Fig. 1

Genome-wide quantification of pig enhancer activity using STARR-seq. A Assessment of the immunoreaction and treatment of TBK1/IKK/PKR inhibitors after DNA was transfected into PK15 cells. Expression levels were assessed by RT-qPCR and normalized to non-transfected cells. Bars represent mean fold change across three independent replicates (grey dots). P-values were calculated from a t-test. B Statistics of functional enhancers identified in PK15 and ST cells. Venn diagram shows that enhancers overlap in the two biological replicates. C STARR-seq cDNA (red) and input plasmid (gray) fragment densities at representative pig genomic loci. Blue boxes denoted the identified enhancers in the PK15 and ST cells. D Correlation analysis of enhancer strength in the two biological replicates of PK15 cells. The correlation was evaluated using the Pearson’s correlation coefficient (PCC). Enhancer strength was calculated based on fold change (FC, cDNA read counts divided by input plasmid read numbers) using 600 bp windows along each chromosome. E STARR-seq enhancer enrichment and RT-qPCR quantification of GFP gene expression was linearly correlated. r, Pearson correlation coefficient; Error bars indicate two independent biological replicates