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 AnnoMiner is a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Arno Meiler ◽  
Fabio Marchiano ◽  
Margaux Haering ◽  
Manuela Weitkunat ◽  
Frank Schnorrer ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Gene Expression Regulation ◽  
Control Cell ◽  
Transcriptional Regulators ◽  
Model Organisms ◽  
Specific Gene ◽  
Epigenetic Events ◽  
Transcription Factor Occupancy

AbstractGene expression regulation requires precise transcriptional programs, led by transcription factors in combination with epigenetic events. Recent advances in epigenomic and transcriptomic techniques provided insight into different gene regulation mechanisms. However, to date it remains challenging to understand how combinations of transcription factors together with epigenetic events control cell-type specific gene expression. We have developed the AnnoMiner web-server, an innovative and flexible tool to annotate and integrate epigenetic, and transcription factor occupancy data. First, AnnoMiner annotates user-provided peaks with gene features. Second, AnnoMiner can integrate genome binding data from two different transcriptional regulators together with gene features. Third, AnnoMiner offers to explore the transcriptional deregulation of genes nearby, or within a specified genomic region surrounding a user-provided peak. AnnoMiner’s fourth function performs transcription factor or histone modification enrichment analysis for user-provided gene lists by utilizing hundreds of public, high-quality datasets from ENCODE for the model organisms human, mouse, Drosophila and C. elegans. Thus, AnnoMiner can predict transcriptional regulators for a studied process without the strict need for chromatin data from the same process. We compared AnnoMiner to existing tools and experimentally validated several transcriptional regulators predicted by AnnoMiner to indeed contribute to muscle morphogenesis in Drosophila. AnnoMiner is freely available at http://chimborazo.ibdm.univ-mrs.fr/AnnoMiner/.

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.

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 NRF-1 and HIF-1α modulate activity of human VDAC1 gene promoter during starvation and hypoxia in HeLa cells

2020 ◽  
Author(s):  
Francesca Guarino ◽  
Federica Zinghirino ◽  
Lia Mela ◽  
Xena Pappalardo ◽  
Angela Messina ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factors ◽  
Promoter Activity ◽  
Gene Expression Regulation ◽  
Anion Channel ◽  
Expression Regulation ◽  
Cell Stress ◽  
Time Data ◽  
Voltage Dependent Anion Channel ◽  
Putative Promoter Region

AbstractVDAC (Voltage Dependent Anion Channel) is a family of pore forming protein located in the outer mitochondrial membrane. Its channel property ensures metabolites exchange between mitochondria and the rest of the cell resulting in metabolism and bioenergetics regulation, and in cell death and life switch. VDAC1 is the best characterized and most abundant isoform, and is involved in many pathologies, as cancer or neurodegenerative diseases. However, little information is available about its gene expression regulation in normal and/or pathological conditions. In this work, we explored VDAC1 gene expression regulation in normal conditions and in the contest of metabolic and energetic mitochondrial dysfunction and cell stress. The most active area of the putative promoter region was characterized in terms of transcription factors responsive elements both by bioinformatic studies and promoter activity experiments. In particular, we found a predominant presence of NRF-1 together with other transcription factors binding sites, involved in cell growth, proliferation, development and we studied their prevalence in gene activity. Furthermore, upon depletion of nutrients or controlled hypoxia, as reported in various pathologies, we found that VDAC1 transcripts levels were significantly increased in a time related manner. VDAC1 promoter activity was also validated by gene reporter assays. According to PCR real-time data, it was confirmed that VDAC1 promoter activity is further stimulated when are exposed to stress. A bioinformatic survey suggested NRF-1 e HIF-1α as the most active TFBS. Their validation was obtained by mutagenesis and overexpression experiments. In conclusion, we demonstrated experimentally the involvement of both NRF-1 and HIF-1α in the regulation of VDAC1 promoter activation at basal level and in cell stress conditions.

scholarly journals AnnoMiner: a new web-tool to integrate epigenetics, transcription factor occupancy and transcriptomics data to predict transcriptional regulators

2021 ◽  
Author(s):  
Arno Meiler ◽  
Fabio Marchiano ◽  
Michaela Weikunat ◽  
Frank Schnorrer ◽  
Bianca H. Habermann
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Gene Expression Regulation ◽  
Control Cell ◽  
Transcriptional Regulators ◽  
Model Organisms ◽  
Specific Gene ◽  
Epigenetic Events ◽  
Transcription Factor Occupancy

AbstractGene expression regulation requires precise transcriptional programs, led by transcription factors in combination with epigenetic events. Recent advances in epigenomic and transcriptomic techniques provided insight into different gene regulation mechanisms. However, to date it remains challenging to understand how combinations of transcription factors together with epigenetic events control cell-type specific gene expression. We developed the AnnoMiner web-server and introduce an innovative and flexible way to annotate and integrate epigenetic, and transcription factor occupancy data. First, AnnoMiner annotates user-provided peaks with gene features. Second, AnnoMiner can integrate genome binding data from two different transcriptional regulators together with gene features. Third, AnnoMiner offers to explore the transcriptional deregulation of 10 genes nearby a user-provided peak. AnnoMiner’s fourth function performs transcription factor or histone mark enrichment analysis for user-provided gene lists by utilizing hundreds of public, high-quality datasets from ENCODE for the model organisms human, mouse, Drosophila and C. elegans. Thus, AnnoMiner can predict transcriptional regulators for a studied process without the strict need for chromatin data from the same process. We compared AnnoMiner to existing tools and experimentally validated several transcriptional regulators predicted by AnnoMiner to indeed contribute to muscle morphogenesis in Drosophila. AnnoMiner is freely available at http://chimborazo.ibdm.univ-mrs.fr/AnnoMiner/.

Subnuclear compartmentalization of sequence-specific transcription factors and regulation of eukaryotic gene expression

2005 ◽  
Vol 83 (4) ◽  
pp. 535-547 ◽  
Author(s):  
Gareth N Corry ◽  
D Alan Underhill
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Transcriptional Activation ◽  
Current Knowledge ◽  
Nuclear Architecture ◽  
Subnuclear Localization ◽  
Modular Structures

To date, the majority of the research regarding eukaryotic transcription factors has focused on characterizing their function primarily through in vitro methods. These studies have revealed that transcription factors are essentially modular structures, containing separate regions that participate in such activities as DNA binding, protein–protein interaction, and transcriptional activation or repression. To fully comprehend the behavior of a given transcription factor, however, these domains must be analyzed in the context of the entire protein, and in certain cases the context of a multiprotein complex. Furthermore, it must be appreciated that transcription factors function in the nucleus, where they must contend with a variety of factors, including the nuclear architecture, chromatin domains, chromosome territories, and cell-cycle-associated processes. Recent examinations of transcription factors in the nucleus have clarified the behavior of these proteins in vivo and have increased our understanding of how gene expression is regulated in eukaryotes. Here, we review the current knowledge regarding sequence-specific transcription factor compartmentalization within the nucleus and discuss its impact on the regulation of such processes as activation or repression of gene expression and interaction with coregulatory factors.Key words: transcription, subnuclear localization, chromatin, gene expression, nuclear architecture.

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