Analysis of the adult and embryonic chicken globin genes in chromosomal DNA

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.

Platypus globin genes and flanking loci suggest a new insertional model for beta-globin evolution in birds and mammals

BACKGROUND

Vertebrate alpha (alpha)- and beta (beta)-globin gene families exemplify the way in which genomes evolve to produce functional complexity. From tandem duplication of a single globin locus, the alpha- and beta-globin clusters expanded, and then were separated onto different chromosomes. The previous finding of a fossil beta-globin gene (omega) in the marsupial alpha-cluster, however, suggested that duplication of the alpha-beta cluster onto two chromosomes, followed by lineage-specific gene loss and duplication, produced paralogous alpha- and beta-globin clusters in birds and mammals. Here we analyse genomic data from an egg-laying monotreme mammal, the platypus (Ornithorhynchus anatinus), to explore haemoglobin evolution at the stem of the mammalian radiation.

RESULTS

The platypus alpha-globin cluster (chromosome 21) contains embryonic and adult alpha- globin genes, a beta-like omega-globin gene, and the GBY globin gene with homology to cytoglobin, arranged as 5'-zeta-zeta'-alphaD-alpha3-alpha2-alpha1-omega-GBY-3'. The platypus beta-globin cluster (chromosome 2) contains single embryonic and adult globin genes arranged as 5'-epsilon-beta-3'. Surprisingly, all of these globin genes were expressed in some adult tissues. Comparison of flanking sequences revealed that all jawed vertebrate alpha-globin clusters are flanked by MPG-C16orf35 and LUC7L, whereas all bird and mammal beta-globin clusters are embedded in olfactory genes. Thus, the mammalian alpha- and beta-globin clusters are orthologous to the bird alpha- and beta-globin clusters respectively.

CONCLUSION

We propose that alpha- and beta-globin clusters evolved from an ancient MPG-C16orf35-alpha-beta-GBY-LUC7L arrangement 410 million years ago. A copy of the original beta (represented by omega in marsupials and monotremes) was inserted into an array of olfactory genes before the amniote radiation (>315 million years ago), then duplicated and diverged to form orthologous clusters of beta-globin genes with different expression profiles in different lineages.

Koelliker haemoglobins in developing chick embryo

1. Three Koelliker haemoglobins, HbKE, HbKA and HbKH, derived from a post-translational loss of alpha-Arg-141, were isolated from red cells of chicken embryos. HbKE is typical of embryos up to 7 days of incubation, HbKA and HbKH are found in mature embryos. 2. All the precursor haemoglobins contain alpha A chains. HbKA derives from adult haemoglobin A whose globin composition is alpha A2 beta 2, HbKH from embryonic haemoglobin H with a globin composition alpha A2 beta H2 and HbKE from embryonic haemoglobin E with globin composition alpha A2 epsilon 2. 3. No Koelliker derivatives of haemoglobins with alpha-like chains other than alpha A were observed.

Erythroid lineage-specific expression and inducibility of the major heat shock protein HSP70 during avian embryogenesis

We have studied the expression of the major heat shock protein HSP70 during maturation of avian erythroid cells. Primitive and definitive erythroid cells were isolated from staged day 3-8 chicken embryos, and the levels of HSP70 mRNA and protein synthesis were examined. The highest levels of HSP70 are detected in polychromatic cells of the day 3-4 primitive erythroid cell. After the initial burst of HSP70 expression the levels of HSP70 mRNA and protein synthesis decline. Although HSP70 is constitutively expressed, neither HSP70 synthesis nor HSP70 mRNA levels were heat shock inducible in primitive red cells. In contrast, definitive red cells respond to heat shock by a 10- to 20-fold increase in HSP70 protein synthesis with little change in HSP70 mRNA levels. These studies reveal that HSP70 expression in erythroid cells is lineage specific, that the levels of HSP70 mRNA are not induced by heat shock, and finally, that the increased expression of HSP70 in definitive cells is due to increased translatability of HSP70 mRNA.

