The β globin gene cluster of the prosimian primate Galago crassicaudatus: Nucleotide sequence determination of the 41-kb cluster and comparative sequence analyses

Tagle, Danilo A.; Stanhope, Michael J.; Siemieniak, David; Benson, Philip; Goodman, Morris; Slightom, Jerry L.

doi:10.1016/0888-7543(92)90150-q

Cited by 26 publications

(26 citation statements)

References 63 publications

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“…1. This alignment has now been extended from -1300 to the polyadenylation signal of the e gene (47). Figure 2 shows portions of this extended alignment done with sequences from three species: human, galago, and rabbit.…”

Section: Resultsmentioning

confidence: 99%

Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes.

Gumucio¹,

Heilstedt-Williamson²,

Gray³

et al. 1992

Mol. Cell. Biol.

179

128

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Tissue-and developmental stage-specific expression of the human 13-like globin genes is regulated by a combination of ubiquitous and erythroid-restricted trans factors that bind to cis elements near each of the five active genes. Additional interactions of these cis and trans factors with sequences located in the far 5' end of the cluster occur by as yet obscure mechanisms. Because of the complexity of this regulatory puzzle, precise identification of the determinants that control hemoglobin switching has proven difficult. Phylogenetic footprinting is an evolutionary approach to this problem which is based on the supposition that the basic mechanisms of switching are conserved throughout mammalian phylogeny. Alignment of the 5' flanking regions of the 'y genes of several species allows the identification of footprints of 100%/ conserved sequence. We have now tested oligomers spanning 13 such phylogenetic footprints and find that 12 are bound by nuclear proteins. One conserved element located at -1086 from the 'y genes exhibits repressor activity in transient transfection studies. The protein that binds this element, CSBP-1 (conserved sequence-binding protein 1), also binds at three sites within a silencer element upstream from the £ globin gene. Further analysis reveals that the CSBP-1 binding activity is identical to that of a recently cloned zinc finger protein that has been shown to act as a repressor in other systems. The binding of CSPB-1 to silencer sequences in the £ and 'y globin genes may be important in the stage-specific silencing of these genes.

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Section: Resultsmentioning

confidence: 99%

Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes.

Gumucio¹,

Heilstedt-Williamson²,

Gray³

et al. 1992

Mol. Cell. Biol.

179

128

View full text Add to dashboard Cite

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“…26,27). In the adult portion of the gene cluster, ectopic recombination between HBB and HBD paralogs has created chimeric ␤/␦ fusion genes in multiple, independent lineages (9,23,(28)(29)(30). In the nonadult portion of the gene cluster, ectopic recombination between HBE and HBG has created a chimeric ␥/ fusion gene in myomorph rodents (24,31).…”

Section: Mode Of Gene Family Evolutionmentioning

confidence: 99%

Differential loss of embryonic globin genes during the radiation of placental mammals

Opazo

Hoffmann

Storz

2008

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

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The differential gain and loss of genes from homologous gene families represents an important source of functional variation among the genomes of different species. Differences in gene content between species are primarily attributable to lineagespecific gene gains via duplication and lineage-specific losses via deletion or inactivation. Here, we use a comparative genomic approach to investigate this process of gene turnover in the ␤-globin gene family of placental mammals. By analyzing genomic sequence data from representatives of each of the main superordinal clades of placental mammals, we were able to reconstruct pathways of gene family evolution during the basal radiation of this physiologically and morphologically diverse vertebrate group. Our analysis revealed that an initial expansion of the nonadult portion of the ␤-globin gene cluster in the ancestor of placental mammals was followed by the differential loss and retention of ancestral gene lineages, thereby generating variation in the complement of embryonic globin genes among contemporary species. The sorting of -, ␥-, and -globin gene lineages among the basal clades of placental mammals has produced species differences in the functional types of hemoglobin isoforms that can be synthesized during the course of embryonic development.

