scholarly journals Widespread inter-individual gene expression variability in Arabidopsis thaliana

2018 ◽  
Author(s):  
Sandra Cortijo ◽  
Zeynep Aydin ◽  
Sebastian Ahnert ◽  
James Locke
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Time Course ◽  
Gene Expression Regulation ◽  
Individual Variability ◽  
Individual Gene ◽  
Expression Variability ◽  
Unicellular Organisms ◽  
Environmental Responses ◽  
The Impact

AbstractA fundamental question in biology is how gene expression is regulated to give rise to a phenotype. However, transcriptional variability is rarely considered and could influence the relationship between genotype and phenotype. It is known in unicellular organisms that gene expression is often noisy rather than uniform and this has been proposed to be beneficial when environmental conditions are unpredictable. However, little is known about transcriptional variability in plants. Using transcriptomic approaches, we analysed gene expression variability between individual Arabidopsis thaliana plants growing in identical conditions over a 24 hour time-course. We identified hundreds of genes that exhibit high inter-individual variability and found that many are involved in environmental responses. We also identified factors that might facilitate gene expression variability, such as gene length, the number of transcription factors regulating the genes and the chromatin environment. These results shed new light on the impact of transcriptional variability in gene expression regulation in plants.

scholarly journals Widespread inter‐individual gene expression variability in Arabidopsis thaliana

2019 ◽  
Vol 15 (1) ◽  
Author(s):  
Sandra Cortijo ◽  
Zeynep Aydin ◽  
Sebastian Ahnert ◽  
James CW Locke
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Individual Gene ◽  
Expression Variability

scholarly journals Lack of Obvious Influence of PLLA Nanofibers on the Gene Expression of BMP-2 and VEGF during Growth and Differentiation of Human Mesenchymal Stem Cells

2009 ◽  
Vol 9 ◽  
pp. 313-319 ◽  
Author(s):  
Markus D. Schofer ◽  
S. Fuchs-Winkelmann ◽  
C. Wack ◽  
M. Rudisile ◽  
R. Dersch ◽  
...  
Keyword(s):  
Gene Expression ◽  
Growth Factor ◽  
Time Course ◽  
Negative Impact ◽  
Fracture Repair ◽  
Bone Morphogenetic Protein 2 ◽  
Vegf Gene ◽  
Down Regulation ◽  
Artificial Graft ◽  
The Impact

Growth factors like bone morphogenetic protein 2 (BMP-2) and vascular endothelial growth factor (VEGF) play an important role in bone remodeling and fracture repair. Therefore, with respect to tissue engineering, an artificial graft should have no negative impact on the expression of these factors. In this context, the aim of this study was to analyze the impact of poly(L-lactic acid) (PLLA) nanofibers on VEGF and BMP-2 gene expression during the time course of human mesenchymal stem cell (hMSC) differentiation towards osteoblasts. PLLA matrices were seeded with hMSCs and cultivated over a period of 22 days under growth and osteoinductive conditions, and analyzed during the course of culture, with respect to gene expression of VEGF and BMP-2. Furthermore, BMP-2–enwoven PLLA nanofibers were used in order to elucidate whether initial down-regulation of growth factor expression could be compensated. Although there was a great interpatient variability with respect to the expression of VEGF and BMP-2, PLLA nanofibers tend to result in a down-regulation in BMP-2 expression during the early phase of cultivation. This effect was diminished in the case of VEGF gene expression. The initial down-regulation was overcome when BMP-2 was directly incorporated into the PLLA nanofibers by electrospinning. Furthermore, the incorporation of BMP-2 into the PLLA nanofibers resulted in an increase in VEGF gene expression. Summarized, the results indicate that the PLLA nanofibers have little effect on growth factor production. An enhancement in gene expression of BMP-2 and VEGF can be achieved by an incorporation of BMP-2 into the PLLA nanofibers.

The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana

2018 ◽  
Vol 35 (16) ◽  
pp. 2718-2723 ◽  
Author(s):  
Tamir Tuller ◽  
Alon Diament ◽  
Avital Yahalom ◽  
Assaf Zemach ◽  
Shimshi Atar ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Arabidopsis Thaliana ◽  
Gene Expression Regulation ◽  
Developmental Pathways ◽  
Cop9 Signalosome ◽  
Supplementary Information ◽  
Loss Of Function ◽  
Genome Wide ◽  
High Level