A Koelliker hemoglobin in chick erythrocytes

1. Adult chicken hemoglobins were analysed by ion exchange chromatography and isoelectric focusing and a minor hemoglobin fraction (HbK) was isolated. 2. Analysis of the constituent chains shows that HbK differs from the two major hemoglobins HbA and HbD in the alpha globin. 3. The amino acid composition, the tryptic peptide maps, the results of carboxypeptidase digestion and the functional properties show that the HbK alpha globin is quite similar to that of HbA except that the C-terminal amino acid Arg 141 is lacking. 4. HbK must then be considered a Koelliker-type hemoglobin.

Absence of gross change in primary DNA sequence during aging process of mice

The possibility of age-associated changes in DNA sequence in terms of amplification and rearrangement was examined in mouse spleen, liver and brain using the method of Southern transfer and filter hybridization. The DNA regions studied were at and around nine cloned sequences, most of which are known to move or amplify in certain situations. No detectable age-associated change, however, was observed in all DNA regions studied. These results suggest that widespread DNA sequence rearrangements or amplifications do not occur during the ageing process in mice.

The rabbit C family of short, interspersed repeats. Nucleotide sequence determination and transcriptional analysis

The C repeat family was first observed in the rabbit beta-like gene family. We have estimated the repetition frequency of the C repeats, determined the nucleotide sequence of three intact members and one truncated member, and have investigated the size, tissue specificity, and intracellular localization of C repeat transcripts. Members of the C repeat family are short (average size of 316 base-pairs) and are repeated about 170,000 times per haploid genome in a widely dispersed pattern. They end in a 3' poly(dA) tract and are flanked by direct repeats that range in size from 8 to 16 base-pairs. The consensus internal control regions for polymerase III transcription are located near the 5' end. Different amounts of C repeat RNA accumulate in a variety of tissues, and most of the transcripts are confined to the nucleus. A heterogeneous distribution of C repeat RNA sizes was found, ranging from about 330 to 8200 nucleotides. These structural and transcriptional properties are similar to those of primate and rodent Alu and Alu-like repeats. However, the C repeats are not similar in sequence to the Alu repeats. Thus two different types of short, interspersed repeats capable of being transcribed and proposed to be transposable elements have now been identified in mammals. The positions of these short repeats in mammalian beta-like globin gene families are not tightly conserved.

Replication, integration and expression of exogenous DNA injected into fertilized eggs of Xenopus laevis

We have analyzed the fate of circular and linear DNA molecules following microinjection into the cytoplasm of fertilized eggs of Xenopus laevis. Recombinant plasmids containing sea urchin histone genes (pSp 102), Drosophila ADH genes (sAC-1), and SV40 (SV2 CAT) replicate during the development of the injected frog embryo. In contrast, pBR322 either as monomers or multimers does not appear to replicate as efficiently. Generally, injected circular DNAs were not detectable by the gastrula stage of development, although there were several examples in which these molecules persisted until larval stages. In 90% of the cases, injected linear DNAs persisted as discrete molecules into early embryonic stages. A portion of the DNA sequences complementary to injected linear and circular molecules was detected comigrating with the high-molecular-weight cellular frog DNA (48 kb or larger) from mid-cleavage stages onward. Restriction enzyme analysis of DNA from injected embryos suggested some copies of the injected DNAs were integrated into the frog genome. This occurred in about 10%-30% of the cases of injected circular DNA and approximately 60%-70% of the cases of injected linear DNA. We were able to rescue circular plasmids from the injected blastulae by retransforming Escherichia coli. Restriction enzyme analysis of this DNA suggested that the majority of injected circular DNAs were not modified following replication in the frog embryo. The DNA of Xenopus embryos was highly methylated. On the other hand, injected DNA sequences were not methylated de novo even after many replication cycles in the frog embryo. Ribonucleic acid (RNA) transcripts from the injected DNAs were detectable by the late blastula stage of development.

Developmental regulation of globin and nonglobin messenger RNAs in avian erythroid cells

During embryonic development in the chicken two morphologically distinct erythroid cell populations sequentially appear. Coincidentally with the change in cell populations that begins on the sixth day of embryonic life, the hemoglobins of the early embryo are gradually replaced by a new set of hemoglobins, which are almost identical to those of the adult chicken. We have used recombinant DNAs to investigate the molecular mechanisms underlying these developmental changes. With respect to the eight nonglobin species of messenger RNA that we have studied, seven are present at approximately equal concentrations in erythroid cells from 5-day embryos and from anemic adults. This suggests that the replacement of erythroid cell populations is not accompanied by a general reorganization of gene expression. With respect to globin gene expression, however, we find that all but one of the globin genes studied (alpha D-globin) undergo dramatic developmental regulation. We have also shown that the expression of the gene for the embryo specific alpha-like globin, pi'-globin, is principally regulated at the level of transcription.

