Fig 1: CVD-associated SNPs alter NKX2-5 and TBX5 in vitro binding. A, DelstaSVM score distribution of the 14,218 CVD-associated SNPs for NKX2-5 (top) and TBX5 (bottom). B, representative EMSA gel for rs59310144 reference/noneffect (Ref) and alternate/effect (Alt) alleles. Source image is available in Fig. S3. C, binding curves of rs59310144, rs6715570, rs61872084, rs76122445, and rs7790964. Experiments were performed in triplicates and binding curves show average bound fraction (X) and error bars are standard error. D, cardiac tissue eQTL analysis of RNASEH2B, BARD1, METTL10, GNB4, and TBX20 expressed in heart atrial appendage or left ventricle when rs59310144, rs6715570, rs61872084, rs76122445, and rs7790964 occur, respectively. CVD, cardiovascular disease; SNP, single nucleotide polymorphism.
Fig 2: Training and testing of LS-GKM SVM predictive model. A, schematic of model training with NKX2-5 and TBX5 ChIP-seq data from HiPSC-CM. B, scoring of ∼520,000 DGF that occur in heart enhancers with the NKX2-5 (top) and TBX5 (bottom) predictive models. C, in vitro testing of predictive model for highest, middle, and lowest scored sequences for NKX2-5 (top) and TBX5 (bottom). For NKX2-5, we tested chr22:25,120,040 to 25,120,058 (circle with blue line), chr3:8,596,782 to 8,596,800 (triangle with green line), and chr7:101,950,814 to 101,950,832 (square with red line). For TBX5, we tested chr2:30,359,836 to 30,359,854 (circle with blue lines), chr1:57,623,182 to 57,623,200 (triangle with green line), and chr4:119,047,319 to 119,047,337 (square with red line). HiPSC-CM, human-induced PSC-derived cardiomyocytes; LS-GKM, large-scale gapped k-mer; SVM, support vector machine; TF, transcription factor.
Supplier Page from DNASU for TBX5 (Homo sapiens) in pDONR221 (Gateway donor/master vector)