Abstract Motivation The COP9 signalosome is a highly conserved multi-protein complex consisting of eight subunits, which influences key developmental pathways through its regulation of protein stability and transcription. In Arabidopsis thaliana, mutations in the COP9 signalosome exhibit a number of diverse pleiotropic phenotypes. Total or partial loss of COP9 signalosome function in Arabidopsis leads to misregulation of a number of genes involved in DNA methylation, suggesting that part of the pleiotropic phenotype is due to global effects on DNA methylation. Results We determined and analyzed the methylomes and transcriptomes of both partial- and total-loss-of-function Arabidopsis mutants of the COP9 signalosome. Our results support the hypothesis that the COP9 signalosome has a global genome-wide effect on methylation and that this effect is at least partially encoded in the DNA. Our analyses suggest that COP9 signalosome-dependent methylation is related to gene expression regulation in various ways. Differentially methylated regions tend to be closer in the 3D conformation of the genome to differentially expressed genes. These results suggest that the COP9 signalosome has a more comprehensive effect on gene expression than thought before, and this is partially related to regulation of methylation. The high level of COP9 signalosome conservation among eukaryotes may also suggest that COP9 signalosome regulates methylation not only in plants but also in other eukaryotes, including humans. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Pathogen Genetic Control of Transcriptome Variation in the Arabidopsis thaliana – Botrytis cinerea Pathosystem

Genetics ◽  
2020 ◽  
Vol 215 (1) ◽  
pp. 253-266 ◽  
Author(s):  
Nicole E. Soltis ◽  
Celine Caseys ◽  
Wei Zhang ◽  
Jason A. Corwin ◽  
Susanna Atwell ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Botrytis Cinerea ◽  
Gene Expression Regulation ◽  
Expression Regulation ◽  
Necrotrophic Pathogen ◽  
Control Of Gene Expression ◽  
Genome Wide ◽  
Pathogen Control ◽  
Transcriptome Variation

In plant–pathogen relations, disease symptoms arise from the interaction of the host and pathogen genomes. Host–pathogen functional gene interactions are well described, whereas little is known about how the pathogen genetic variation modulates both organisms’ transcriptomes. To model and generate hypotheses on a generalist pathogen control of gene expression regulation, we used the Arabidopsis thaliana–Botrytis cinerea pathosystem and the genetic diversity of a collection of 96 B. cinerea isolates. We performed expression-based genome-wide association (eGWA) for each of 23,947 measurable transcripts in Arabidopsis (host), and 9267 measurable transcripts in B. cinerea (pathogen). Unlike other eGWA studies, we detected a relative absence of locally acting expression quantitative trait loci (cis-eQTL), partly caused by structural variants and allelic heterogeneity hindering their identification. This study identified several distantly acting trans-eQTL linked to eQTL hotspots dispersed across Botrytis genome that altered only Botrytis transcripts, only Arabidopsis transcripts, or transcripts from both species. Gene membership in the trans-eQTL hotspots suggests links between gene expression regulation and both known and novel virulence mechanisms in this pathosystem. Genes annotated to these hotspots provide potential targets for blocking manipulation of the host response by this ubiquitous generalist necrotrophic pathogen.

scholarly journals The Impact of MicroRNAs on Brain Aging and Neurodegeneration

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Stephan P. Persengiev ◽  
Ivanela I. Kondova ◽  
Ronald E. Bontrop
Keyword(s):  
Gene Expression ◽  
Target Genes ◽  
Gene Expression Regulation ◽  
Brain Aging ◽  
Functional Decline ◽  
System Level ◽  
Model Organisms ◽  
Small Noncoding Rnas ◽  
The Impact ◽  
Gene Expression Levels

The molecular instructions that govern gene expression regulation are encoded in the genome and ultimately determine the morphology and functional specifications of the human brain. As a consequence, changes in gene expression levels might be directly related to the functional decline associated with brain aging. Small noncoding RNAs, including miRNAs, comprise a group of regulatory molecules that modulate the expression of hundred of genes which play important roles in brain metabolism. Recent comparative studies in humans and nonhuman primates revealed that miRNAs regulate multiple pathways and interconnected signaling cascades that are the basis for the cognitive decline and neurodegenerative disorders during aging. Identifying the roles of miRNAs and their target genes in model organisms combined with system-level studies of the brain would provide more comprehensive understanding of the molecular basis of brain deterioration during the aging process.

The impact of space environment on gene expression in Arabidopsis thaliana seedlings

2017 ◽  
Vol 60 (6) ◽  
pp. 902-910 ◽  
Author(s):  
HuaSheng Li ◽  
JinYing Lu ◽  
Hui Zhao ◽  
Qiao Sun ◽  
FuTong Yu ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Space Environment ◽  
The Impact

scholarly journals Time Course of Microbiologic Outcome and Gene Expression in Candida albicans during and following In Vitro and In Vivo Exposure to Fluconazole

2006 ◽  
Vol 50 (4) ◽  
pp. 1311-1319 ◽  
Author(s):  
A. Lepak ◽  
J. Nett ◽  
L. Lincoln ◽  
K. Marchillo ◽  
D. Andes
Keyword(s):  
Gene Expression ◽  
Candida Albicans ◽  
Time Course ◽  
Dependent Manner ◽  
Time Points ◽  
In Vivo Expression ◽  
The Impact ◽  
The Relationship

