Genomic organization and expression during embryogenesis of the chicken CR1 repeat

Cytogenetic repartition of chicken CR1 sequences evidenced by PRINS in Galliformes and some other birds

Chicken repeat 1 (CR1) belongs to the non-long repeat class of retrotransposons. Nearly 100000 repeats interspersed in the chicken genome are subdivided into at least six distinct subfamilies, each 300 bp long and all sharing substantial sequence similarity. CR1-like elements were found in genomes from invertebrates to mammals, suggesting their importance for genome structure and/or function. Moreover, numerous data support the hypothesis of their implication in regulation of gene expression. So, the chromosomal distribution of these CR1 sequences in vertebrates is of great interest to improve our knowledge about the genome structure, function and evolution. A comparison of the cytogenetic distribution of CR1 sequences was performed by PRINS using consensus chicken primers on the chromosomes of chicken and species of several bird orders: Galliformes, Anseriformes, Passeriformes and Falconiformes. The study revealed that CR1 repeats are spread over nearly all chicken chromosomes with a higher density on the macrochromosomes and in particular with hot spots on subtelomeric regions of chromosome 1, 2, 3q, 4q, 5q. Their distribution on the macrochromosomes forms a kind of banding pattern, which was not systematically matched with R- or G-banding. This banding pattern appears to be conserved on the chromosomes of the Galliformes studied, irrespective of their karyotypes, rearranged or not. CR1 primers also show similar signals on the chromosomes of birds phylogenetically more distant (Anseriformes, Passeriformes and Falconiformes). This fact confirms the importance of these sequences at the large scale of bird evolution and in the chromosomal structure. The location of CR1 sequences, and in particular of the hot spots, mainly within the richest CG areas are in conformity with the data on an epigenetic role of these highly conserved sequences.

A sequence with homology to human HPFH-linked enhancer elements and to a family of G-protein linked membrane receptor genes is located downstream of the chicken beta-globin locus

We report 5805bp of novel sequence (GenBank/EMBL Accession No. AJ012570) from a region starting approx. 11.5kb downstream of the chicken beta-globin locus (map position approx. +30.8 to +36.6kb), which contains a 945bp open reading frame (map position approx. +33 to +33.9kb). This is predicted to encode a 315-residue protein containing seven hydrophobic helical regions and a 17 amino acid motif characteristic of the R7G family of G-protein coupled membrane-bound receptors. The open reading frame and some surrounding sequence also have significant homology with the breakpoint enhancer elements, which also contain open reading frames, implicated in the HPFH-1/2 and HPFH-6 deletional forms of the human syndrome, hereditary persistence of foetal haemoglobin (HPFH). The existence of similar sequences at similar distances downstream of the beta-globin genes in chickens and HPFH patients is intriguing.

Sequence scanning chicken cosmids: a methodology for genome screening

The chicken genome is relatively poorly studied at the molecular level. The karyotype 2n=78 is divided into three main chromosomal sub-groups: the macrochromosomes (six pairs), the intermediate microchromosomes (four pairs) and the microchromosomes (29 pairs). Whilst the microchromosome group comprise only 25% of the DNA, increasing evidence is proving that this is disproportionate to their gene content. This paper demonstrates the utility of cosmid sequence scanning as a potential method for analysing the chicken genome, providing an economical method for the production of a molecular map. The GC content, gene density and repeat distribution are analysed relative to chromosomal origin. Results indicate that gene density is higher on the microchromosomes. During the scanning process an example of conserved linkage between chicken and human (12q34.2) has been demonstrated.