Repetitive DNA of Candida albicans: nuclear and mitochondrial components

We report the isolation and analysis of the rapidly reassociating DNA of the pathogenic, dimorphic fungus Candida albicans. Minicot analysis of whole-cell repetitive DNA suggested that a significant portion of this component was mitochondrial DNA. Genomic blot hybridizations in which radioactive whole-cell repetitive DNA was used as a probe revealed eight major EcoRI bands in the molecular weight range resolved by the gel system used. Isolation and analysis of high-purity mitochondrial DNA have shown that five of these bands are of mitochondrial origin. The remaining three bands are of nuclear origin and represent repetitive sequences that are found in the nuclear genome. Attempts to isolate nuclear DNA that was completely free of mitochondrial DNA contamination were unsuccessful.

Transmission of integrated sea urchin histone genes by nuclear transplantation in Xenopus laevis

Sea urchin histone genes contained in a recombinant plasmid pSp102 were microinjected into the cytoplasm of fertilized eggs of Xenopus laevis. By the late blastula stage, plasmid DNA sequences were detected comigrating with the high molecular weight cellular DNA (greater than 48 kilobases). Analysis of the DNA from injected embryos digested with various restriction endonuclease demonstrated that the injected DNA was integrated into the frog genome. Clones of embryos containing the pSp102 DNA sequences were produced by means of nuclear transplantation. Individuals of the same clone contain the pSp102 sequences integrated into similar chromosomal locations. These sites vary between different clones.

Theoretical mechanism for synthesis of carcinogen induced embryonic proteins: VIII. Transcriptional theory

In this paper an extension of prior writings on the mechanism by which changes in genic expression is presented. The previous development of these ideas led to a unifying concept of alterations in heterochromatin due to a variety of carcinogenic agents as a pivital process leading to potential re-expressions of genes (1). The following deals just with structural features of chromatin before continuing to finer control levels of gene expression, especially in reference to cancer cells. The DNA methylation status is presented as being an important step in an intermediate stage of chromatin expression along with protein acetylation, phosphorylation and methylation as other means of modifying chromatin status.

Restriction patterns of adult chicken globin genes at early and late stages of embryonic development

Globin mRNA isolated from anemic chicken was transcribed into cDNA and integrated into the Pst I cleavage site of plasmid pBR 322. After cloning in E. coli strain HB 101 and colony hybridization with 125I-labelled globin mRNA the plasmids of individual clones were characterized by hybrid arrested cell-free translation. Thus we could isolate clones containing alpha or beta globin chain nucleotide sequences. DNA was isolated from chicken blastoderms incubated for 18-20 h and from 11 d chicken embryos. A comparison of the restriction maps of the DNA from the two developmental stages with labelled nick translated plasmids and labelled cDNA did not indicate any globin gene rearrangements between these two stages of embryonic development. We conclude, that the adult chicken globin genes show a constant genomic organization during embryonic development. However, the restriction patterns of the globin gene family of the chicken strain investigated revealed some differences after 2 generations of propagation.

Chromosomal arrangement of the chicken beta-type globin genes

We have isolated the chicken beta-type globin genes from a library of chicken DNA--lambda Charon 4A recombinant bacteriophage. There are four beta-type genes within this segment of the genome; we believe this represents all of the beta-type genes of the chicken. The recombinant lambda C beta G1 contains the embryonic epsilon- and adult beta-globin genes. The hatching beta H- and embryonic rho-globin genes are found in the recombinant lambda C beta G2. Although lambda C beta G1 and lambda C beta G2 do not physically overlap, we present evidence that all four genes are closely linked and transcribed from the same DNA strand. These experiments demonstrate that the chromosomal regions represented by lambda C beta G1 and lambda C beta G2 lie approximately 1.6 kb apart in the chicken genome. A third recombinant lambda C beta G3 extends the genomic locus studied in the vicinity of the beta-type globin genes to approximately 39 kb. The physical order of the chicken beta-type globin genes within this segment of the chromosome is 5' ... rho--beta H--beta--epsilon ... 3'. This arrangement is unique among the vertebrate beta-type globin gene clusters thus far examined, in that embryonic genes are located at the 5' and 3' ends of the cluster while the hatching and adult genes occupy central positions.

