Figure 7

Small gaps between LEM-2 subdomains are exceptionally transcriptionally active. (a) A representative genomic region showing enrichment of RNA polymerase II (RNAPII), H3K4me3 and HTZ-1 in gaps between LEM-2 subdomains. The top panel indicates the chromosomal position of the enlarged region. RNAPII and HTZ-1 ChIP-chip data are shown as z-scores of log₂ (ChIP/Input), whereas H3K4me3 ChIP-seq data are shown as normalized base counts. (b) Average RNAPII, H3K4me3, HTZ-1 and LEM-2 levels in subdomain-gap boundaries. For RNAPII and HTZ-1, sliding window averages (100-bp window; 50-bp offset) are shown, whereas for H3K4me3 the average of each base position is plotted. (c) Expression status of genes located near the boundaries. Each dot represents a transcript, whose abundance is shown on the y-axis and the distance from a boundary is shown on the x-axis. Boundaries between LEM-2 subdomains and medium gaps (left) or between subdomains and small gaps (right) are shown. The horizontal dashed bars indicate median transcript levels across 5-kb or 10-kb regions in gaps or subdomains. (d) RNA interference (RNAi) phenotypes of genes in LEM-2 subdomains and gaps. Numbers of genes with indicated RNAi phenotypes are shown. Chi-square test was used for statistical analysis with distribution of all genes with phenotypic annotations (shown in the header) as a background probability. Phenotypes annotated for more than 500 genes are listed.