Figure 3

ChIP-seq signal near TSS for mouse liver and HeLa cells. (a, b) ChIP-seq profiles near TSS (mm9 genome) for highly expressed transcripts in mouse liver, separated into the following categories: all expressed (red, 10,111 genes, >6.0 microarray units), expressed and isolated with no other TSS or PAS within 1 kb (black, 3,070 genes), those expressed with an oppositely directed TSS less than 1 kb upstream (green, 1,605 genes) and those expressed with an oppositely directed TSS between 170 and 200 bp upstream (blue, 91 genes). (a) PolII averaged signal, arbitrary units. (b) H3K4me3 averaged signal, arbitrary units. (c, d) The promoter-proximal bimodal profile with separation of 110 bp is apparent also for HeLa cells [23]. Vertical lines are given at the consensus TSS (hg19 genome) and at TSS + 110 bp. (c) Profiles of PolII in mouse liver (black) and HeLa cells using a different antibody (sc-899 instead of our sc-67318) (red). Transcripts are chosen to be isolated from nearby transcripts and to have non-zero RNA-seq signal (see Materials and methods). HeLa coverage is multiplied by 35 to be on the same scale as the higher coverage mouse liver data. (d) In HeLa cells, both pausing factors NELF and DSIF co-localize with PolII as expected, with a peak at TSS + 110 bp. DSIF coverage is multiplied by 3 to be on the same scale as NELF. a.u., arbitrary units.