Eukaryotic genomes are organized into domains of differential structure and activity. Through chromatin state mapping using 17 chromatin marks in L3 larvae, we identify 20 states that correlate with many biological features as seen previously in other systems. Investigating patterns of states on a larger scale, we observe extended active and inactive domains corresponding with regions of low and high H3K27me3, and we characterize two types of border regions separating domains. Marked borders are associated with higher levels of H3K36me3 and germline active chromatin. These borders show spreading of H3K27me3 into neighboring active regions in animals with reduced H3K36me3 germline marking, suggesting that germline events contribute to domain definition. Regulatory borders are enriched for characteristics of transcriptional regulatory regions. The domain organization shows similarities to topological domains in humans and Drosophila, where insulator proteins such as CTCF show enrichment at boundaries. Using large modENCODE and ENCODE collections of transcription factor binding data, we find that the binding of most transcription factors is enriched at C. elegans borders and Drosophila and human topological boundaries, indicating that the previously observed topological boundary enrichment of insulator proteins is not specific to these factors. We propose that these regulatory regions may help to organize chromatin into domains.
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