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.