Intergenic DNA sequences flanking the pseudo alpha globin genes of human and chimpanzee

Sawada, Ikuhisa; Beal, Marc P.; Shen, Chc-Kun James; Chapman, Barbara S.; Wilson, Allan C.; Schmid, Carl W.

doi:10.1093/nar/11.22.8087

Cited by 35 publications

(12 citation statements)

References 29 publications

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“…There is evidence of the same phenomena in the interspersed GGA repeats. The generation of tandem repeats and their divergence to more complex forms can be explained by several models, including unequai crossover (29) or polymerase slippage during replication (26). These models are consistent with the observation in satellite and the GGA repeats that adjoining repeat units tend to share common changes from the repeat consensus, as if amplification occurred predominantly in a local region.…”

Section: Cloningsupporting

confidence: 72%

“…This doubled the length of the repeat unit through the region. Some of the divergence observed in the repeats may have emerged by a simple amplification through unequal crossover or replication slippage (26,29).…”

Section: Cloningmentioning

confidence: 99%

“…Isolated examples of other simple sequence repeats have been found in noncentromeric locations (2,4,10,21,24,26,28). Small clusters of (CA), have been implicated as hot spots for recombination or gene conversion (28).…”

Section: Cloningmentioning

confidence: 99%

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Repeat arrays in cellular DNA related to the Epstein-Barr virus IR3 repeat.

Heller¹,

Flemington²,

Kieff³

et al. 1985

Mol. Cell. Biol.

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We isolated clones and determined the sequence of portions of mouse and human cellular DNA which cross-hybridize strongly with the IR3 repetitive region of Epstein-Barr virus. The sequences were found to be tandem arrays of a simple sequence based on the triplet GGA, very similar to the IR3 repeat. The cellular repeats have distinct differences from the viral repeat region, however, and their sequences do not appear capable of being translated into a purely glycine-plus-alanine protein domain like the portion of the Epstein-Barr nuclear antigen coded by IR3. Although the relationship between IR3 anid the cellular repeats is left unclear, the cellular repeats have many interesting features. The tandem arrays are about 1 to several kilobases long, much shorter than satellite tandem repeats and larger than other interspersed, tandem repeats. Each of the repeats is a distinct variation, perhaps diverged from a common sequence, (GGA)n. This family is present in the genomes of all species tested and appears to be a ubiquitous feature of all higher eucaryotic genomes.Epstein-Barr virus (EBV) is a B-lymphotrophic human herpesvirus. The EBV genome consists of unique and repetitive sequences (1, 17). One of the internal direct repeats, IR3, is a 708-base-pair (bp) region (in the B95-8 strain of EBV) which contains only three nucleotide triplets: GGG, GGA, and GCA (7, 14). The three triplets are arrayed as a single or repetitive 9-bp sequence, GGG GCA GGA, interspersed with a 6-bp sequence, GCA GGA, or a 9-bp sequence, GCA GGA GGA. There is no regular pattern of interspersion of these repeating units. Interestingly, IR3 encodes a repetitive glycine-alanine domain of a protein, EBNA-1, found in the nucleus of all EBV latently infected cells (15). The functions of EBNA-1 are not entirely known. Recent data indicate that EBNA-1 acts in trans to permit replication of episomes containing a putative origin of EBV DNA replication (J. Yates and B. Sugden, personal communication).Southern blot analysis indicates that EBV IR3 is homologous to moderately reiterated and interspersed sequences in mouse and human DNA (14). The heterogeneity of the IR3 homologous cellular DNA fragment sizes suggests that the genomic sequences are interspersed in the cellular genomes and are not organized as large tandem arrays like satellite DNA. This was further confirmed by in situ hybridization of IR3 to human chromosomes (12). IR3-related human sequences are found on every chromosome except the Y chromosome. The chromosomal loci are primarily euchromatic with no enrichment at the centromeres as is observed for most previously described simple sequence repeats (reviewed in reference 27).The homology to an EBV sequence which encodes part of EBNA raises the possibility of a genetic or functional relatedness to the cellular sequences. To further define the IR3-related cellular sequence elements, we isolated several independent regions from the human and mouse genomes which hybridize to EBV IR3 and sequenced the regions of * Corresponding author.

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Section: Cloningsupporting

confidence: 72%

Section: Cloningmentioning

confidence: 99%

See 1 more Smart Citation

Repeat arrays in cellular DNA related to the Epstein-Barr virus IR3 repeat.

Heller¹,

Flemington²,

Kieff³

et al. 1985

Mol. Cell. Biol.

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“…In contrast, 21 substitutions are found in the coding regions of the orangutan (Table 1). The intergenic regions of the human and orangutan a-globin cluster diverge by -6.0% (data not shown), in contrast to the value of 2.6% divergence for human and chimpanzee intergenic DNA derived from elsewhere in the a-globin cluster (41). While these comparisons are phenetic, and await the sequence determination of appropriate out-groups (e.g., rhesus macaque, olive baboon, etc.)…”

Section: Discussionmentioning

confidence: 93%

The orangutan adult alpha-globin gene locus: duplicated functional genes and a newly detected member of the primate alpha-globin gene family.

Marks

Shaw

Shen

1986

Proc. Natl. Acad. Sci. U.S.A.

