Figure 3

Most genes are unpoised in undifferentiated cells of bam testis. (a) Scatter plot for H3K4me3 and RNA Pol II enrichment of all annotated genes. All labels and the definition of up-regulated genes are the same as in Figure 2d, except that a -250 to +250-bp window with respect to the TSS was used to calculate reads for RNA Pol II. (b) Scatter plot for RNA Pol II enrichment and RPKM values for all annotated genes. All labels are the same as in Figure 2d, except that RPKM ≥ 1 is used as a cutoff for expressed genes. (c) RPKM values for genes that have three absent calls (3A) in the microarray. (d) Analysis of the RPKM values of transcripts demonstrates that genes with stalled Pol II are weakly transcribed genes. Genes that show an active Pol II profile are expressed at significantly higher levels. Genes with no Pol II profile are expressed at significantly lower levels. The box represents the 25th and 75th percentiles, with the 50th percentile as a black bar. The whiskers refer to outliers that are at least 1.5× the interquartile range from the box. The y-axis represents the RPKM value.