ABSTRACT Pharmacodynamics (PD) considers the relationship between drug exposure and effect. The two factors that have been used to distinguish the PD behaviors of antimicrobials are the impact of concentration on the extent of organism killing and the duration of persistent microbiologic suppression (postantibiotic effect). The goals of these studies were (i) to examine the relationship between antimicrobial PD and gene expression and (ii) to gain insight into the mechanism of fluconazole effects persisting following exposure. Microarrays were used to estimate the transcriptional response of Candida albicans to a supra-MIC F exposure over time in vitro. Fluconazole at four times the MIC was added to a log-phase C. albicans culture, and cells were collected to determine viable growth and for microarray analyses. We identified differential expression of 18% of all genes for at least one of the time points. More genes were upregulated (n = 1,053 [16%]) than downregulated (174 [3%]). Of genes with known function that were upregulated during exposure, most were related to plasma membrane/cell wall synthesis (18%), stress responses (7%), and metabolism (6%). The categories of downregulated genes during exposure included protein synthesis (15%), DNA synthesis/repair (7%), and transport (7%) genes. The majority of genes identified at the postexposure time points were from the protein (17%) and DNA (7%) synthesis categories. In subsequent studies, three genes (CDR1, CDR2, and ERG11) were examined in greater detail (more concentration and time points) following fluconazole exposure in vitro and in vivo. Expression levels from the in vitro and in vivo studies were congruent. CDR1 and CDR2 transcripts were reduced during in vitro fluconazole exposure and during supra-MIC exposure in vivo. However, in the postexposure period, the mRNA abundance of both pumps increased. ERG11 expression increased during exposure and fell in the postexposure period. The expression of the three genes responded in a dose-dependent manner. In sum, the microarray data obtained during and following fluconazole exposure identified genes both known and unknown to be affected by this drug class. The expanded in vitro and in vivo expression data set underscores the importance of considering the time course of exposure in pharmacogenomic investigations.

scholarly journals Involvement of FLOWERING LOCUS T in microgravity response of Arabidopsis thaliana plants under long- and short-day conditions

2021 ◽  
Author(s):  
Lihua Wang ◽  
Junyan Xie ◽  
Yuanyuan Wu ◽  
Chenghong Mou ◽  
Yuwei Jiao ◽  
...  
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Fluorescent Protein ◽  
Higher Plants ◽  
Reproductive Stage ◽  
Vegetative Stage ◽  
Green Fluorescent Protein Gene ◽  
Flowering Locus T ◽  
Flowering Locus ◽  
The Impact

Abstract Microgravity have an impact on growth and development of higher plants in space at both vegetative stage and reproductive stage. A great deal of information has been available on the vegetative stage in space, but relatively little is known about the influence of microgravity on plants at the reproductive stage. In this study, we constructed a transgenic Arabidopsis thaliana plants expressing flowering control gene, FLOWERING LOCUS T (FT), together with green fluorescent protein gene(GFP) under control of a heat shock-inducible promoter (HSP17.4), by which we induced FT expression inflight through remote controlling heating shock treatment. Inflight photography data showed that induction of FT expression in plants in space could counteract the impact of microgravity and promote flowering. Whole-genome microarray analysis of gene expression changes in leaves of wild-type and these transgenic plants grown under different photoperiod conditions in space indicated that the function of the photoperiod-related microgravity response genes are mainly involved in protein synthesis and post-translation protein modulation, notably protein phosphorylation. In addition, changes of circadian component gene expression in response to microgravity under different photoperiod indicated that role of circadian oscillator could act as integrators of microgravity response and photoperiodic signals in Arabidopsis plant grown in space.

scholarly journals Floral pathway integrator gene expression mediates gradual transmission of environmental and endogenous cues to flowering time

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3197 ◽  
Author(s):  
Aalt D.J. van Dijk ◽  
Jaap Molenaar
Keyword(s):  
Gene Expression ◽  
Arabidopsis Thaliana ◽  
Genetic Variation ◽  
Reproductive Success ◽  
Environmental Factors ◽  
Flowering Time ◽  
Genetic Networks ◽  
Expression Levels ◽  
Quantitative Level ◽  
The Impact

The appropriate timing of flowering is crucial for the reproductive success of plants. Hence, intricate genetic networks integrate various environmental and endogenous cues such as temperature or hormonal statues. These signals integrate into a network of floral pathway integrator genes. At a quantitative level, it is currently unclear how the impact of genetic variation in signaling pathways on flowering time is mediated by floral pathway integrator genes. Here, using datasets available from literature, we connect Arabidopsis thaliana flowering time in genetic backgrounds varying in upstream signalling components with the expression levels of floral pathway integrator genes in these genetic backgrounds. Our modelling results indicate that flowering time depends in a quite linear way on expression levels of floral pathway integrator genes. This gradual, proportional response of flowering time to upstream changes enables a gradual adaptation to changing environmental factors such as temperature and light.

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