test). In contrast, we observed levels of transcription just upstream of genes (−1800 bp to transcription start site) and in intronic regions that were indistinguishable from the baseline. These data indicate that the signals observed by our microarray accurately detect known transcribed regions. Second, many previous studies in a variety of cell types have shown that active transcription is associated with low levels of DNA methylation in the 5′ ends of genes [23]. CpG islands also show lower than average levels of DNA methylation compared to other genomic regions [24]. As expected, we observed lower DNA methylation levels in 5′ gene ends (P = 1.34×10−78 by Wilcoxon Rank Sum test) and within CpG islands (P = 7.15×10−200 by Wilcoxon Rank Sum test) than the overall levels of methylation across the locus (Fig. S3b–c). Third, actively transcribed genes have been associated with reduced nucleosome occupancy near transcription start sites [25], [26], [27]. We similarly found lower H3K9 acetylation levels in 5′ gene ends (P = 9.22×10−47 by Wilcoxon Rank Sum test; Fig. S3b). Computational prediction of nucleosome density from DNA sequence [28] showed a significant correlation between nucleosome position and H3K9 acetylation levels observed by microarray (R = 0.2, P =
