Technical Comments

Comment on “Drosophila Dosage Compensation Involves Enhanced Pol II Recruitment to Male X-Linked Promoters”

See allHide authors and affiliations

Science  19 Apr 2013:
Vol. 340, Issue 6130, pp. 273
DOI: 10.1126/science.1231815

Figures

  • Fig. 1 Effect of the erroneous multiplication step on the ratio of Pol II binding on X-linked genes compared with autosomal genes.

    (A) We have reproduced the analysis pipeline in (5). The upper plot reports the average Pol II ChIP over input log2 enrichment ratio along X-linked (red) and autosomal (gray) genes in male salivary glands. The lower plot reports the ratio between X and autosomes. The same annotations and gene lists from figure 2 by Conrad et al. (5) are used here. (B) Same data as in (A), but processed without the erroneous multiplication step. (C) Average Pol II binding ratios between X and autosomal genes in male (black) and female (gray) salivary glands, as measured at the promoter, gene body, and 3′-end regions. Male over female ratios are also indicated. The data were processed using the ChIP-seq processing pipeline in (5). (D) Same as (C), but processed without the erroneous amplification step.

  • Fig. 2

    Additional analyses of ChIP-seq and paused RNAs fail to support the initiation model for dosage compensation.(A) Average Pol II binding ratios between X and autosomal genes in untreated wild-type (black) and MSL2 RNAi–treated (gray) male cells, using the same annotations and gene lists as in figure 4 by Conrad et al. (5). (B) The same as in (A), but processed without the erroneous amplification step. (C) Average Pol II binding ratios between chromosome X and autosomal genes in male (black) and female (gray) 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 software 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.

Navigate This Article