi Hartanto ◽  
Ronny V. L. Joosen ◽  
Basten L. Snoek ◽  
Leo A. J. Willems ◽  
Mark G. Sterken ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Network Analysis ◽  
Seed Germination ◽  
Recombinant Inbred Lines ◽  
Genetic Regulation ◽  
Regulation Of Gene Expression ◽  
Regulatory Genes ◽  
Regulation Of Expression ◽  
Trait Locus

AbstractSeed germination is characterized by a constant change of gene expression across different time points. These changes are related to specific processes, which eventually determine the onset of seed germination. To get a better understanding on the regulation of gene expression during seed germination, we performed a quantitative trait locus mapping of gene expression (eQTL) at four important seed germination stages (primary dormant, after-ripened, six-hour after imbibition, and radicle protrusion stage) using Arabidopsis thaliana Bay x Sha recombinant inbred lines (RILs). The mapping displayed the distinctness of the eQTL landscape for each stage. We found several eQTL hotspots across stages associated with the regulation of expression of a large number of genes. Interestingly, an eQTL hotspot on chromosome five collocates with hotspots for phenotypic and metabolic QTLs in the same population. Finally, we constructed a gene co-expression network to prioritize the regulatory genes for two major eQTL hotspots. The network analysis prioritizes transcription factors DEWAX and ICE1 as the most likely regulatory genes for the hotspot. Together, we have revealed that the genetic regulation of gene expression is dynamic along the course of seed germination.One-sentence summaryTwo transcription factors, DEWAX and ICE1, may be important regulators of gene expression during seed germination, based on network analysis of eQTL hotspots.

scholarly journals On Using Local Ancestry to Characterize the Genetic Architecture of Human Phenotypes: Genetic Regulation of Gene Expression in Multiethnic or Admixed Populations as a Model

2018 ◽  
Author(s):  
Yizhen Zhong ◽  
Minoli Perera ◽  
Eric R. Gamazon
Keyword(s):  
Gene Expression ◽  
Complex Traits ◽  
Genetic Architecture ◽  
Genetic Regulation ◽  
Regulation Of Gene Expression ◽  
Type I ◽  
Eqtl Mapping ◽  
Entire Genome ◽  
Local Ancestry ◽  
Heritability Estimation

AbstractBackgroundUnderstanding the nature of the genetic regulation of gene expression promises to advance our understanding of the genetic basis of disease. However, the methodological impact of use of local ancestry on high-dimensional omics analyses, including most prominently expression quantitative trait loci (eQTL) mapping and trait heritability estimation, in admixed populations remains critically underexplored.ResultsHere we develop a statistical framework that characterizes the relationships among the determinants of the genetic architecture of an important class of molecular traits. We estimate the trait variance explained by ancestry using local admixture relatedness between individuals. Using National Institute of General Medical Sciences (NIGMS) and Genotype-Tissue Expression (GTEx) datasets, we show that use of local ancestry can substantially improve eQTL mapping and heritability estimation and characterize the sparse versus polygenic component of gene expression in admixed and multiethnic populations respectively. Using simulations of diverse genetic architectures to estimate trait heritability and the level of confounding, we show improved accuracy given individual-level data and evaluate a summary statistics based approach. Furthermore, we provide a computationally efficient approach to local ancestry analysis in eQTL mapping while increasing control of type I and type II error over traditional approaches.ConclusionOur study has important methodological implications on genetic analysis of omics traits across a range of genomic contexts, from a single variant to a prioritized region to the entire genome. Our findings highlight the importance of using local ancestry to better characterize the heritability of complex traits and to more accurately map genetic associations.

scholarly journals Cold priming uncouples light- and cold-regulation of gene expression in Arabidopsis thaliana

2020 ◽  
Author(s):  
Andras Bittner ◽  
Jörn van Buer ◽  
Margarete Baier
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Plant Pathogens ◽  
Cold Treatment ◽  
Regulation Of Gene Expression ◽  
Light Regulation ◽  
High Light ◽  
Cold Stimulus ◽  
Expression Of Genes ◽  
Specific Manner

