Figure 2.

Monovalent chromatin signature is prevalent in undifferentiated cells of bam testis. (a) UCSC genome browser screenshot showing the H3K4me3 monovalency at the E(z) gene locus in undifferentiated cells. The read counts are labeled on the y-axis and the genomic region used to calculate the enrichment of modified histones (0 to +500 bp with respect to the TSS) is shaded in grey. (b) Transcription level of two representative monovalent genes, E(z) and sa, in bam and wild-type (wt) testis, respectively. According to the RNA-seq data, the RPKM for E(z) mRNA is four-fold higher in bam testis, and that for sa mRNA is 113-fold higher in wild-typetestis. (c) UCSC genome browser snapshot showing the H3K27me3 monovalency at the sa gene locus in undifferentiated cells. The read counts are labeled on the y-axis and the genomic region used to calculate the enrichment of modified histones (0 to +500 bp with respect to the TSS) is shaded in grey. (d) Scatter plot for H3K4me3 and H3K27me3 enrichment of all annotated genes. A common window (0 to +500 bp with respect to the TSS) was used to calculate H3K4me3 and H3K27me3 reads. The blue dashed lines indicate the statistical cutoff line - P < 0.05 in a 1-kb window per 1 million total reads. Gene numbers in each quadrant are labeled in black. Differentiation genes are defined as those with RPKM in bam testis < 0.5 and RPKM in wild-type testis ≥ 1 and are labeled as red dots. Among the 1,894 differentiation genes, 1,304 genes are applicable for ChIP-seq analysis (Materials and methods). Up-regulated genes are defined as those with RPKM in wild-typetestis/bam testis ≥ 2 (if the RPKM in bam testis < 0.5, the value is raised to 0.5) and are labeled as green inverted triangles. Among the 3,377 up-regulated genes, 2,188 genes are applicable for ChIP-seq analysis (Materials and methods).

Gan et al. Genome Biology 2010 11:R42   doi:10.1186/gb-2010-11-4-r42
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