Figure 2

Transcription in K562 leukemia cell lines shows a complex dependence on the distance from pairs of TSSs, their intragenic position, and the transcriptional activity of the gene. (A, B), two-dimensional density of normalized RNA-seq signal for pairs of the first (TSS 1) and second (TSS 2) TSSs (A) and the second (TSS 2) and third (TSS 3) TSSs (B) of genes with high, medium, and low levels of transcription. (C), seven representative regions of the two-dimensional (density) signal used to characterize the interdependence on pairs of TSSs. TSSs are ordered according to their genomic position. Regions A and B correspond to transcription at the upstream TSS (\(0 \le x \le 200\)) when the downstream TSS is far away (\(- 20{\text{k}} \le y \le - 10{\text{k}}\)) and at an intermediate distance (\(- 900 \le y \le - 200\)), respectively. Regions Af and Bf correspond to transcription at intermediate distances from the upstream TSS (\(300 \le x \le 1k\)) when the downstream TSS is far away (\(- 20{\text{k}} \le y \le - 10{\text{k}}\)) and at an intermediate distance (\(- 900 \le y \le - 200\)), respectively. Regions C, D, and E correspond to transcription at the downstream TSS (\(0 \le y \le 200\)) when the upstream TSS is nearby (\(0 \le x \le 200\)), at an intermediate distance (\(300 \le x \le 1{\text{k}}\)), and far away (\(10{\text{k}} \le x \le 20{\text{k}}\)), respectively. For the quantification of proximal, intermediate, and distal effects between TSSs, we define the average transcription \(T_{W}\) in a given region \(W\) as \(T_{W} = \left\langle {g\left( {x + z_{U} } \right)\delta_{{y, x + z_{U} - z_{D}}} } \right\rangle_{{ \left\{ {z_{U} ,z_{D} } \right\},\left( {x,y} \right)}}\) with \(\left( {x,y} \right) \in W\) (see “Materials and Methods” section). Selecting \(W\) as one of the representative regions leads to the definitions of proximal cooperativity as \(T_{C} /T_{E}\); upstream effects as \(T_{B} /T_{A}\); downstream effects as \(T_{D} /T_{E}\); positional dominance as \(T_{E} /T_{A}\); persistence with a distal downstream TSS as \(T_{Af} /T_{A}\); persistence with a non-distal downstream TSS as \(T_{Bf} /T_{B}\); and signal dominance as \(T_{Bf} /T_{Af}\). Data is available from the ENCODE consortium (experiment accession number ENCSR000AEL, Thomas Gingeras lab, CSHL). The accession numbers of the minus and plus strand RNA-seq signals and gene quantifications are ENCFF652ZSN, ENCFF091RAW, and ENCFF782PCD, respectively.