ABSTRACT Long noncoding RNAs (lncRNAs) are connected with various biomolecular functions including gene regulation. They are mainly linked with various kinds of RNA processing mechanisms with the help of RNA binding proteins (RBPs). Recent studies on the configuration and function of lncRNAs have described that they are inevitable for the functioning of the cellular transcriptome. As per studies reported by Genome-wide association studies (GWAS), the noncoding region present within the genome incorporates most of single nucleotide polymorphisms (SNPs). Transcription of such SNP containing lncRNAs may give rise to numerous diseases. So, the study of SNPs linked with lncRNAs is crucial to decipher the possible mechanism behind the association among SNP, lncRNA, and RBP. In our research, we have investigated the SNP effect of on the configuration and function of lncRNA. Along with this, we have detected the position of N6-Methyladenosine (m6A) modification present within lncRNAs and have also examined whether these lncRNAs make contact with the chromatin. From in silico work, SNPs are found to be associated with the alteration in the structure of lncRNA using software like RNA structure, RNAfold and Centroidfold. From molecular docking, they are found to impact the function of lncRNA by changing the interaction of lncRNA-RBP. Using the published data acquired from the Encyclopedia of RNA Elements (ENCORE), we have obtained the RBPs interacting with lncRNAs. We have identified m6A position near the SNP in the lncRNA employing the published m6A- atlas data. In addition to this, we have also observed that lncRNAs are making contact with the chromatin at different locations within the cellular genome, obtained from the RNA-Chrom analytical database. Further study of SNP-lncRNA-RBP will improve our understanding related to the underlying molecular mechanism of disease pathogenesis and be helpful in predicting effective therapeutics for different human diseases.

KEYWORDS: SNP, lncRNA, RBP, RNA structure, m6A, ENCORE, RNA-Chrom