Mapping of IS1 elements flanking the argF gene region on the Escherichia coli K-12 chromosome

Two directly-repeated IS1 elements have been mapped on the Escherichia coli K-12 chromosome at positions 23.2 kb and 34.5 kb counterclockwise of the IS3 element alpha3beta3 by using F-prime plasmids (including the F lac- proAB+ plasmid F128) that carry different portions of the bacterial chromosome in the purE to proA region. Mapping was accomplished in part by construction of EcoRI, BamHI, and BglII restriction enzyme cleavage maps. Electron microscope heteroduplex and hybridization studies indicate that the chromosomal region flanked by these IS1 elements is completely homologous to the IS1-argF-IS1 region (Tn2901) on the P1argF5 transducing phage (York and Stodolsky, 1981), which suggests that the argF gene region in the usual E. coli K-12 strains has a transposon-like structure.

An immunoglobulin heavy chain variable region gene is generated from three segments of DNA: VH, D and JH

We have determined the sequences of separate germline genetic elements which encode two parts of a mouse immunglobulin heavy chain variable region. These elements, termed gene segments, are heavy chain counterparts of the variable (V) and joining (J) gene segments of immunoglobulin light chains. The VH gene segment encodes amino acids 1-101 and the JH gene segment encodes amino acids 107-123 of the S107 phosphorylcholine-binding VH region. This JH gene segment and two other JH gene segments are located 5' to the mu constant region gene (Cmu) in germline DNA. We have also determined the sequence of a rearranged VH gene encoding a complete VH region, M603, which is closely related to S107. In addition, we have partially determined the VH coding sequences of the S107 and M167 heavy chain mRNAs. By comparing these sequences to the germline gene segments, we conclude that the germline VH and JH gene segments do not contain at least 13 nucleotides which are present in the rearranged VH genes. In S107, these nucleotides encode amino acids 102-106, which form part of the third hypervariable region and consequently influence the antigen-binding specificity of the immunoglobulin molecule. This portion of the variable region may be encoded by a separate germline gene segment which can be joined to the VH and JH gene segments. We term this postulated genetic element the D gene segment, referring to its role in the generation of heavy chain diversity. Essentially the same noncoding sequences are found 3' to the VH gene segment and as inverse complements 5' to two JH gene segments. These are the same conserved nucleotides previously found adjacent to light chain V and J gene segments. Each conserved sequence consists of blocks of seven and ten conserved nucleotides which are separated by a spacer of either 11 or 22 nonconserved nucleotides. The highly conserved spacing, corresponding to one or two turns of the DNA helix, maintains precise spatial orientations between blocks of conserved nucleotides. Gene segments which can join to one another (VK and JK, for example) always have spacers of different lengths. Based on these observations, we propose a model for variable region gene rearrangement mediated by proteins which recognize the same conserved sequences adjacent to both light and heavy chain immunoglobulin gene segments.

The linkage arrangement of four rabbit beta-like globin genes

Four different regions of rabbit beta-like globin gene sequences designated beta 1, beta 2, beta 3 and beta 4 were identified in a set of clones isolated from a bacteriophage lambda library of chromosomal DNA fragments (Maniatis et al., 1978). Restriction mapping and blot hybridization (Southern, 1975) studies indicate that a subset of these clones containing beta 1 and beta 2 hybridizes to an adult beta-globin cDNA clone (Maniatis et al., 1976) more efficiently than to a human gamma-globin cDNA clone (Wilson et al., 1978), while another subset containing beta 3 and beta 4 displays the converse hybridization specificity. beta 1 was identified as the adult beta-globin gene, while beta 2, beta 3 and beta 4 have not been identified with any known rabbit globin polypeptides. Cross-hybridization and transcriptional orientation experiments indicate that the set of beta-like gene clones contains overlapping restriction fragments encompassing 44 kb of rabbit chromosomal DNA. In addition, all four genes have the same transcriptional orientation and are arranged in the order 5'-beta 4-beta 3-beta 2-beta 1-3'.

