Conservation and variation in the large scale organisation of the globin gene domains of duck and chicken

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.

Silencer and enhancer elements located at the 3'-side of the chicken and duck alpha-globin-encoding gene domains

Enhancer activities have been observed in DNA fragments up to 1.36 kb long located on the 3'-side of the cluster of the three alpha-type globin-encoding genes in duck [Kretsovali et al., C.R. Acad. Sci. Paris 307 (1988) 563-568] and chicken [Knezetic and Felsenfeld, Mol. Cell. Biol. 9 (1989) 893-901]. We report here the identification of a chicken silencer element placed upstream from the three GATA-1 sites which constitute the core enhancer element in both species. This silencer element can autonomously reduce the activity of promoters for thymidine kinase and alpha D globin. Band shifts and DNase I footprinting experiments using nuclear extracts from thermosensitive avian erythroblastosis virus-transformed chicken erythroblasts led to the delineation of three sites for DNA-binding proteins within the silencer element.

Matrix attachment sites in the murine alpha-globin gene

DNA sequences with a high affinity for nuclear matrix proteins have been identified and localized in the mouse alpha-globin gene. These matrix association regions (MARs) are adjacent, covering the first intron and part of the 5'-coding sequence. The binding sites are in close proximity to DNase I hypersensitive sites and other important signal sequences. The proteins of the nuclear lamina do not bind the alpha-globin gene MARs in the in vitro binding assay. The finding of MARs in the mouse alpha-globin gene creates an apparent paradox, since works from other authors and our results presented here indicate that this gene is not bound to the nuclear matrix in vivo. This contradiction is difficult to explain at present but different possibilities are accounted for in the text.

The presence of sequence-specific protein binding sites correlate with replication activity and matrix binding in a 1.7 Kb-long DNA fragment of the chicken alpha-globin gene domain

Several recognition sites for novel sequence-specific DNA-binding proteins were found at the 5'-side of the chicken alpha-globin gene domain in a 1.7 Kbp DNA fragment. This fragment includes the replication origin, a non tissue-specific transcriptional enhancer, a DNAse I hypersensitive site and a permanent site of DNA attachment to the nuclear matrix. Most of the identified protein binding sites differ from previously known consensus sequences. Two sites coincide with MARs located at the 5'-end of the 1.7 kbp fragment. The proteins interacting with these two recognition sites were observed only in proliferating cells and were virtually absent in the extracts obtained from the nonreplicating differentiated form of the same cells. One of them seems to belong to the GATA protein family, but its presence in nuclear extracts correlates with cell proliferation rather than expression of the domain.

Protein-binding A + T-rich motifs flank the duck beta A-globin enhancer

The duck beta A-globin (beta GLB) enhancer DNA was analysed by footprinting for sites of specific binding of proteins extracted from duck erythrocytes. The results were compared with previously determined protein binding to the homologous region in chicken DNA. Two A + T-rich protein-binding sites, not recognized in chicken, were found at the 5'-end and the 3'-end of the duck beta GLB enhancer. The 5'-motif (designated BS-1; 5'-AAACAAAATGAA) binds proteins extracted from both embryonic and adult erythrocytes, while the 3'-motif (BS-2; 5'-ATAAACAAGGTC) binds protein from embryonic cells only.

Mapping of structural and transcription-related matrix attachment sites in the alpha-globin gene domain of avian erythroblasts and erythrocytes

The positions of preferential DNA interaction with the nuclear matrix were mapped within the domain of the chicken alpha-globin genes in transcriptionally active erythroblast nuclei and inactive nuclei of mature erythrocytes. In the latter, only two major distinct attachment sites were observed, close to the A + T-rich sequences previously found at the boundaries of the domain. Sequencing of these structural matrix attachment points revealed several known DNA motifs; some of them were present on both sides of the domain. In actively transcribing erythroblast nuclei of adult animals, a large fraction of the transcribed area was represented in nuclear matrix DNA, including upstream and downstream elements. In particular, adult alpha A- and alpha D-globin genes were found in matrix DNA, while the transcribed but translationally unexpressed embryonic pi gene was underrepresented. The data are discussed in terms of the existence of stable or structural and expression-related matrix attachment sites; correlations to the origin of replication and the units of transcription of the domain are shown.

