JIL-1 and Transcriptionn Figure 3. JIL-1–dependent H3S10phK14ac is enriched on the compensated X chromosome together with JIL-1. (A) Genome-wide distribution of H3S10phK14ac in comparison to JIL-1 and H4K16ac on a 140 kb X-chromosomal locus close to the gene phl. (B) Fractional distribution of probes significantly enriched for H3S10phK14ac (n = 4478) with respect to chromosomal location. As a comparison, the distribution of all probes (n = 384680) represented on the array is shown. (C) Cumulative binding profiles of H3S10phK14ac along genes that are either bound (n = 3362) or not bound (n = 2050) by JIL-1. (D) Decrease of H3S10phK14ac ChIP signal at the 39 end of the genes phl, CG12467, Suv4.20, CG14804 and RpII215 after JIL-1 RNAi as compared to a control GST RNAi. The intergenic region close to ptr and the inactive gene Fz3 are shown as negative control regions. Results are the mean of 3 biological replicates and error bars represent the standard error of the mean. In the insert, we showed that the difference of the H3S10phK14ac ChIP signal after JIL-1 depletion is 4 times higher for target loci compared to control loci after normalization. This difference is statistically significant since the 2-sided unpaired t-test applied to the data gave a p value ,0.05. doi:10.1371/journal.pgen.1001327.g003 upper panels). The distribution of ePol along the transcribed regions is similar for autosomal and X-linked genes with a modest enrichment towards the 39 end. Monitoring the binding of JIL-1 along the gene bodies as a function of ePol density, we found that while JIL-1 clearly associated with active genes, its binding was not proportional to ePol levels (Figure 5A centre panels). Rather, three out of the four groups with significant association of ePol showed the same average binding of JIL-1, except that there was roughly twice as much JIL-1 on X-chromosomal genes compared to autosomal genes, as observed before. This property was also illustrated when the density per gene was plotted against the corresponding steady-state transcript levels. Whereas the ePol density and transcript levels correlated well, JIL-1 binding was characterized by two clouds representing autosomal and X chromosomal genes (Figure S3B). These two representations show that the density of JIL-1 on active genes is not proportional to their transcription level. This was also observed for H3K36me3 and MSL1 distributions using the same representations (Figure S3C, S3D; Figure S8B, S8C) whereas the density of H3K4me2 and ePol were roughly proportional (Figure S8D). The discordance between ePol and JIL-1 distributions along gene bodies was even more pronounced when monitored as a function of gene length (Figure 5B). On autosomes, ePol was found enriched towards the 39 end of short genes, but for genes longer than 1.8 kb the maximal density of ePol gradually shifted towards their 59 ends as a function of length. This is also illustrated by visual inspection of very long genes both on the X and on autosomes (Figure S9). It is conceivable that the risk of premature transcription termination increases with gene length and thus leads to relative depletion of ePol at 39 ends. Interestingly, this trend was less pronounced on the X chromosome, in keeping with the attractive hypothesis that dosage compensation facilitates transcriptional elongation through PLoS Genetics | www.plosgenetics.org 6 March 2011 | Volume 7 | Issue 3 | e1001327