First insights into the molecular basis association between promoter polymorphisms of the IL1B gene and Helicobacter pylori infection in the Sudanese population: computational approach

Autor: Ali Elbagir Ali Mohamed, Mohamed Hassan, Bashir M. Osman Arbab, Einas Babiker Idris, Abeer Babiker Idris, El-Amin Mohamed Ibrahim, Amany Eltayib Ataelmanan
Rok vydání: 2021
Předmět:
Male
Interleukin-1beta
lcsh:QR1-502
In silico analysis
lcsh:Microbiology
Sudan
0302 clinical medicine
Gene expression
Promoter Regions
Genetic
Conserved Sequence
Aged
80 and over
Genetics
0303 health sciences
education.field_of_study
Middle Aged
Female
030211 gastroenterology & hepatology
Research Article
5′- region
Adult
Microbiology (medical)
Adolescent
Pan troglodytes
In silico
Population
Single-nucleotide polymorphism
Biology
Polymorphism
Single Nucleotide
Microbiology
Helicobacter Infections
Young Adult
03 medical and health sciences
Dogs
Animals
Humans
Computer Simulation
Genetic Predisposition to Disease
education
Gene
Genotyping
Aged
030304 developmental biology
Helicobacter pylori
Computational Biology
IL1B
biology.organism_classification
Macaca mulatta
Rats
DNA binding site
Cattle
H. pylori
Zdroj: BMC Microbiology, Vol 21, Iss 1, Pp 1-15 (2021)
BMC Microbiology
ISSN: 1471-2180
Popis: Background: Helicobacter pylori (H. pylori) infects nearly half of the world’s population with a variation in incidence among different geographic regions. Genetic variants in the promoter regions of IL1B gene can affect cytokine expression and creates a condition of hypoacidity which favors the survival and colonization of H. pylori. Aim: To characterize the polymorphic sites in the 5’- region [-687_+297] of IL1B in H. pylori infection using in silico tools.Methods: Genomic DNA was extracted from 122 gastric biopsies and genotyping of IL1B-31 polymorphism was performed using PCR with confronting two-pair primer (PCR-CTPP) to investigate its association with the susceptibility to H. pylori infection in the Sudanese population. In addition, Sanger sequencing was applied to detect SNPs in the 5’-region [-687_+297] of IL1B in 14 H. pylori-infected patients; and bioinformatics analyses were used to predict whether these mutations would alter transcription factor binding sites (TFBSs) or composite regulatory elements (CEs) in this region. Also, comparative analysis was conducted for this region in 11 species using ECR browser and Mulan search engine. Results: A total of five nucleotide variations were detected in the 5’-regulatory region which led to the addition or alteration of the TFBSs and CEs. Genotyping of IL1B-31 C>T revealed a significant association between -31T and susceptibility to H. pylori infection in the studied population (P=0.0363). Comparative analysis showed conservation rates of IL1B upstream [−368_+10] region above 70% in chimpanzee, rhesus monkey, a domesticated dog, cow and rat.Conclusion: In H. pylori-infected patients, three detected SNPs (-338, -155 and -31) located in the IL1B promoter were predicted to alter TFBSs and CE, thereby might affecting gene expression. These in silico predictions provide insight for further experimental in vitro and in vivo studies of the regulation of IL1B expression and its relationship to H. pylori infection. However, recognition of regulatory motifs by computer algorithms is fundamental for understanding gene expression patterns.
Databáze: OpenAIRE
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