Transcription of lampbrush chromosomes of a centromerically localized highly repeated DNA in pigeon (Columba) relates to sequence arrangement

A highly repetitive, centromerically localized DNA sequence (PR1) has been isolated from the genomic DNA of two species of pigeon (Columba livia and C. palumbus). PR1 is approximately 900 bp long. It includes a sequence that is similar to the CENP-B box of mammals. It represents about 5% of the genome in C. livia and 2% in C. palumbus. In both species, tandem arrays of PR1 form part of larger repeating units. The organization of PR1 repeats and the larger repeating units is strikingly different in the two species. The large repeating units in C. livia include long (at least 14 units) tandem arrays of PR1 interspersed with relatively short intervening sequences. The large repeats of C. palumbus have much shorter (4 units or fewer) PR1 arrays interspersed with longer sections of non-PR1 DNA. PR1 is transcribed on short lampbrush loops in the centromeric regions of all lampbrush bivalents of C. palumbus. In C. livia, it is not transcribed at any of the major pericentromeric sites at which it is known to be present, although it is transcribed at one minor centromeric site on chromosome 2. It is proposed that transcription of the noncoding PR1 sequence on lampbrush chromosomes of pigeons relates to its genomic organization. The proposal is discussed with regard to the 'read-through' hypothesis for transcription on lampbrush loops.

Two chicken repeat one (CR1) elements lacking a silencer-like region upstream of the chicken avidin-related genes Avr4 and Avr5

Two repetitive elements of the chicken CR1 family, each located in the 5' flanking region of the avidin-related genes Avr4 and Avr5, have been cloned and sequenced. Both elements are 721 bp in length with 72% identity to a CR1 consensus sequence. They had a 191 bp deletion in a region corresponding to the functional silencer regions previously detected within the CR1 elements upstream of the chicken lysozyme and apoVLDLII genes.

Primary sequence, evolution, and repetitive elements of the Gallus gallus (chicken) beta-globin cluster

The DNA sequence of the Gallus gallus (chicken) beta-globin cluster was completed and analyzed. This G + C-rich region is 23.7 kb in length and includes the rho-, beta H-, beta A-, and epsilon-globin genes, the enhancer found between the beta A and epsilon genes, and three upstream DNase I hypersensitive sites. The CpG dinucleotides are nonrandomly distributed, being present at an increased relative frequency near the promoters and upstream hypersensitive sites. The cluster has an unusually low TA dinucleotide frequency. The upstream hypersensitive sites (5'HS1, 5'HS2, and 5'HS3) contain DNA sequence motifs recognized by erythroid transcription factors. However, no significant sequence similarity was found among the upstream hypersensitive sites and the beta A/epsilon enhancer. The G. gallus upstream site sequences were not similar to the upstream sites of the mammalian globin clusters, probably due to the small size of the functional regions and large evolutionary distance between the classes. The avian cluster evolved by gene duplication from an ancestor beta-globin gene, first producing the epsilon and the rho/beta H/beta A ancestor genes, then the rho and the beta H/beta A ancestor genes, and finally the beta H- and beta A-globins. Four probable gene conversions can be documented: beta A to beta H, epsilon to beta H, and rho/epsilon (twice). The cluster shows a massive overrepresentation of a non-LTR retrotransposon, CR1, which accounts for 16% of the DNA. We suggest that the locus is a preferred site for CR1 insertion.

Arginine vasotocin gene expression and hormone synthesis during ontogeny of the chicken embryo and the newborn chick

Chicken embryos at different developmental stages (embryonal day (E) 6 to 21) and chicks at posthatch day 1 (D1) were monitored for the development of their hypothalamo-neurohypophysial system as indicated by the kinetics of arginine vasotocin (AVT) gene expression via mRNA concentration and brain AVT content. Our data concerning the onset of gene expression support previous results from our laboratory and others about an early activation of the AVT gene transcriptional and translational activity around E6. We could detect measurable amounts of AVT in chicken embryo brains at E6 and an exponential increase during further development until D1. Dot blots of hypothalamic RNA extracts indicated that AVT gene transcript concentrations rose between E12 and E17 and slightly dropped thereafter. Northern hybridization showed that this drop was caused by a decrease of full length message and an increase of smaller transcripts during late embryonal and D1 stages, probably an AVT mRNA specific degradation phenomenon. The dissociation between the increase of AVT concentration and AVT mRNA concentration visible at the D1 stage might be due to accumulation and storage of AVT in the magnocellular neurons, preferentially in their axon terminals in the neurohypophysis. Blood samples taken from E14 onwards revealed a constant increase in plasma osmolality and plasma AVT concentration. Our data suggest that, in the chicken, AVT seems to be required early during embryonal development, either for osmoregulatory or further unknown functions.