JIL-1 and Transcriptionn Figure 2. JIL-1 is enriched at the 39 end of phl and is twofold enriched at X-linked loci in male flies. Comparison of the distribution of JIL- 1, ePol, H4K16ac and H3K36me3 on the X-linked gene phl in SL2 cells. (A) Signals as revealed by ChIP-chip profiling were compared to (B) the qPCR- based quantification of unamplified material. The position of the amplicons used for qPCR is indicated above the gene annotations. The relative enrichments from amplicons A to D were calculated using the intergenic region located ,2 kb left of the gene ptr (ptr_IG) as a reference. (C) Comparison of the enrichment of JIL-1, H3K36me3 and H4K16ac at the 39 end of the active X-linked genes phl, CG14804, sta, Pgd, RpII215 and of the active autosomal gene Cortactin. The inactive X-linked gene runt, the promoter region of the annexin IX gene flanking the Cortactin gene and the intergenic region close to ptr served as negative control regions. Signals were normalized to the annexin IX locus and error bars represent the standard error of the mean for 3 independent biological replicates. doi:10.1371/journal.pgen.1001327.g002 effects incorporates the results of all experiments. Among several thousand active genes bound by JIL-1 in SL2 cells, we found that after JIL-1 depletion the expression level was significantly reduced for 276 genes and increased for 25 genes. Globally, transcription of X-linked genes was significantly reduced as compared to the autosomal genes (p-value 1.2e-06) suggesting that the enrichment of JIL-1 on X-linked genes is functionally relevant for dosage compensation (Figure 4D). Interestingly, the few active genes on the fourth chromosome also appear to be particularly affected. We observed that total amount (Figure 4B) and distribution of ePol (not shown) were not changed after RNAi against JIL-1 and suggest that in SL2 cells, JIL-1 is probably not essential for the release of RNA polymerase II in productive elongation. Alterna- tively, the few percent of JIL-1 remaining after RNAi may be sufficient to fulfil this function. It is also noteworthy that, contrary to many proteins having a function in transcriptional activation, those genes whose transcription is sensitive to JIL-1 depletion tend to have lower JIL-1 levels to start with (Figure 4E). JIL-1 association to genes does not follow ePol To compare the distribution of ePol and JIL-1 along genes, we scaled all genes to equal length and aligned them from transcriptional start sites (TS) to transcriptional termination sites (TT). The genes were furthermore divided into six equally sized groups based on their average ePol enrichment and average distribution profiles were computed for each group (Figure 5A PLoS Genetics | www.plosgenetics.org 5 March 2011 | Volume 7 | Issue 3 | e1001327