Effect of HCFC1 depletion on mRNA levels. Percentages of HCFC1 unbound (1 and 3) or bound (2 and 4) TSSs that display a significant differential expression upon depletion of HCFC1 for both the up-regulated (1 and 2) and the down-regulated genes (3 and 4). The number of TSSs used here is 20,571 because 7% of TSSs identified by ChIP-seq analyses were not present on the Affymetrix chip.