Mapping of structural and transcription-related matrix attachment sites in the alpha-globin gene domain of avian erythroblasts and erythrocytes

The positions of preferential DNA interaction with the nuclear matrix were mapped within the domain of the chicken alpha-globin genes in transcriptionally active erythroblast nuclei and inactive nuclei of mature erythrocytes. In the latter, only two major distinct attachment sites were observed, close to the A + T-rich sequences previously found at the boundaries of the domain. Sequencing of these structural matrix attachment points revealed several known DNA motifs; some of them were present on both sides of the domain. In actively transcribing erythroblast nuclei of adult animals, a large fraction of the transcribed area was represented in nuclear matrix DNA, including upstream and downstream elements. In particular, adult alpha A- and alpha D-globin genes were found in matrix DNA, while the transcribed but translationally unexpressed embryonic pi gene was underrepresented. The data are discussed in terms of the existence of stable or structural and expression-related matrix attachment sites; correlations to the origin of replication and the units of transcription of the domain are shown.

Nuclear matrix attachment occurs in several regions of the IgH locus

The genome is thought to be divided into domains by DNA elements which mediate anchorage of chromosomal DNA to the nuclear matrix or chromosome scaffold. The positions of nuclear matrix anchorage regions (MARs) have been mapped within the 200 kb mouse immunoglobulin heavy chain constant region locus, thereby allowing an estimate of the size of DNA domains within a segment of the genome. MARs were identified in four regions, which appear to divide the locus into looped DNA domains of 30, 20, 30 and greater than 70 kb in length. These DNA domain sizes fall within the range of DNA loop sizes observed in histone-extracted nuclei and chromosomes. In two regions, large clusters of MARs were identified, and many of these MARs lie on DNA fragments that include repetitive DNA elements, perhaps indicating that repetitive DNA integrates into the genome close to MARs, or that some classes of repeats could themselves act as MARs.

Organization of the 3'-boundary of the chicken alpha globin gene domain and characterization of a CR 1-specific protein binding site

The sequence of a DNA fragment about 1 Kbp long located at the 3' boundary of the chicken alpha globin gene domain, including the 3'-side matrix attachment point and the site of transcription termination, was determined. It contains a repetitive DNA element and the AT-rich (easily denaturable) DNA segment conserved at the same position in the duck genome. The repetitive sequence was identified by computer analysis as being a member of the CR1 family. Within the non-repetitive part of the AT-rich DNA fragment, four topoisomerase II recognition sites were found which might be indicative of matrix attachment. Furthermore, two distinct regions were identified, possessing strong homology to a number of noncoding consensus sequences, one of them to a limited part of the LTR of HTLVIII, and the other to the replication origin of Polyoma virus JC. DNA shift experiments showed that the CR1 repeat binds specifically an abundant nuclear protein factor. The binding site for this factor was identified by footprinting and turned out to be closely related to the previously described recognition site for the TGGCA-binding protein, the chicken analog of nuclear factor 1 (NF-1). Finally, the CR1 repeats within the chicken alpha and beta globin gene domains were mapped. All these observations are discussed in terms of the organization of the 5' and 3' boundaries of the functional genomic domains forming a chromatin loop including all avian alpha type globin genes.

The chicken alpha-globin gene domain is transcribed into a 17-kilobase polycistronic RNA

The 5' start sites and the 3' ends of giant transcripts of the approximately 20-kilobase (kb)-long chicken alpha-globin gene domain were identified by reverse transcription with specific primers and by nuclease S1 mapping using cloned and sequenced restriction fragments of the domain. A transcriptional unit of approximately 17 kb was found that includes all three embryonic and adult genes of the cluster. The largest transcript initiates 8 kb upstream of the gene, within a cluster of A + T-rich sequences placed upstream of a matrix attachment point, at one of several CAA(A)T boxes framing a cluster of four TATA boxes. The 5' ends of a group of 2.5-, 5-, and 12-kb globin transcripts accumulating in avian erythroblastosis virus-transformed cells, which transcribe globin genes abortively, map to the sequence ATATATAATAA 1 kb upstream of the embryonic pi-globin gene. This sequence might correspond to a site of RNA processing or of alternative transcription initiation. Transcription of the domain ends about 2 kb downstream of the last gene of the cluster, downstream of an enhancer and immediately upstream of a CR1 repetitive element in an A + T-rich sequence that includes a matrix attachment site. These data indicate that full-domain transcripts including embryonic as well as adult alpha-globin genes exist, and that the region transcribed is framed by A + T-rich linkers and matrix attachment points.

The duck beta-globin gene cluster contains a single enhancer element

An erythroid-specific enhancer was previously identified in the 3'-flanking region of the beta adult gene in chicken and duck, by transfection into AEV transformed chicken erythroblasts. Here we show that the duck enhancer is equally active in erythroid human K562 cells, presenting an embryonic/fetal program of globin gene expression. Furthermore, no other enhancer was found within the 20 kb of DNA including four beta-like globin genes as well as a 1.5 kb upstream and a 3 kb downstream sequence.

