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Background  The zinc finger (ZF) protein CTCF (CCCTC-binding factor) is highly conserved in  Drosophila  and vertebrates where it has been shown to mediate chromatin insulation at a genomewide level. A mode of genetic regulation that involves insulators and insulator binding proteins to establish independent transcriptional units is currently not known in nematodes including  Caenorhabditis elegans . We therefore searched in nematodes for orthologs of proteins that are involved in chromatin insulation.    Results  While orthologs for other insulator proteins were absent in all 35 analysed nematode species, we find orthologs of CTCF in a subset of nematodes. As an example for these we cloned the  Trichinella spiralis  CTCF-like gene and revealed a genomic structure very similar to the  Drosophila  counterpart. To investigate the pattern of CTCF occurrence in nematodes, we performed phylogenetic analysis with the ZF protein sets of completely sequenced nematodes. We show that three ZF proteins from three basal nematodes cluster together with known CTCF proteins whereas no zinc finger protein of  C. elegans  and other derived nematodes does so.    Conclusion  Our findings show that CTCF and possibly chromatin insulation are present in basal nematodes. We suggest that the insulator protein CTCF has been secondarily lost in derived nematodes like  C. elegans . We propose a switch in the regulation of gene expression during nematode evolution, from the common vertebrate and insect type involving distantly acting regulatory elements and chromatin insulation to a so far poorly characterised mode present in more derived nematodes. Here, all or some of these components are missing. Instead operons, polycistronic transcriptional units common in derived nematodes, seemingly adopted their function.

Loss of the insulator protein CTCF during nematode evolution