The chicken beta globin gene region. Delineation of transcription units and developmental regulation of interspersed DNA repeats

TMEM8 - a non-globin gene entrapped in the globin web

For more than 30 years it was believed that globin gene domains included only genes encoding globin chains. Here we show that in chickens, the domain of α-globin genes also harbor the non-globin gene TMEM8. It was relocated to the vicinity of the α-globin cluster due to inversion of an ∼170-kb genomic fragment. Although in humans TMEM8 is preferentially expressed in resting T-lymphocytes, in chickens it acquired an erythroid-specific expression profile and is upregulated upon terminal differentiation of erythroblasts. This correlates with the presence of erythroid-specific regulatory elements in the body of chicken TMEM8, which interact with regulatory elements of the α-globin genes. Surprisingly, TMEM8 is not simply recruited to the α-globin gene domain active chromatin hub. An alternative chromatin hub is assembled, which includes some of the regulatory elements essential for the activation of globin gene expression. These regulatory elements should thus shuttle between two different chromatin hubs.

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.

Poly(A)-driven and poly(A)-assisted termination: two different modes of poly(A)-dependent transcription termination

We mapped the elements that mediate termination of transcription downstream of the chicken betaH- and betaA-globin gene poly(A) sites. We found no unique element and no segment of 3'-flanking DNA to be significantly more effective than any other. When we replaced the native 3'-flanking DNA with bacterial DNA, it too supported transcription termination. Termination in the bacterial DNA depended on a functional poly(A) signal, which apparently compelled termination to occur in the downstream DNA with little regard for its sequence. We also studied premature termination by poorly processive polymerases close to the promoter. The rate of premature termination varied for different DNA sequences. However, the efficiencies of poly(A)-driven termination and promoter-proximal premature termination varied similarly on different DNAs, suggesting that poly(A)-driven termination functions by returning the transcription complex to a form which resembles a prior state of low processivity. The poly(A)-driven termination described here differs dramatically from the poly(A)-assisted termination previously described for the simian virus 40 (SV40) early transcription unit. In the SV40 early transcription unit, essentially no termination occurs downstream of the poly(A) site unless a special termination element is present. The difference between the betaH-globin and SV40 modes of termination is governed by sequences in the upstream DNA. For maximum efficiency, the betaH-globin poly(A) signal required the assistance of upstream enhancing sequences. Moreover, the SV40 early poly(A) signal also drove termination in betaH-globin style when it was placed in a betaH-globin sequence context. These studies were facilitated by a rapid, improved method of run-on transcription analysis, based on the use of a vector containing two G-free cassettes.

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.

Nucleosome spacing is compressed in active chromatin domains of chick erythroid cells

We have cleaved the chromatin of embryonic and adult chicken erythroid cells using a novel nuclease that is capable of resolving clearly the nucleosomes of active chromatin. We found that in active chromatin, nucleosomes are spaced up to 40 base pairs closer together than in inactive chromatin. This was true for both "housekeeping" and "luxury" genes and was observed whether the digestion was carried out on isolated nuclei in vitro or by activating the endogenous nuclease in vivo. The close spacing extended several kilobases into flanking chromatin, indicating that this is a domain property of active chromatin, not just a characteristic of regions disrupted by transcription. A simple interpretation of our results is that the nucleosomes of active chromatin are mobile in vivo and, not being constrained by linker histones, freely move closer together.

An apparent pause site in the transcription unit of the rabbit alpha-globin gene

Transcription of the rabbit alpha-globin gene begins primarily at the cap site, although some upstream start sites are also observed. Analysis by RNA polymerase run-on assays in nuclei shows that transcription continues at a high level past the polyadenylation site, after which the polymerase density actually increases in a region of about 400 nucleotides, followed by a gradual decline over the 700 nucleotides. These features are also observed in the transcription unit of the rabbit beta-globin gene. The region with the unexpectedly high nascent RNA hybridization signal in the 3' flank contains a conserved sequence, KGCAGCWGGR (K = G or T, W = A or T, R = A or G), followed by an inverted repeat. The inverted repeat (perhaps with the conserved sequence) may be a pause site for RNA polymerase II, thus accounting for the increase in polymerase density. This sequence and inverted repeat are found in the 3' flank of several globin genes and the simian virus 40 (SV40) early genes, as well as in the regions implicated in pausing or termination of transcription of eight different genes. Deletion of the conserved sequence and inverted repeat from the 3' flank of the SV40 early region causes a small increase in the levels of transcription downstream from this site. Replacement with the conserved sequence and inverted repeat from the rabbit alpha-globin gene causes an accumulation of polymerases, supporting the hypothesis that polymerases pause at this site. This proposed pause site may affect the efficiency of termination at some sites further downstream, perhaps by loss of a processivity factor.

Decline in histone H5 phosphorylation during erythroid senescence in chick embryos

Previous studies have implicated histone H5 dephosphorylation as a causal factor in genetic inactivation and chromatin condensation during erythroid senescence in adult chickens. We show that histone H5 phosphorylation declines in two stages as various cohorts of erythroid cells senesce in chick embryos. The first decline occurs between 5 and 6 days and coincides with the senescence of primitive erythrocytes. The second decline in H5 phosphorylation occurs between 17 and 19 days of chicken development, when the definitive erythrocytes undergo senescence and chromatin condensation. These results point to a role for histone dephosphorylation during the programmed senescence of erythroid cells.

