A chicken middle-repetitive DNA sequence which shares homology with mammalian ubiquitous repeats

Abstract

We have identified and sequenced two members of a chicken middle repetitive DNA sequence family. By reassociation kinetics, members of this family (termed CRl) are estimated to be present in 1500-7000 copies per chicken haploid genome. The first family member sequenced (CRlUla) is located approximately 2 kb upstream from the previously cloned chicken Ul RNA gene. The second CRl sequence (CRl)Va) is located approximately 12 kb downstream from the 3' end of the chicken ovalbumin gene. The region of homology between these two sequences extends over a region of approximately 160 base pairs. In each case, the 160 base pair region is flanked by imperfect, but homologous, short direct repeats 10-15 base pairs in length. When the CRl sequences are compared with mammalian ubiquitous interspersed repetitive DNA sequences (human Alu and Mouse Bl families), several regions of extensive homology are evident. In addition, the short nucleotide sequence CAGCCTGG which is completely conserved in ubiquitous repetitive sequence families from several mammalian species is also conserved at a homologous position in the chicken sequences. These data imply that at least certain aspects of the sequence and structure of these interspersed repeats must predate the avian-mammalian divergence. It seems that the CRl family may possibly represent an avian counterpart of the mammalian ubiquitous repeats.

Sequence conservation in avian CR1: an interspersed repetitive DNA family evolving under functional constraints.

“…It is unlikely that this high degree of sequence conservation occurred by chance alone in such distantly related species as the emu and chicken. In fact, it has already been pointed out that these regions were also well conserved among the chicken CR1 members (9,18). The region between 284 and 292 matches a consensus silencer and is included in a 172-bp restriction fragment upstream of the chicken lysozyme gene with demonstrable effects on transcription: it exerts a strong repressing effect on weak promoters but has a weak effect on strong transcription units (14).…”

“…Therefore, we undertook a screen of the crane genome, hoping to identify repetitive sequence elements that were present in many other avian species. The first clone we identified: turned out to be a member of the interspersed repetitive DNA family CR1, discovered by Stumph et al (9) in domestic fowl (chickens, Gallus gallus).…”

“…It is composed of approximately 7000-20,000 repeats per haploid genome, the lengths of individual members varying from 160 to 850 base pairs (bp) (9,10). Interestingly, the 5' ends of the known CR1 members are all truncated at various positions, reminiscent of the Li family in mammals (11).…”

Genomic structure and possible retroviral origin of the chicken CR1 repetitive DNA sequence family.

“…We have previously identified and characterized a family of short dispersed repetitive DNA sequences in the chicken genome, and this family of repeats has been named the CR1 family (2,3). The first CRI family sequence that was characterized lies -2 kilobase pairs (kb) upstream from a chicken UJ RNA gene (2).…”

“…We have previously identified and characterized a family of short dispersed repetitive DNA sequences in the chicken genome, and this family of repeats has been named the CR1 family (2,3). The first CRI family sequence that was characterized lies -2 kilobase pairs (kb) upstream from a chicken UJ RNA gene (2). Molecular cloning methods have revealed that members of the CRI family also exist at defined locations both upstream and downstream of the chicken X-Y-ovalbumin multigene cluster (3).…”