scholarly journals Analysis of Sequence Variation Underlying Tissue-specific Transcription Factor Binding and Gene Expression

2013 ◽  
Vol 34 (8) ◽  
pp. 1140-1148 ◽  
Author(s):  
Karen M. Lower ◽  
Marco De Gobbi ◽  
Jim R. Hughes ◽  
Christopher J. Derry ◽  
Helena Ayyub ◽  
...  
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Sequence Variation ◽  
Transcription Factor Binding ◽  
Tissue Specific ◽  
Specific Transcription Factor ◽  
Factor Binding

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 CpG-depleted promoters harbor tissue-specific transcription factor binding signals—implications for motif overrepresentation analyses

2009 ◽  
Vol 37 (19) ◽  
pp. 6305-6315 ◽  
Author(s):  
Helge G. Roider ◽  
Boris Lenhard ◽  
Aditi Kanhere ◽  
Stefan A. Haas ◽  
Martin Vingron
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Binding ◽  
Tissue Specific ◽  
Specific Transcription Factor ◽  
Factor Binding

scholarly journals Restriction of chromatin accessibility is necessary for appropriate enhancer expression

2018 ◽  
Author(s):  
Daniel W. Hagey ◽  
Susanne Klum ◽  
Cecile Zaouter ◽  
Jonas Muhr
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Common Factor ◽  
Transcription Factor Binding ◽  
Chromatin Accessibility ◽  
Specific Gene ◽  
Reporter Expression ◽  
Enhancer Activity ◽  
Tissue Specific ◽  
Factor Binding

AbstractTissue specific gene expression underpins cell type diversity, and arises from the cooperative activities of transcription factors and the chromatin landscape. It has been previously demonstrated that enhancers with specific arrangements of transcription factor binding motifs can bring together commonly and specifically expressed factors in order to stabilize chromatin accessibility and drive spatially restricted reporter expression within different regions of the CNS. However, when reporters were used to analyse the activity of enhancers bound differentially by a common factor in the endoderm and CNS, several examples of non-tissue specific reporter expression were observed. In order to judge whether or not this may have been due to the unregulated chromatin environment of exogenously delivered enhancer reporters, here we have analysed the chromatin landscape of cells from the CNS and endodermal tissues and find that this reflects neighbouring gene expression to a greater degree than transcription factor binding. This work demonstrates that chromatin accessibility plays an essential role in defining enhancer activity in distantly related cell types.

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.

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