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. Author manuscript; available in PMC: 2014 Apr 15.
Published in final edited form as: Dev Cell. 2013 Mar 21;25(1):55–68. doi: 10.1016/j.devcel.2013.01.028

Figure 1. PolII-S5p but not PolII-S2p occupancy is enhanced at expressed X-linked genes in female ES cells.

Figure 1

(A–L) ChIP-chip analyses using genome tiling arrays to survey X-linked (X) and autosomal (A) genes in undifferentiated female ES cells PGK12.1.

(A–B) Metagene analyses of 355 X-linked and 387 chr19-linked expressed genes (≥1RPKM). Average PolII-S5p occupancy (log2 ChIP/input) was plotted 3kb up- and downstream of the TSS (transcriptional start site) (A) and TES (transcriptional end site) (B) in a 500bp sliding window (100bp intervals).

(C–E) Average binding scores of PolII-S5p in a 1kb region downstream of the TSS (C) or in a 3kb region upstream of the TES (3’ gene body) (E) plotted for 50 expression-ranked bins, each containing 10 X-linked and 9 chr19-linked genes. A total of 506 X-linked and 456 chr19-linked genes (>0RPKM) were examined. Regression values (R2) and trend lines are shown.

(D–F) Box plots of PolII-S5p occupancy at the promoter (D) and at the 3’ gene body (F) of expressed X-linked and chr19-linked genes (≥1RPKM). P values from Wilcoxon-test are shown.

(G–L) Occupancy of PolII-S2p at the 5’ or 3’ end of X-linked and chr19-linked genes. Same analyses as described in (A–F).

See also Figure S1.