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We have cloned and sequenced the complete al-and a2-globin genes of the orangutan, and here we compare them to the homologous genes of the human. The pattern of similarity apparent among the genes is most consistent with a model of gene correction operating on the primate a-globin cluster. This correction breaks down in both human and orangutan in the 3'-untranslated region at 14 base pairs downstream from the termination codon. The unit evolutionary period values calculated for either the replacement substitution or the silent substitutions are only slightly higher than the previously established molecular clock predicts. The 7-base-pair insertion in intron 2 of the human al-globin gene is not present in either orangutan gene, suggesting that this insertion is not the cause of the sequence divergence in the 3'-untranslated regions of primate a2-and al-globin genes. Finally, blotting hybridization and partial DNA sequencing reveal a newly detected member of the primate a-globin gene family, which is located downstream from the duplicated adult a-globin genes.Genetic studies over the past quarter of a century have shown that while human, chimpanzee, and gorilla are virtually indistinguishable at the genetic level, they cluster as a group somewhat more distantly from their Asian relative, the orangutan (1-3). The exact nature of the evolutionary relationship between humans and the apes has been debated for decades, however, and continues to be debated (4-6). As many conflicting genetic phylogenies have been suggested in recent years, it now seems likely that satisfactory resolution of the problem will be achieved only by careful analyses of the homologous nucleotide sequences from the nuclear genomes of human, chimpanzee, gorilla, and orangutan (7). The a-globin-like gene locus is an ideal choice for this purpose.One of the most intensively studied regions of the primate nuclear genomes is the human a-globin gene cluster (for a review, see ref. 8). This cluster consists of five globin genes arranged in the order 5'-6+q-4al-a2-al-3' (9) and at least eight Alu family repeats (10). The three functional genes (embryonic, {; adult, a2 and al) are all transcribed on the same DNA strand and are arranged in the order of their expression during development. Both qial and 4if are pseudogenes (11,12). One of the most interesting structural aspects of the a-globin cluster is the evolution of its adult globin gene region. Heteroduplex mapping and nucleotide sequence analysis have revealed extensive homology within (9, 13-15) and flanking the a2-and al-globin genes (9,(15)(16)(17). Each of the two homologous sequences spans a region of 4 kilobases (kb) and is interrupted by two blocks of nonhomology (9,16). This extensive sequence homology is thought to be the product of an ancient duplication event and subsequent gene correction (9,(13)(14)(15)(16).The organization of the human adult a-globin-like gene region makes it an excellent model for investigating the processes of molecular evolution, by using the modem techniqu...

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“…The newly discovered 01 has only been sequenced in orangutan and a1 and a2 are known for orangutan and human (Marks et al, 1986a,b). Sawada et al (1983Sawada et al ( , 1985 sequenced Alu family repeats 5' to the human and chimp $a. While these data are useful in assessing modes and rates of evolution, until holes in the data are filled, phylogenetic applications are minimal.…”

mentioning

confidence: 99%

Nucleic acid evidence bearing on hominoid relationships

Weiss

1987

Am. J. Phys. Anthropol.

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Molecular approaches to primate evolutionary relationships have been in use for 25 years. Recent advances in nucleic acid technology have permitted increasing resolution in assessing the topology and timing of primate phylogeny. The basics of these new approaches and their possibilities and limitations are set forth in reference to hominoid evolution. Specific reference is made to recent research involving DNA-DNA liquid hybridization, restriction mapping, and nucleic acid sequencing. These approaches are unanimous in establishing an African ape-human clade within the hominoids; orangutans share a more recent common ancestor with this clade than does the gibbon. Present data on the form of the tree uniting chimps, gorilla, and human are not compelling. Currently, it appears somewhat more likely that chimps and humans shared a most recent common ancestor, but a strong case can be made for a tree that joins chimp and gorilla. The tree uniting humans and gorillas cannot be disregarded. For present purposes, a trifurcation, though probably not literally correct, is a reasonable reconstruction. Molecular information is proving especially useful in setting the time frame for hominoid evolution as well as drastically limiting the number of trees that can be reasonably entertained. As the technology becomes more sophisticated, it can be hoped that the ability to discriminate between trees will increase. It will be necessary to maintain a continuing dialogue between morphological and molecular biologists to insure cross-fertilization of ideas about hominoid relations.The persistence of the chemical blood relationships between the various groups of animals serves to carry us back into geological times, and I believe . , . that it will lead to valuable results in the study of various problems of evolution. Nuttall, 1904The outline of hominoid evolution has undergone a major reappraisal in recent years. The grouping of African apes with the orangutan in the family Pongidae and the positioning of humans in the family Hominidae has been the taxonomic convention. This grouping also has been presumed to reflect phylogenetic relationships. This framework for viewing hominoid evolution and taxonomy persisted for many years, from prior to World War 11 (e.g., Schultz, 1936) to well afterward (Le Gros Clark, 19591, though the possibility of other trees was entertained (Straus, 1949). In the 1960s the last common ancestor of humans and the African apes was being placed in the late Oligocene-early Miocene, roughly 25 MYA, by authorities such as YEARBOOK OF PHYSICAL ANTHROPOLOGY[Vol. 30, 1987 Simons (1967). The mainstream view in the late 1970s still involved a close relationship between Pongo, Pa% and Gorilla (Tuttle, 1975;Pilbeam, 1979). Yet there had been for some time a minority that advocated a much closer relationship between humans and the African apes. Dubois (1896) was of this opinion, as were Elliot Smith (1924) and, seemingly, Gregory (1916. In the 1960s, this view received new impetus with the publication of ext...

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Intergenic DNA sequences flanking the pseudo alpha globin genes of human and chimpanzee

Cited by 35 publications

References 29 publications

Repeat arrays in cellular DNA related to the Epstein-Barr virus IR3 repeat.

Repeat arrays in cellular DNA related to the Epstein-Barr virus IR3 repeat.

The orangutan adult alpha-globin gene locus: duplicated functional genes and a newly detected member of the primate alpha-globin gene family.

Nucleic acid evidence bearing on hominoid relationships

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