Abstract Background: The majority of stress-sensitive genes responds to cold and high light in the same direction, if plants face the stresses for the first time. As shown recently for a small selection of genes of the core environmental stress response cluster, pre-treatment of Arabidopsis thaliana with a 24 h long 4 °C cold stimulus modifies cold regulation of gene expression for up to a week at 20 °C, although the primary cold effects are reverted within the first 24 h. Such memory-based regulation is called priming. Here, we analyse the effect of 24 h cold priming on cold regulation of gene expression on a transcriptome-wide scale and investigate if and how cold priming affects light regulation of gene expression.Results: Cold-priming affected cold and excess light regulation of a small subset of genes. In contrast to the strong gene co-regulation observed upon cold and light stress in not-primed plants, most priming-sensitive genes were regulated in a stressor-specific manner in cold-primed plant. Furthermore, almost as much genes were inversely regulated as co-regulated by a 24 h long 4 °C cold treatment and exposure to heat-filtered high light (800 µmol quanta m-2 s-1). Gene ontology enrichment analysis revealed that cold priming preferentially supports expression of genes involved in the defence against plant pathogens upon cold triggering. The regulation took place on the cost of the expression of genes involved in growth regulation and transport. On the contrary, cold priming resulted in stronger expression of genes regulating metabolism and development and weaker expression of defence genes in response to high light triggering. qPCR with independently cultivated and treated replicates confirmed the trends observed in the RNASeq guide experiment.Conclusion: A 24 h long priming cold stimulus activates a several days lasting stress memory that controls cold and light regulation of gene expression and adjusts growth and defence regulation in a stressor-specific manner.

scholarly journals How (Epi)Genetic Regulation of the LIM-Domain Protein FHL2 Impacts Multifactorial Disease

Cells ◽  
2021 ◽  
Vol 10 (10) ◽  
pp. 2611
Author(s):  
Jayron J. Habibe ◽  
Maria P. Clemente-Olivo ◽  
Carlie J. de Vries
Keyword(s):  
Gene Expression ◽  
Genetic Variation ◽  
Current Knowledge ◽  
Genetic Regulation ◽  
Regulation Of Gene Expression ◽  
Lim Domain ◽  
Multifactorial Diseases ◽  
Lim Domains ◽  
Age Related

Susceptibility to complex pathological conditions such as obesity, type 2 diabetes and cardiovascular disease is highly variable among individuals and arises from specific changes in gene expression in combination with external factors. The regulation of gene expression is determined by genetic variation (SNPs) and epigenetic marks that are influenced by environmental factors. Aging is a major risk factor for many multifactorial diseases and is increasingly associated with changes in DNA methylation, leading to differences in gene expression. Four and a half LIM domains 2 (FHL2) is a key regulator of intracellular signal transduction pathways and the FHL2 gene is consistently found as one of the top hyper-methylated genes upon aging. Remarkably, FHL2 expression increases with methylation. This was demonstrated in relevant metabolic tissues: white adipose tissue, pancreatic β-cells, and skeletal muscle. In this review, we provide an overview of the current knowledge on regulation of FHL2 by genetic variation and epigenetic DNA modification, and the potential consequences for age-related complex multifactorial diseases.

scholarly journals Tissue specific regulation of transcription in endometrium and association with disease

2020 ◽  
Vol 35 (2) ◽  
pp. 377-393 ◽  
Author(s):  
Sally Mortlock ◽  
Raden I Kendarsari ◽  
Jenny N Fung ◽  
Greg Gibson ◽  
Fei Yang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Association Study ◽  
Genetic Variants ◽  
Genetic Regulation ◽  
Regulation Of Gene Expression ◽  
Enrichment Analysis ◽  
Reproductive Traits ◽  
Genetic Effects ◽  
Genotype Data ◽  
Tissue Specific

