Abeer Babiker Idris1, Einas Babiker Idris2, Amany Eltayib Ataelmanan3, Ali Elbagir Ali Mohamed4, Bashir M Osman Arbab5, El-Amin Mohamed Ibrahim6, Mohamed A Hassan7,8,9. 1. Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan. abeer.babiker89@gmail.com. 2. Medical Laboratory Specialist, Department of Medical Microbiology, Rashid Medical Complex, Riyadh, Saudi Arabia. 3. Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Al-Gazirah, Wad Madani, Sudan. 4. Faculty of Medicine, University of Khartoum, Khartoum, Sudan. 5. Department of Internal Medicine, Modern Medical Centre, Khartoum, Sudan. 6. Department of Medical Microbiology, Faculty of Medical Laboratory Sciences, University of Khartoum, Khartoum, Sudan. 7. Department of Bioinformatics, Africa city of technology, Khartoum, Sudan. 8. Department of Bioinformatics, DETAGEN Genetic Diagnostics Center, Kayseri, Turkey. 9. Department of Translation Bioinformatics, Detavax Biotech, Kayseri, Turkey.
Abstract
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 the IL1B gene can affect cytokine expression and creates a condition of hypoacidity which favors the survival and colonization of H. pylori. Therefore, the aim of this study was to characterize the polymorphic sites in the 5'- region [-687_ + 297] of IL1B in H. pylori infection using in silico tools. RESULTS: A total of five nucleotide variations were detected in the 5'-regulatory region [-687_ + 297] of IL1B which led to the addition or alteration of transcription factor binding sites (TFBSs) or composite regulatory elements (CEs). Genotyping of IL1B - 31 C > T revealed a significant association between -31 T 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. CONCLUSIONS: In H. pylori-infected patients, three detected SNPs (- 338, - 155 and - 31) located in the IL1B promoter were predicted to alter TFBSs and CE, which might affect the 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, the recognition of regulatory motifs by computer algorithms is fundamental for understanding gene expression patterns.
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 the IL1B gene can affect cytokine expression and creates a condition of hypoacidity which favors the survival and colonization of H. pylori. Therefore, the aim of this study was to characterize the polymorphic sites in the 5'- region [-687_ + 297] of IL1B in H. pyloriinfection using in silico tools. RESULTS: A total of five nucleotide variations were detected in the 5'-regulatory region [-687_ + 297] of IL1B which led to the addition or alteration of transcription factor binding sites (TFBSs) or composite regulatory elements (CEs). Genotyping of IL1B - 31 C > T revealed a significant association between -31 T and susceptibility to H. pyloriinfection 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. CONCLUSIONS: In H. pylori-infectedpatients, three detected SNPs (- 338, - 155 and - 31) located in the IL1B promoter were predicted to alter TFBSs and CE, which might affect the 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. pyloriinfection. However, the recognition of regulatory motifs by computer algorithms is fundamental for understanding gene expression patterns.
Entities:
Keywords:
5′- region; H. pylori; IL1B; In silico analysis; Sudan
Authors: M Zamani; F Ebrahimtabar; V Zamani; W H Miller; R Alizadeh-Navaei; J Shokri-Shirvani; M H Derakhshan Journal: Aliment Pharmacol Ther Date: 2018-02-12 Impact factor: 8.171
Authors: Nuri Kodaman; Alvaro Pazos; Barbara G Schneider; M Blanca Piazuelo; Robertino Mera; Rafal S Sobota; Liviu A Sicinschi; Carrie L Shaffer; Judith Romero-Gallo; Thibaut de Sablet; Reed H Harder; Luis E Bravo; Richard M Peek; Keith T Wilson; Timothy L Cover; Scott M Williams; Pelayo Correa Journal: Proc Natl Acad Sci U S A Date: 2014-01-13 Impact factor: 11.205
Authors: Yoshan Moodley; Bodo Linz; Robert P Bond; Martin Nieuwoudt; Himla Soodyall; Carina M Schlebusch; Steffi Bernhöft; James Hale; Sebastian Suerbaum; Lawrence Mugisha; Schalk W van der Merwe; Mark Achtman Journal: PLoS Pathog Date: 2012-05-10 Impact factor: 6.823
Authors: Abeer Babiker Idris; Alaa B Idris; Manal A Gumaa; Mohammed Babiker Idris; Amanda Elgoraish; Mohamed Mansour; Dalia Allam; Bashir Mo Arbab; Nazar Beirag; El-Amin M Ibrahim; Mohamed A Hassan Journal: World J Gastroenterol Date: 2022-01-14 Impact factor: 5.742