Fig. 1

Advantages of studying BPs at single-cell level. a An illustration of a BP, defined based on two genes located on opposing strands of DNA (Watson and Crick). Bulk RNA measurements at the BP may hide complexity of BP gene regulation. This is shown in the left single-cell expression scenario, where one of the genes is expressed and the other is silent in the same cell compared to the other scenario where single-cell expression agrees with bulk measurements. b Heatmaps of 65 single-cell RNA-seq expression measured in four bidirectional promoters (TPM, HepG2 cells). c After single-cell sequencing and estimating the gene expression of all genes in a cell, a set of 1242 BPs was extracted. Single-cell expression of either genes of a BP was arranged in two separate matrices for which the rows represent the BPs and columns the cells. Next, we swap the higher expressed gene to the matrix on the right and lower expressed one to the left. The resulting matrices are combined into one joint BP single-cell expression matrix