Abstract STUDY QUESTION Are genetic effects on endometrial gene expression tissue specific and/or associated with reproductive traits and diseases? SUMMARY ANSWER Analyses of RNA-sequence data and individual genotype data from the endometrium identified novel and disease associated, genetic mechanisms regulating gene expression in the endometrium and showed evidence that these mechanisms are shared across biologically similar tissues. WHAT IS KNOWN ALREADY The endometrium is a complex tissue vital for female reproduction and is a hypothesized source of cells initiating endometriosis. Understanding genetic regulation specific to, and shared between, tissue types can aid the identification of genes involved in complex genetic diseases. STUDY DESIGN, SIZE, DURATION RNA-sequence and genotype data from 206 individuals was analysed and results were compared with large publicly available datasets. PARTICIPANTS/MATERIALS, SETTING, METHODS RNA-sequencing and genotype data from 206 endometrial samples was used to identify the influence of genetic variants on gene expression, via expression quantitative trait loci (eQTL) analysis and to compare these endometrial eQTLs with those in other tissues. To investigate the association between endometrial gene expression regulation and reproductive traits and diseases, we conducted a tissue enrichment analysis, transcriptome-wide association study (TWAS) and summary data-based Mendelian randomisation (SMR) analyses. Transcriptomic data was used to test differential gene expression between women with and without endometriosis. MAIN RESULTS AND THE ROLE OF CHANCE A tissue enrichment analysis with endometriosis genome-wide association study summary statistics showed that genes surrounding endometriosis risk loci were significantly enriched in reproductive tissues. A total of 444 sentinel cis-eQTLs (P < 2.57 × 10−9) and 30 trans-eQTLs (P < 4.65 × 10−13) were detected, including 327 novel cis-eQTLs in endometrium. A large proportion (85%) of endometrial eQTLs are present in other tissues. Genetic effects on endometrial gene expression were highly correlated with the genetic effects on reproductive (e.g. uterus, ovary) and digestive tissues (e.g. salivary gland, stomach), supporting a shared genetic regulation of gene expression in biologically similar tissues. The TWAS analysis indicated that gene expression at 39 loci is associated with endometriosis, including five known endometriosis risk loci. SMR analyses identified potential target genes pleiotropically or causally associated with reproductive traits and diseases including endometriosis. However, without taking account of genetic variants, a direct comparison between women with and without endometriosis showed no significant difference in endometrial gene expression. LARGE SCALE DATA The eQTL dataset generated in this study is available at http://reproductivegenomics.com.au/shiny/endo_eqtl_rna/. Additional datasets supporting the conclusions of this article are included within the article and the supplementary information files, or are available on reasonable request. LIMITATIONS, REASONS FOR CAUTION Data are derived from fresh tissue samples and expression levels are an average of expression from different cell types within the endometrium. Subtle cell-specifc expression changes may not be detected and differences in cell composition between samples and across the menstrual cycle will contribute to sample variability. Power to detect tissue specific eQTLs and differences between women with and without endometriosis was limited by the sample size in this study. The statistical approaches used in this study identify the likely gene targets for specific genetic risk factors, but not the functional mechanism by which changes in gene expression may influence disease risk. WIDER IMPLICATIONS OF THE FINDINGS Our results identify novel genetic variants that regulate gene expression in endometrium and the majority of these are shared across tissues. This allows analysis with large publicly available datasets to identify targets for female reproductive traits and diseases. Much larger studies will be required to identify genetic regulation of gene expression that will be specific to endometrium. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by the National Health and Medical Research Council (NHMRC) under project grants GNT1026033, GNT1049472, GNT1046880, GNT1050208, GNT1105321, GNT1083405 and GNT1107258. G.W.M is supported by a NHMRC Fellowship (GNT1078399). J.Y is supported by an ARC Fellowship (FT180100186). There are no competing interests.

Cytokinin Regulation of Gene Expression in the AHP Gene Family in Arabidopsis thaliana

2007 ◽  
Vol 26 (3) ◽  
pp. 229-244 ◽  
Author(s):  
Jana Hradilová ◽  
Jiří Malbeck ◽  
Břetislav Brzobohatý
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Gene Family ◽  
Regulation Of Gene Expression

scholarly journals Synchronization of senescence and desynchronization of flowering in Arabidopsis thaliana

AoB Plants ◽  
2020 ◽  
Vol 12 (3) ◽  
Author(s):  
Matin Miryeganeh
Keyword(s):  
Arabidopsis Thaliana ◽  
Recombinant Inbred Lines ◽  
Life Stage ◽  
Reproductive Traits ◽  
Reproductive Timing ◽  
Qtl Detection ◽  
Timing Of Reproduction ◽  
Temperature Regimes ◽  
Trait Locus ◽  
Germination Timing

Abstract In a recent publication, we proposed that adjusting lifespan in order to synchronize senescence is important for timing of reproduction, and we quantified the synchrony of reproductive timing relative to germination timing. Here, in a second sequential seeding experiment (SSE), the germination timing of Arabidopsis thaliana accessions was manipulated and plants were then grown under two different temperature regimes. Life stage traits of plants in each temperature regime were analysed and it was evaluated whether the cohorts were grouped according to age and/or environmental conditions. While flowering-related traits showed desynchrony among cohorts, striking synchrony in the timing of senescence among cohorts for each group was found. A quantitative trait locus (QTL) analysis using a genotyped population of ‘Cvi/Ler’ recombinant inbred lines (RILs) was then conducted. Novel and known loci were assigned to flowering and senescence timing. However, senescence synchrony resulted in low variation in senescence time and weak QTL detection for flowering termination. Overlapping flowering and senescence genes with loci affecting either of those traits were found and suggest a potential interdependency of reproductive traits.

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