scholarly journals Ordering up gene expression by slowing down transcription factor binding kinetics

2018 ◽  
Vol 65 (2) ◽  
pp. 401-406 ◽  
Author(s):  
Matthew J. Culyba
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Binding Kinetics ◽  
Factor Binding ◽  
Slowing Down

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

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

scholarly journals Extensive Divergence of Transcription Factor Binding in Drosophila Embryos with Highly Conserved Gene Expression

PLoS Genetics ◽  
2013 ◽  
Vol 9 (9) ◽  
pp. e1003748 ◽  
Author(s):  
Mathilde Paris ◽  
Tommy Kaplan ◽  
Xiao Yong Li ◽  
Jacqueline E. Villalta ◽  
Susan E. Lott ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Factor Binding ◽  
Conserved Gene ◽  
Drosophila Embryos

scholarly journals Methylation QTLs Are Associated with Coordinated Changes in Transcription Factor Binding, Histone Modifications, and Gene Expression Levels

PLoS Genetics ◽  
2014 ◽  
Vol 10 (9) ◽  
pp. e1004663 ◽  
Author(s):  
Nicholas E. Banovich ◽  
Xun Lan ◽  
Graham McVicker ◽  
Bryce van de Geijn ◽  
Jacob F. Degner ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Histone Modifications ◽  
Transcription Factor Binding ◽  
Expression Levels ◽  
Factor Binding ◽  
Gene Expression Levels

scholarly journals Allele-specific transcription factor binding to common and rare variants associated with disease and gene expression

2016 ◽  
Vol 135 (5) ◽  
pp. 485-497 ◽  
Author(s):  
Marco Cavalli ◽  
Gang Pan ◽  
Helena Nord ◽  
Ola Wallerman ◽  
Emelie Wallén Arzt ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Rare Variants ◽  
Transcription Factor Binding ◽  
Specific Transcription Factor ◽  
Factor Binding ◽  
Allele Specific

scholarly journals WAPL maintains dynamic cohesin to preserve lineage specific distal gene regulation

2019 ◽  
Author(s):  
Ning Qing Liu ◽  
Michela Maresca ◽  
Teun van den Brand ◽  
Luca Braccioli ◽  
Marijne M.G.A. Schijns ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Regulation ◽  
Transcription Factor ◽  
Binding Sites ◽  
Transcription Factor Binding ◽  
Ctcf Binding ◽  
Release Factor ◽  
Factor Binding ◽  
Active Enhancer ◽  
Lineage Specific Genes

SUMMARYThe cohesin complex plays essential roles in sister chromatin cohesin, chromosome organization and gene expression. The role of cohesin in gene regulation is incompletely understood. Here, we report that the cohesin release factor WAPL is crucial for maintaining a pool of dynamic cohesin bound to regions that are associated with lineage specific genes in mouse embryonic stem cells. These regulatory regions are enriched for active enhancer marks and transcription factor binding sites, but largely devoid of CTCF binding sites. Stabilization of cohesin, which leads to a loss of dynamic cohesin from these regions, does not affect transcription factor binding or active enhancer marks, but does result in changes in promoter-enhancer interactions and downregulation of genes. Acute cohesin depletion can phenocopy the effect of WAPL depletion, showing that cohesin plays a crucial role in maintaining expression of lineage specific genes. The binding of dynamic cohesin to chromatin is dependent on the pluripotency transcription factor OCT4, but not NANOG. Finally, dynamic cohesin binding sites are also found in differentiated cells, suggesting that they represent a general regulatory principle. We propose that cohesin dynamically binding to regulatory sites creates a favorable spatial environment in which promoters and enhancers can communicate to ensure proper gene expression.HIGHLIGHTSThe cohesin release factor WAPL is crucial for maintaining a pluripotency-specific phenotype.Dynamic cohesin is enriched at lineage specific loci and overlaps with binding sites of pluripotency transcription factors.Expression of lineage specific genes is maintained by dynamic cohesin binding through the formation of promoter-enhancer associated self-interaction domains.CTCF-independent cohesin binding to chromatin is controlled by the pioneer factor OCT4.

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