Occupancy of the majority of DNA in the chicken W chromosome by bent-repetitive sequences.

Another family of repetitive sequences, designated the EcoRI family, was found in the DNA of the chicken W chromosome by hybridization with the W chromosome-specific XhoI family probe under conditions of low stringency. A 1.2 kb EcoRI fragment, the major repeating unit of the family, was cloned and sequenced. The 1.2 kb unit showed an overall sequence similarity of about 68% to the 0.7 kb XhoI family repeating unit and it consisted of tandem repeats of average length 21 bp, most of which contained (A)3-5 and (T)3-4 clusters separated by 6-8 G + C-rich sequences. These features and its behavior as a strongly bent molecule in solution were very similar to those found for other W chromosome-specific repetitive sequences in the order Galliformes: XhoI family of chicken, PstI family of turkey and TaqI family of pheasant. The cloned 1.2 kb unit contained 78 CpG dinucleotide sequences and those that were in HapII, HhaI and BstUI sites were shown to be extensively methylated in the genomic DNA. Repetition frequencies of the 1.2 kb unit among the female population of chicken fell into high- and low-level classes, which accounted for about 30% and 10%, respectively, of the DNA in the W chromosome. Thus, 70% to 90% of the DNA in the chicken W chromosome was shown to be occupied by bent-repetitive sequences. The EcoRI and XhoI family sequences were not intermingled over the short range but each family formed a unique domain ranging from one to several million base pairs.