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Chromatin insulators are eukaryotic genome elements that upon binding of specific proteins display barrier and/or enhancer-blocking activity. Although several insulators have been described throughout various metazoans, much less is known about proteins that mediate their functions. This article deals with the identification and functional characterization in  Paracentrotus lividus  of COMPASS-like (CMPl), a novel echinoderm insulator binding protein. Phylogenetic analysis shows that the CMPl factor, encoded by the alternative spliced  Cmp / Cmpl  transcript, is the founder of a novel ambulacrarian-specific family of Homeodomain proteins containing the Compass domain. Specific association of CMPl with the  boxB cis -element of the  sns5  chromatin insulator is demonstrated by using a yeast one-hybrid system, and further corroborated by ChIP-qPCR and  trans -activation assays in developing sea urchin embryos. The  sns5  insulator lies within the early histone gene cluster, basically between the  H2A  enhancer and  H1  promoter. To assess the functional role of CMPl within this locus, we challenged the activity of CMPl by two distinct experimental strategies. First we expressed in the developing embryo a chimeric protein, containing the DNA-binding domain of CMPl, which efficiently compete with the endogenous CMPl for the binding to the  boxB  sequence. Second, to titrate the embryonic CMPl protein, we microinjected an affinity-purified CMPl antibody. In both the experimental assays we congruently observed the loss of the enhancer-blocking function of  sns5 , as indicated by the specific increase of the  H1  expression level. Furthermore, microinjection of the CMPl antiserum in combination with a synthetic mRNA encoding a forced repressor of the  H2A  enhancer-bound MBF1 factor restores the normal  H1  mRNA abundance. Altogether, these results strongly support the conclusion that the recruitment of CMPl on  sns5  is required for buffering the  H1  promoter from the  H2A  enhancer activity, and this, in turn, accounts for the different level of accumulation of early linker and nucleosomal transcripts.

The Compass-like Locus, Exclusive to the Ambulacrarians, Encodes a Chromatin Insulator Binding Protein in the Sea Urchin Embryo