Presence of globin gene transcripts in chicken oocytes and of a partially processed globin RNA in early embryos

RNA isolated from chicken oocytes and early embryos of various stages of development were probed with cloned cDNA of the alpha type (pi, alpha D and alpha A) and beta type (beta A, globin genes. Transcripts of all genes were present, although at a very low level, in the RNA of oocytes, and of embryos of the blastula and gastrula stages, prior to the onset of globin synthesis at about 30 h incubation. Interestingly, Northern blotting of electrophoretically fractionated embryonic RNA made it possible to observe, at all stages of development and for all genes tested, RNA molecules several hundred nucleotides longer than mature mRNA. PCR amplification of the pi globin transcripts indicates that these additional sequences are localized upstream of the CAP site. These higher-MW forms were found to be replaced by normal-size globin mRNA several hours after the onset of globin synthesis. The relevance of these data to comprehension of how globin gene expression is controlled during development is discussed.

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.

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

The genomic DNA of cloned recombinants containing the duck globin genes was compared to that of the analogous domains of the chicken. A 36 kb insert including the three alpha-type globin genes was isolated from a newly prepared duck genomic library in the cosmid PJB8; another recombinant contained a 45 kb insert with the four beta globin genes. In the alpha globin gene domain, the relative positions of genes, of repetitive sequences, and of the A + T-rich segments (AT-rich linkers, ATRLs) which frame the gene cluster (Moreau et al. 1982), were found to be closely maintained between duck and chicken. Although ATRLs and repetitive sequences also frame the gene cluster in the beta globin domains of duck and chicken, there is more genetic drift in their relative positions than in the alpha domain. It is of interest that several repetitive DNA segments were detected in the chicken beta globin domain which do not exist in corresponding positions in the duck. In view of the strict conservation in both species of genes and their relative positions in the cluster, this observation seems to exclude a simple function of repetitive sequences in the control of individual genes. The data are discussed with regard to the possible significance of repetitive and AT-rich DNA segments in genome organisation and function.

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.

Transcription termination within the E1A gene of adenovirus induced by insertion of the mouse beta-major globin terminator element

In induced erythroleukemia cells, transcription of the beta-globin gene terminates in a region 600-1500 nucleotides downstream of the poly(A) site. To determine whether this region of the mouse DNA functions to terminate transcription when moved to another genomic site, portions of the putative termination region have been inserted into the E1A transcription unit of the adenovirus (type 5) chromosome. Analysis of RNA labeled either in isolated nuclei or in whole cells early after infection with reconstructed viruses indicated that transcription is terminated if the inserted DNA is oriented in the same direction as in the beta-globin transcription unit and contains the globin poly(A) site plus an additional 1395 nucleotides downstream. In addition to halting transcription within the E1A unit, the insertion of the terminator region had a negative cis effect on the E1B transcription unit, which normally initiates 363 bp downstream of the site of the globin insert. The E1B transcription unit was the only early gene affected, and complementation of the terminator virus with a wild-type E1A gene did not restore transcription of the E1B gene.

Torsional stress promotes the DNAase I sensitivity of active genes

Active genes are known to have an altered chromatin structure that is preferentially sensitive to digestion with DNAase I. We find that when chicken red blood cells are incubated in media containing the topoisomerase II inhibitor novobiocin, the preferential DNAase I sensitivity of the active beta-globin genes is reversed in vivo with as little as 20 min of drug treatment. Control experiments suggest that inhibition of a topoisomerase II is responsible for this alteration in active gene conformation. Reversal of DNAase I sensitivity can also be induced in vitro by partial cleavage of the nuclear DNA with staphylococcal nuclease. We propose that the altered structure around active genes is maintained by continuous DNA supercoiling and that in the absence of this superhelical tension active chromatin reverts to a less DNAase I-sensitive ground state.

Induced differentiation of murine erythroleukemia cells: cellular and molecular mechanisms

Study of inducer-mediated differentiation of murine erythroleukemia cells provides insights into the cellular and molecular mechanisms implicated in cell differentiation. The loss of proliferative capacity is revealed to be a complex multistep process during which the cells progress through a series of stages, including a precommitment "initiation" stage, a stage suggestive of the accumulation of commitment-related factors, and, finally, a stage of expression of the characteristics of the differentiated state. Cell cycle arrest in G1 phase of the cell cycle may, in part at least, be related to down-regulation of protein p53 synthesis. Expression of induced differentiation is accompanied by an acceleration of transcription at the globin loci, and possibly by posttranscriptional modulation of globin mRNA accumulation, as well. Cells at the stage of erythroid cell development represented by the transformed, differentiation-arrested MELC, have acquired a unique DNA structure and chromatin configuration around the globin genes which distinguish them from other, nonerythroid cells; additional complex changes in chromatin configuration accompany, and probably precede, inducer-mediated acceleration of globin gene transcription during terminal differentiation. Passage through G1 and early S phase of the cell cycle, in the presence of inducer, is critical for subsequent globin gene expression and may be important in establishing the chromatin reconfiguration required for gene expression.