Enter Note Done


H. Shiferaw1, C. Hong2, J. J. Johnston3, L. G. Biesecker4; 1NIH, Gaithersburg, MD, 2Natl. Inst.S OF HEALTH, BETHESDA, MD, 3NIH, Rockville, MD, 4Bethesda, MD

Polyadenylation is essential in maintaining nascent mRNA stability. Variants in polyadenylation signal (PAS) hexamers can cause reduced polyadenylation at the normal polyA sites and lead to reduced gene expression or expression of transcripts with aberrant 3’ UTR sequences. Only 34 PAS hexamer variants in 20 genes have been associated with Mendelian disorders. Of the 20 genes, 12 have at least one PAS hexamer variant as damaging assertion (‘DM’) in HGMD. We hypothesize that this is under-representative of this class of variants. Here, we aimed to comprehensively identify clinically important PAS hexamers, which are most commonly AATAAA, but other PAS hexamers are included. Clusters of polyadenylated 3’ UTRs in ESTs were identified from the PolyA Site 2.0 and examined for dominant polyA site usage activity (defined by >50% of overall EST representation). We filtered for inclusion of polyA sites with PAS hexamers closest to -21 nucleotides relative to the polyadenylation site. We identified 15,212 PAS hexamers for further examination. To understand constraint in the identified PAS hexamers, we compared the number of variants in the AATAAA and ATTAAA PAS hexamers of interest vs. control sequences in 3’ UTR by examining variants in gnomAD population. For quality control, we included regions with ≥20x coverage in >90% of gnomAD samples and removed regions of low complexity and mappability. The AATAAA and ATTAAA PAS hexamers were significantly more constrained than control nucleotides found upstream of our PAS hexamers (p < .001, Mann-Whitney U test). To understand the effects of variants occurring in polyA hexamers, RNA sequencing and 3’ end sequencing was performed on 76 ClinSeq® individuals with variants in these hexamers. Twenty-five of 64 genes with PAS hexamer variants showed alternative polyadenylation, which suggests that variants in PAS hexamers can lead to reduced gene function. Additionally, of the 15,212 PAS hexamers, 4,532 were in disease-associated genes, suggesting that PAS hexamer variants may lead to aberrant transcripts in these genes with clinical implications. Further analyses are ongoing to investigate the clinical effects of PAS hexamer variants. These data reinforce that PAS hexamer sequences are critical in polyadenylation and that variants in these sequences are candidates for pathogenic, disease-associated variation.
Session Type
Poster Presentations
Molecular Effects of Genetic Variation