Heterogeneity of genetic loci in chickens: analysis of endogenous viral and nonviral genes by cleavage of DNA with restriction endonucleases

Restriction endonucleases can be used to define the structure and position of genetic loci for which specific molecular hybridization reagents are available. We have used this approach to compare 18 chicken embryos with respect to several cellular genes; endogenous viral DNA related to the replicative genes of avian sarcoma virus (ASV) or to RAV-O, an endogenous virus of chickens; and sequences related to the transforming (src) gene of ASV. Each cellular gene eas remarkably homogeneous within our test population. We found little or no variation in globin and ovomucoid genes; ovalbumin and transferrin (with one exception) showed variation which is probably allelic in nature. The endogenous viral DNA which has homology with RAV-O was found at several different positions in host DNA and its structure resembled that of proviruses acquired by experimental infection, with sequences from both ends of viral RNA repeated near both ends of viral DNA. Within the population of 18 chickens, one endogenous provirus was always present, whereas the several other proviruses were each found in only a few members of this group. However, screening of additional chickens identified individuals lacking the provirus common to the initial 18 animals surveyed; in at least one embryo no RAV-O-related DNA was detected. These findings suggest that the endogenous RAV-O-related sequences have entered the germ line by relatively recent infection and are still segregating in several contemporary chicken flocks. The sequences in the chicken genome which have homology with the src gene of ASV are invariant from bird to bird and in this sense resemble a cellular gene rather than a viral sequence.

Specificity in formation of type II F' plasmids

Eight new F' plasmids derived from Hfr strains in which F is integrated at the chromosomal element alpha 3 beta 3 have been isolated and subjected to restriction enzyme, hybridization, and electron microscope heteroduplex analysis. Plasmids carrying extensive amounts of bacterial deoxyribonucleic acid were produced even though they were obtained by selection for transfer of lac, which is closely linked to F in the parental Hfr strains. Seven plasmids were type II Flac+ proC+ purE+ plasmids, and one was a type I Flac+ proC+ plasmid. Five of the Flac+ proC+ purE+ plasmids contain approximately 284 kilobases of bacterial deoxyribonucleic acid, which is identical for all five within the resolution of the restriction enzyme analysis. Theses results indicate that type II F' plasmids are the predominant tra+ F' type from this region of the Escherichia coli K-12 chromosome and that the recombination events leading to formation of these plasmids exhibit site specificity.

On pre-messenger RNA and transcriptions. A review

From the present review integrating old and new data emerge a few principles of gene expression in eukaryotes, and an infinite variety of possible mechanistic details generating the overal pattern. The few principles, most of which are not fundamentally new, may thus be summarized. 1) The eukaryotic genome is subdivided into transcriptional units: into transcriptons which are subject to individual activation controlled at DNA level. 2) Viral genomes may contain one or a few transcriptons, while cells of multicellular organisms contain from 3 x 10(3) in diptera up to an estimated 2 x 10(5) in birds and mammals. 3) Transcriptons may include one or several coding sequences. 4) Transcriptons vary considerably in size: in mammals and birds their size spectrum falls into the 2,000 to 20,000 bp range. 5) Units of coding information constituting one message (genes) and, possibly, units of regulative information are frequently broken up and stored within the transcripton in sub-genic blocks (of so far unknown significance) in general located at a certain distance from the 5' and 3' transcript terminals which are determined by the promotor and terminator signals. 6) The gene, in its specific definition as the functional unit underlying the phenotype, is in general constituted posttranscriptionally by the processing mechanisms from the mosaic of its genomic subunits in the transcripton; segments of coding, service and regulative sequences are recombined within themselves and with each other, polygenic transcripts separate into their unit messages. 7) Activated transcriptons produce pre-mRNA; these primary transcripts are colinear with the DNA of the transcriptional unit. 8) Primary pre-mRNA is processed into secondary pre-mRNA's by extragenic cleavage and intragenic ("splicing") processing, giving rise stepwise to functional mRNA. During this process chemical modifications as methylation, 5'-terminal capping and 3'-terminal polyadenylation take place. 9) Translation yields either potentially functional polypeptides or polycistronic polyproteins subject to further processing. 10) Processing is a regulated process; it involves many of the possible phases and mechanisms of post-transcriptional regulation (cf. 39, 40).