scholarly journals Integrative analysis of SF-1 transcription factor dosage impact on genome-wide binding and gene expression regulation

2013 ◽  
Vol 41 (19) ◽  
pp. 8896-8907 ◽  
Author(s):  
Mabrouka Doghman ◽  
Bonald C. Figueiredo ◽  
Marco Volante ◽  
Mauro Papotti ◽  
Enzo Lalli
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Gene Expression Regulation ◽  
Expression Regulation ◽  
Integrative Analysis ◽  
Genome Wide

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 Uncovering divergence in gene expression regulation in the adaptation of yeast to nitrogen scarcity

2021 ◽  
Author(s):  
Carlos A. Villarroel ◽  
Paulo Canessa ◽  
Macarena Bastias ◽  
Francisco A Cubillos
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Gene Expression Regulation ◽  
Transcription Factor Binding ◽  
Chromatin Accessibility ◽  
Expression Regulation ◽  
Factor Binding ◽  
Allele Specific ◽  
The Impact ◽  
Allelic Bias

Saccharomyces cerevisiae rewires its transcriptional output to survive stressful environments, such as nitrogen scarcity under fermentative conditions. Although divergence in nitrogen metabolism has been described among natural yeast populations, the impact of regulatory genetic variants modulating gene expression and nitrogen consumption remains to be investigated. Here, we employed an F1 hybrid from two contrasting S. cerevisiae strains, providing a controlled genetic environment to map cis factors involved in the divergence of gene expression regulation in response to nitrogen scarcity. We used a dual approach to obtain genome-wide allele-specific profiles of chromatin accessibility, transcription factor binding, and gene expression through ATAC-seq and RNA-seq. We observed large variability in allele-specific expression and accessibility between the two genetic backgrounds, with a third of these differences specific to a deficient nitrogen environment. Furthermore, we discovered events of allelic bias in gene expression correlating with allelic bias in transcription factor binding solely under nitrogen scarcity, where the majority of these transcription factors orchestrates the Nitrogen Catabolite Repression regulatory pathway and demonstrates a cis x environment-specific response. Our approach allowed us to find cis variants modulating gene expression, chromatin accessibility and allelic differences in transcription factor binding in response to low nitrogen culture conditions.

Antibody free ELISA-like assay for the detection of transcription factors based on double-stranded DNA thermostability

The Analyst ◽  
2020 ◽  
Vol 145 (9) ◽  
pp. 3339-3344
Author(s):  
Yue Sun ◽  
Zhiyan Li ◽  
Choiwan Lau ◽  
Jianzhong Lu
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Gene Expression Regulation ◽  
Expression Regulation ◽  
Disease Development ◽  
Chemiluminescence Assay ◽  
Double Stranded Dna

Transcription factors (TFs) play critical roles in gene expression regulation and disease development. Herein we report a chemiluminescence assay for the detection of transcription factor based on double-stranded DNA thermostability.

scholarly journals Genome-wide gene expression regulation as a function of genotype and age in C. elegans

2010 ◽  
Vol 20 (7) ◽  
pp. 929-937 ◽  
Author(s):  
A. Vinuela ◽  
L. B. Snoek ◽  
J. A. G. Riksen ◽  
J. E. Kammenga
Keyword(s):  
Gene Expression ◽  
Gene Expression Regulation ◽  
Expression Regulation ◽  
C Elegans ◽  
Genome Wide ◽  
Genome Wide Gene Expression
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