Abstract 490: Single nucleotide variations within and around microRNA-binding sites

* equally contributed Grant #5P20GM103443 (NIGMS). Single nucleotide polymorphisms (SNPs) can either create or destroy microRNA binding sites. We analyzed 200 previously reported cancer associated SNPs within microRNA binding sites and found that more than 90% of them were surrounded by single and multiple low-frequency SNPs. The low-frequency SNPs were positioned within the expected microRNAs seed matching areas (58%), within the whole microRNA matching regions (71% incidence), and within the distance where they potentially can affect microRNA-mRNA interaction (36% incidence). We further analyzed the presence of SNPs within microRNA-binding sites in the 3'UTRs of mRNAs encoding the human V-set domain containing T-cell activation inhibitor 1 (VTCN1) and an AT-rich interaction domain 5B (ARID5B). In VTCN1 single SNPs were present in 36% of microRNAs seed matching areas, and two and more SNPs in 8% of microRNA seed matching sites. For ARID5B, single SNPs were present in 42%, and two and more SNPs in 26% of microRNA seed matching sites. In both VTCN1 and ARID5B, some microRNA seed matching areas harbored as many as 4 SNPs. The predicted binding site for microRNA-6870-5p (miR-6870) within the VTCN1 3'UTR consists of 11 uninterrupted and 2 additional Watson-Crick pairs. The length of mature miR-6870 is 19 bases, and the corresponding VTCN1 mRNA fragment harbors 6 nucleotide variations: rs758251859, rs1001277215, rs551576201, rs539444165, rs949692788, and indel rs9055595515. Hypothetically, the rs1001277215 minor allele (MA) eliminates the miR-6870-mRNA complementarity between the corresponding nucleotides. The rs551576201 MA weakens miR-6870-mRNA complementarity by creating a wobble G-U pair, the rs949692788 MA enhances miR-6870-mRNA complementarity by switching from a non-canonical G-U to canonical Watson-Crick A-U pair, and for indel rs9055595515, the absence of deletion preserves miR-6870-mRNA complementarity between CA and GU nucleotides. The probabilities of the “best” and “worst” matches between miR-6870 and VTCN1 mRNA are 0.009995% and 0.000006% correspondingly. The binding between miR-6870 and VTCN1mRNA may also be affected by variations between A and G within rs758251859 (MA frequency is unknown). As microRNA-binding efficacy depends on the mRNA sequences outside the target region, the indels rs35182629 (located 5 nucleotides upstream and covers 2 bases) and rs896747700 (located 1 nucleotide downstream and covers 1 base) may also impact miR-6870-mediat