Transcription of the alpha globin gene domain in normal and AEV-transformed chicken erythroblasts: mapping of giant globin-specific RNA including embryonic and adult genes

The genomic domain of about 20 kbp of the chicken alpha-type globin genes, framed by AT-rich linkers (ATRLs; Moreau et al. 1982) and repetitive sequences (Broders et al. 1986), was cut into 13 fragments and subcloned. The in vitro labelled individual restriction fragments were used to test the extent of the transcribed domain by blot-hybridization of nuclear RNA in large excess from normal adult chicken and Avian Erythroblastosis Virus (AEV)-transformed erythroblasts. In both these types of cells, the AT-rich segments situated 6 kbp upstream of the first gene as well as all the domain including the embryonic pi and the adult alpha D and alpha A genes down to the AT-rich segment placed 3 kbp downstream were found to be transcribed. Electrophoresis of nuclear RNA, Northern blotting and hybridization with most of the nick-translated DNA probes revealed in all cases the presence of heterogeneous globin RNA molecules in the 3-12 kb range, as well as some distinct RNA bands. Single-stranded RNA probes of some genomic segments indicated asymmetrical transcription of the minus strand. A 12 kb globin-specific RNA including the pi and alpha A genes but not the intervening alpha D gene was observed in AEV-transformed cells: it includes sequences located far upstream and downstream from the alpha globin genes and might represent a processing product of a full length transcript spanning the whole domain. Reverse transcription by extension of primers placed in the first exon of each of the three globin genes confirmed the presence of continuous transcripts of the domain including the two adult and the embryonic globin genes.

Co-evolution of base composition and codon usage in Xenopus laevis and human globin genes with long-range DNA organization of their genome

Eucaryotic DNA is punctuated by many A+T-rich segments that we named A+T-rich linkers. Two types of these A+T-rich linkers can be distinguished: (i) isolated A+T-rich linkers, and (ii) A+T-rich linkers crowded in clusters. We have analysed the distribution of A+T-rich linker across the alpha- and beta-globin gene domain in Xenopus laevis and human genomes using isodenaturation and electron microscopy. Comparison of our data with those previously obtained for the avian globin genes leads us to conclude that genes can be harboured indifferently in either domain. A correlation is established between the presence of A+T-rich linker inside introns and flanking regions and the A+T content of the coding sequence. For the coding sequence, a high A+T content is strongly correlated with high A+T content in the codon's third position and weakly in the first position.

A transcriptional enhancer located between adult beta-globin and embryonic epsilon-globin genes in chicken and duck

We have detected a transcriptional enhancer sequence downstream from the adult beta-globin (beta A-globin) genes of chicken and duck. DNA segments from the beta-globin coding and flanking sequences were cloned into expression vectors containing the SV40 promoter linked to either the T antigen gene or the cat gene. The expression of these genes was measured in a chicken erythroid cell line transfected with the recombinant plasmids. We found that segments located about 400 bp downstream from the poly(A) site of both the chicken and duck beta A-globin genes (and about 1.5 kb upstream from the embryonic epsilon-globin gene) stimulate transcription of the test genes about five-fold. In chicken essentially the same segment was also found by others to act as an erythroid cell-specific enhancer [Hesse et al., Proc. Natl. Acad. Sci. USA 83 (1986) 4312-4316; Choi and Engel, Nature 323 (1986) 731-734]. The sequence containing this enhancer is conserved in evolution. A high degree of homology, reaching 84% in a segment 180 bp in length, was found between chicken and duck despite an evolutionary divergence of 70 myr.

Correlations of repetitive and AT-rich DNA segments within the chicken globin gene domains

The repetitive DNA segments were mapped within a 30 Kbp genomic domain including (in 5' to 3' order) the chicken embryonic pi and adult alpha D (minor) and alpha A (major) globin genes. Two repeats map 5 and 8 Kbp upstream from the embryonic pi gene and another 3 Kbp downstream of the adult alpha A gene. These repetitive DNA sequences are placed within, or immediately adjacent to the AT-rich DNA segments framing this domain. Similar correlations exist also within the chicken beta globin gene domain. The positions of these AT-rich and repetitive DNA segments framing the alpha globin gene domain also correlate with other already explored features of long range DNA organisation, as clusters of sites of DNAse I hypersensitivity and differential methylation, sites of Matrix-DNA attachment, and with the beginning and end of the transcribed domain.