Regulation of Gene Expression and Transcription Factor Binding Activity during Cellular Aging

Neurosignals ◽  
1996 ◽  
Vol 5 (3) ◽  
pp. 130-138 ◽  
Author(s):  
Muthupalaniappan Meyyappan ◽  
Peter W. Atadja ◽  
Karl T. Riabowol
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Regulation Of Gene Expression ◽  
Transcription Factor Binding ◽  
Binding Activity ◽  
Cellular Aging ◽  
Factor Binding

scholarly journals Quantitative models for accelerated protein dissociation from nucleosomal DNA

2014 ◽  
Vol 42 (15) ◽  
pp. 9753-9760 ◽  
Author(s):  
Cai Chen ◽  
Ralf Bundschuh
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factors ◽  
Specific Binding ◽  
Regulation Of Gene Expression ◽  
Transcription Factor Binding ◽  
General Mechanism ◽  
Binding Model ◽  
Factor Binding ◽  
Protein Dissociation

Abstract Binding of transcription factors to their binding sites in promoter regions is the fundamental event in transcriptional gene regulation. When a transcription factor binding site is located within a nucleosome, the DNA has to partially unwrap from the nucleosome to allow transcription factor binding. This reduces the rate of transcription factor binding and is a known mechanism for regulation of gene expression via chromatin structure. Recently a second mechanism has been reported where transcription factor off-rates are dramatically increased when binding to target sites within the nucleosome. There are two possible explanations for such an increase in off-rate short of an active role of the nucleosome in pushing the transcription factor off the DNA: (i) for dimeric transcription factors the nucleosome can change the equilibrium between monomeric and dimeric binding or (ii) the nucleosome can change the equilibrium between specific and non-specific binding to the DNA. We explicitly model both scenarios and find that dimeric binding can explain a large increase in off-rate while the non-specific binding model cannot be reconciled with the large, experimentally observed increase. Our results suggest a general mechanism how nucleosomes increase transcription factor dissociation to promote exchange of transcription factors and regulate gene expression.

scholarly journals Bioinformatics Analysis of SNPs in IL-6 Gene Promoter of Jinghai Yellow Chickens

Genes ◽  
2018 ◽  
Vol 9 (9) ◽  
pp. 446 ◽  
Author(s):  
Shijie Xin ◽  
Xiaohui Wang ◽  
Guojun Dai ◽  
Jingjing Zhang ◽  
Tingting An ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Binding Sites ◽  
Promoter Region ◽  
Bioinformatics Analysis ◽  
Cpg Islands ◽  
Regulatory Region ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Factor Binding

The proinflammatory cytokine, interleukin-6 (IL-6), plays a critical role in many chronic inflammatory diseases, particularly inflammatory bowel disease. To investigate the regulation of IL-6 gene expression at the molecular level, genomic DNA sequencing of Jinghai yellow chickens (Gallus gallus) was performed to detect single-nucleotide polymorphisms (SNPs) in the region −2200 base pairs (bp) upstream to 500 bp downstream of IL-6. Transcription factor binding sites and CpG islands in the IL-6 promoter region were predicted using bioinformatics software. Twenty-eight SNP sites were identified in IL-6. Four of these 28 SNPs, three [−357 (G > A), −447 (C > G), and −663 (A > G)] in the 5′ regulatory region and one in the 3′ non-coding region [3177 (C > T)] are not labelled in GenBank. Bioinformatics analysis revealed 11 SNPs within the promoter region that altered putative transcription factor binding sites. Furthermore, the C-939G mutation in the promoter region may change the number of CpG islands, and SNPs in the 5′ regulatory region may influence IL-6 gene expression by altering transcription factor binding or CpG methylation status. Genetic diversity analysis revealed that the newly discovered A-663G site significantly deviated from Hardy-Weinberg equilibrium. These results provide a basis for further exploration of the promoter function of the IL-6 gene and the relationships of these SNPs to intestinal inflammation resistance in chickens.

MGMT DNA repair gene promoter/enhancer haplotypes alter transcription factor binding and gene expression

2016 ◽  
Vol 39 (5) ◽  
pp. 435-447 ◽  
Author(s):  
Meixiang Xu ◽  
Courtney E. Cross ◽  
Jordan T. Speidel ◽  
Sherif Z. Abdel-Rahman
Keyword(s):  
Gene Expression ◽  
Dna Repair ◽  
Transcription Factor ◽  
Gene Promoter ◽  
Transcription Factor Binding ◽  
Repair Gene ◽  
Factor Binding ◽  
Dna Repair Gene

Age-Associated Changes in Basal c-fos Transcription Factor Binding Activity in Rat Hearts

1996 ◽  
Vol 229 (2) ◽  
pp. 432-437 ◽  
Author(s):  
Hui Tsou ◽  
Gohar Azhar ◽  
Xiu Gui Lu ◽  
Suzanne Kovacs ◽  
Monica Peacocke ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Binding Activity ◽  
Factor Binding ◽  
Rat Hearts

scholarly journals Disease-gene discovery by integration of 3D gene expression and transcription factor binding affinities

2012 ◽  
Vol 29 (4) ◽  
pp. 468-475 ◽  
Author(s):  
Rosario M. Piro ◽  
Ivan Molineris ◽  
Ferdinando Di Cunto ◽  
Roland Eils ◽  
Rainer König
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Disease Gene ◽  
Gene Discovery ◽  
Transcription Factor Binding ◽  
Binding Affinities ◽  
Factor Binding ◽  
Disease Gene Discovery ◽  
3D Gene
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