scholarly journals Transcription factor binding sites in the pol gene intragenic regulatory region of HIV-1 are important for virus infectivity

2005 ◽  
Vol 33 (13) ◽  
pp. 4285-4310 ◽  
Author(s):  
V. Goffin
Keyword(s):  
Transcription Factor ◽  
Binding Sites ◽  
Regulatory Region ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Virus Infectivity ◽  
Factor Binding ◽  
Hiv 1

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.

scholarly journals Genetic Diversity in HIV-1 Subtype C LTR from Brazil and Mozambique Generates New Transcription Factor-Binding Sites

Viruses ◽  
2014 ◽  
Vol 6 (6) ◽  
pp. 2495-2504 ◽  
Author(s):  
José Boullosa ◽  
Mahesh Bachu ◽  
Dulce Bila ◽  
Udaykumar Ranga ◽  
Theodoro Süffert ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Transcription Factor ◽  
Binding Sites ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
Subtype C ◽  
Factor Binding ◽  
Hiv 1

scholarly journals DNA Replication Efficiency Depends on Transcription Factor-Binding Sites

2001 ◽  
Vol 75 (12) ◽  
pp. 5638-5645 ◽  
Author(s):  
William J. Turner ◽  
Mary E. Woodworth
Keyword(s):  
Transcription Factor ◽  
Dna Replication ◽  
Binding Sites ◽  
Regulatory Region ◽  
Simian Virus 40 ◽  
Transcription Factor Binding Sites ◽  
Transcription Factor Binding ◽  
T Antigen ◽  
Replication Efficiency ◽  
Factor Binding

ABSTRACT Naturally arising variants of simian virus 40 (SV40), generated by serial passage of the virus at high multiplicities of infection, provide important insight into the role of transcription factor-binding sites in enhancing DNA replication. Although the variants that arise from numerous recombination events are the result of selective pressure to replicate more efficiently than the other variants in the infection, there is no transcription pressure. Therefore, it is interesting that a minimum of two viral Sp1 transcription factor-binding sites are retained and that host AP-1 and NF-1 transcription factor-binding sites are incorporated into the 100-bp regulatory region that maximizes DNA replication in these variants. We cotransfected COS-1 cells (that provide viral large T antigen for DNA replication) to examine the effect of transcription factor-binding sites on the replication of plasmid constructs that contain the SV40 origin of replication (ori). The level of relative replication efficiency (RRE) depends on the number and type of transcription factor-binding sites. Replication increases as the number of transcription factor-binding sites increases within the regulatory region of the variants; AP-1 sites are more effective than NF-1 transcription factor-binding sites. Competition between constructs in transfections magnifies the difference in their RREs. The results indicate that transcription factor-binding sites play an important role in enhancing DNA replication.

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