Fig. 2.

(A) Average Pol II binding ratios between X and autosomal genes in untreated wild type (black) and MSL2 RNAi treated (grey) male cells, using the same annotations and gene lists as in Figure 4 by Conrad et al. (5). (B) The same as panel B, but processed without the erroneous amplification step. (C) Average Pol II binding ratios between chromosome X and autosomal genes in male (black) and female (grey) salivary glands, analyzed with an alternative pipeline. Normalized ChIP over Input enrichment was computed using the maximum likelihood estimate (MLE) analysis implemented in the SPP package (6). The promoter, gene body and 3'-end regions are analyzed. The numbers on top specify the ratio of male over female values. (D) Short RNAs associated with paused Pol II from (8) show similar density per gene copy around the transcription start sites (TSS) on active X-linked and autosomal genes in males. The same annotations and gene lists from Figure 2 by Conrad et al. (5) were used; data were processed with SPP (6); normalization over genomic control was used to account for differences in copy number.