Figure 2.

RNA polymerase II shows a variety of gene-specific enrichment patterns. Graphs plot 10log(p-value) mapped to chromosome position with the significant p-values greater than 40 indicated by the rectangle blocks below the graph. Values are plotted at every probe location. Flat lines indicate weak p-values and gaps indicate the absence of probes. The high density of probes across these genes suggest that the observed patterns are not due to probe bias. A scale bar is shown for each panel to reflect the different gene lengths displayed. RefSeq genes and knownGenes are annotated in green and blue, respectively, with thick bars representing exons and thin lines introns. Genes above the white bar are ordered 5' to 3', whereas those below the white bar are 3' to 5'. (a) On the highly expressed SF1 gene, PolIIa localizes to the first exon only. PolII accumulates across the gene with a distinctive pattern. (b) No significant signal is observed across the inactive NRXN2 locus which is near SF1 on chromosome 11. Graphs are plotted on the same scale as (a). (c) The moderately expressed gene KIAA1932 also reveals distinct accumulations across the gene. The red box highlights alternatively spliced exons. At the 3' end of the gene, some PolIIa signal is observed, probably indicative of the expression of a small gene antisense to KIAA1932. (d) Another commonly observed pattern is exemplified by the EHD1 gene. Both anti-polymerase antibodies recognize the first exon, but no other significant signal is observed across the gene until the 3' end.