Binding of nuclear factors to a satellite DNA of retroviral origin with marked differences in copy number among species of the rodent Ctenomys

The major satellite DNA of the subterranean rodent Ctenomys, named RPCS, contains several consensus sequences characteristic of the U3 region of retroviral long terminal repeats (LTRs), such as a polypurine tract, CCAAT boxes, binding sites for the CC-AAT/enhancer-blnding protein (C/EBP), a TATA box and putative polyadenylatlon signals. RPCS presents an enormous variation in abundance between species of the same genus: while C.australls or C.talarum have approximately 3×106 copies per genome, C.opimus has none. A sequence (RPCS-I) with Identity to the SV40-enhancer core element, present In all the repeating units of the satellite is specifically protected In DNase I footprlntings. Competitions of band-shift assays with different transcription factor binding sites Indicate that binding to RPCS-I is specific and involves CCAAT proteins related to NF-1, but not to C/EBP. By the use of quantitative protein/DNA binding assays we determined that, despite of their conspicuous difference in RPCS copy number, C.talarum and C.opimus have equivalent amounts and Identical quality of RPCS-bindlng proteins. These results are consistent with the observation, by in situ hybridization, that RPCS is clustered in heterochromatic regions, where it might have restricted accessibility to transcription factors in vivo. This is the first report of the binding of transcription factors to a satellite DNA of retroviral origin.