Computational Investigation of Regulatory Region SNPs of Autophagy Gene BECN1

Sargeet Kaur; Jitendraa Vashistt; Harish Changotra

doi:10.14429/dlsj.9.19452

Sargeet Kaur Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh- 173 234, India https://orcid.org/0000-0001-5868-3084
Jitendraa Vashistt Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Waknaghat, Solan, Himachal Pradesh- 173 234, India https://orcid.org/0000-0002-8702-3170
Harish Changotra Department of Molecular Biology and Biochemistry, Guru Nanak Dev University, Amritsar, Punjab- 143 005, India https://orcid.org/0000-0002-1465-5257

DOI: https://doi.org/10.14429/dlsj.9.19452

Keywords: Hypoxia, BECN, Single nucleotide polymorphism, Promoter variants, 3'UTR

Abstract

The autophagy process plays a cytoprotective role and ensures the healthy survival of a cell. The role of autophagy has been implicated in various diseases, making it an essential candidate for therapeutic interventions. Beclin 1, a candidate autophagy protein, plays a critical role during autophagy initiation and maturation by interacting with various other autophagy proteins. Beclin1 has been reported to be involved in various human diseases. This study uses a computational approach to study the effect of non-coding region single nucleotide polymorphisms (SNPs) of gene encoding beclin1. RegulomeDB, SNP2TFBS, and PROMO ALLGEN were used to predict the effect of promoter region variants on transcription factor binding sites. SNPs located within 3'UTR were analyzed by miRdSNP, PolymiRTS Database 3.0, miRNASNP-V3, MicroSNIPER, and miRmap. Nine promoter region variants that alter the transcription factor binding sites and 4 variants in 3'UTR were identified that either create a new target site for miRNA or disrupt an existing one. The functional analysis of these identified SNPs could be done experimentally to unravel their relation with a particular disease and the genetic predisposition of human subjects for a disease.