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“…Batzer et al (64) showed that the frequency of a SINE insertion at four different loci in the human genome distinguished human population groups and used their results to further support the African origin of modern humans. Comparisons between mammalian ␤-globin loci have shown that different species can be distinguished by the pattern of L1 insertions at this site (4,65,66). For example, an ancient L1 insertion between the ⑀ and ␥ genes distinguishes eutherians (mammals) from metatherians (marsupials) (4, 66), and two independent L1 insertions flank the ␥-globin gene in simians but not in prosimians (66).…”

Section: Discussionmentioning

confidence: 99%

“…Comparisons between mammalian ␤-globin loci have shown that different species can be distinguished by the pattern of L1 insertions at this site (4,65,66). For example, an ancient L1 insertion between the ⑀ and ␥ genes distinguishes eutherians (mammals) from metatherians (marsupials) (4,66), and two independent L1 insertions flank the ␥-globin gene in simians but not in prosimians (66). However, independent insertional events could be problematic for phylogenetic analysis.…”

Section: Discussionmentioning

confidence: 99%

DNA “Fossils” and Phylogenetic Analysis

Furano

Usdin

1995

Journal of Biological Chemistry

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The L1 element (LINE-1, long interspersed repeated DNA) is the mammalian version of the non-long terminal repeat class of transposable elements that replicate via an RNA intermediate (retrotransposons) (1). Every modern mammalian species studied to date contains a distinctive L1 family consisting of tens of thousands of members, which are interspersed throughout the genome. Despite their distinctiveness, all full-length mammalian L1 elements share the same organization: a 5Ј-UTR, 1 which includes a regulatory sequence; ORF I, which encodes a protein of unknown function; ORF II, which encodes an RT (2); and a 3Ј-UTR that contains a G-rich polypurine:polypyrimidine tract and terminates in an A-rich sequence (Fig. 1).Each of the modern L1 families evolved independently in the various mammalian lineages from a common ancestral L1 element that dates back to sometime before the mammalian radiation ϳ100 million years ago (3-5). Being capable of prodigious amplification, the modern L1 elements and their evolutionary antecedents (see below) now account for at least 30% of the mass of mammalian DNA. In addition, L1 elements are active in present day species and are a frequent cause of genetic polymorphisms including a number of non-inherited genetic defects in humans (6 -8). It is also possible that the L1 RT catalyzed the retrotransposition of elements that do not encode their own RT such as the mammalian SINE families (e.g. Alu in primates, B1, B2, ID, etc., in rodents) (5, 9 -11). Since these families can reach copy numbers as high as 1 ϫ 10 6 and alone contribute up to 5% of mammalian DNA (e.g. Alu (9)), L1 elements quite likely have had, and continue to have, a profound effect on the structure, function, and evolution of mammalian genomes.In spite of their prominence, most of the biochemical and molecular details of L1 regulation, replication, and transposition remain unknown. To a large extent, what is known has been derived from evolutionary studies, and these have yielded two kinds of information. The first is derived from comparisons between different mammalian L1 families or between L1 elements and their counterparts in other organisms. This comparative biochemical approach identified and assigned possible functional significance to different features of non-long terminal repeat retrotransposons.The second type of information, generated by the analytical techniques of evolutionary biology, revealed the evolutionary dynamics of L1 families. These studies suggest that L1 evolution is a paradigm for a novel, but as yet incompletely understood, evolutionary process that is taking place within the "ecosystem" of the mammalian genome and that L1 evolution is quite dynamic, with novel L1 variants continually emerging over relatively short periods of time. As a consequence, L1 evolution has generated a rather complex family structure, and it has become apparent that this feature of L1 evolution can be exploited to examine the evolutionary (phylogenetic) history of the mammalian hosts that harbor these elements (12)(13)...

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The β globin gene cluster of the prosimian primate Galago crassicaudatus: Nucleotide sequence determination of the 41-kb cluster and comparative sequence analyses

Cited by 26 publications

References 63 publications

Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes.

Phylogenetic footprinting reveals a nuclear protein which binds to silencer sequences in the human gamma and epsilon globin genes.

Differential loss of embryonic globin genes during the radiation of placental mammals

DNA “Fossils” and Phylogenetic Analysis

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