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Abbott JK, Nordén AK, Hansson B. Sex chromosome evolution: historical insights and future perspectives. Proc Biol Sci 2018; 284:rspb.2016.2806. [PMID: 28469017 PMCID: PMC5443938 DOI: 10.1098/rspb.2016.2806] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 04/04/2017] [Indexed: 12/26/2022] Open
Abstract
Many separate-sexed organisms have sex chromosomes controlling sex determination. Sex chromosomes often have reduced recombination, specialized (frequently sex-specific) gene content, dosage compensation and heteromorphic size. Research on sex determination and sex chromosome evolution has increased over the past decade and is today a very active field. However, some areas within the field have not received as much attention as others. We therefore believe that a historic overview of key findings and empirical discoveries will put current thinking into context and help us better understand where to go next. Here, we present a timeline of important conceptual and analytical models, as well as empirical studies that have advanced the field and changed our understanding of the evolution of sex chromosomes. Finally, we highlight gaps in our knowledge so far and propose some specific areas within the field that we recommend a greater focus on in the future, including the role of ecology in sex chromosome evolution and new multilocus models of sex chromosome divergence.
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Affiliation(s)
- Jessica K Abbott
- Department of Biology, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
| | - Anna K Nordén
- Department of Biology, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
| | - Bengt Hansson
- Department of Biology, Lund University, Sölvegatan 37, 223 62 Lund, Sweden
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Marks J. Hominoid cytogenetics and evolution. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012. [DOI: 10.1002/ajpa.1330260507] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Babcock M, Yatsenko S, Stankiewicz P, Lupski JR, Morrow BE. AT-rich repeats associated with chromosome 22q11.2 rearrangement disorders shape human genome architecture on Yq12. Genome Res 2007; 17:451-60. [PMID: 17284672 PMCID: PMC1832092 DOI: 10.1101/gr.5651507] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Low copy repeats (LCRs; segmental duplications) constitute approximately 5% of the sequenced human genome. Nonallelic homologous recombination events between LCRs during meiosis can lead to chromosomal rearrangements responsible for many genomic disorders. The 22q11.2 region is susceptible to recurrent and nonrecurrent deletions, duplications as well as translocations that are mediated by LCRs termed LCR22s. One particular DNA structural element, a palindromic AT-rich repeat (PATRR) present within LCR22-3a, is responsible for translocations. Similar AT-rich repeats are present within the two largest LCR22s, LCR22-2 and LCR22-4. We provide direct sequence evidence that the AT-rich repeats have altered LCR22 organization during primate evolution. The AT-rich repeats are surrounded by a subtype of human satellite I (HSAT I), and an AluSc element, forming a 2.4-kb tripartite structure. Besides 22q11.2, FISH and PCR mapping localized the tripartite repeat within heterochromatic, unsequenced regions of the genome, including the pericentromeric regions of the acrocentric chromosomes and the heterochromatic portion of Yq12 in humans. The repeat is also present on autosomes but not on chromosome Y in other hominoid species, suggesting that it has duplicated on Yq12 after speciation of humans from its common ancestor. This demonstrates that AT-rich repeats have shaped or altered the structure of the genome during evolution.
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Affiliation(s)
- Melanie Babcock
- Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
| | - Svetlana Yatsenko
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Pawel Stankiewicz
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - James R. Lupski
- Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas 77030, USA
| | - Bernice E. Morrow
- Department of Molecular Genetics, Albert Einstein College of Medicine, Bronx, New York 10461, USA
- Corresponding author.E-mail ; fax (718) 430-8778
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Marchal JA, Acosta MJ, Bullejos M, Díaz de la Guardia R, Sánchez A. A repeat DNA sequence from the Y chromosome in species of the genus Microtus. Chromosome Res 2005; 12:757-65. [PMID: 15702414 DOI: 10.1007/s10577-005-5079-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Accepted: 08/03/2004] [Indexed: 11/30/2022]
Abstract
In most mammals, the Y chromosome is composed of a large amount of constitutive heterochromatin. In some Microtus species, this feature is also extended to the X chromosome, resulting in enlarged (giant) sex chromosomes. Several repeated DNA sequences have been described in the gonosomal heterochromatin of these species, indicating that it has heterogeneous and species-specific composition and distribution. We have cloned an AT-rich, 851-bp long, repeated DNA sequence specific for M. cabrerae Y chromosome heterochromatin. The analysis of other species of the genus Microtus indicated that this sequence is also located on the Y chromosome (male-specific) in three species (M. agrestis, M. oeconomus and M. nivalis), present on both Y and X chromosomes and on some autosomes in M. arvalis and absent in the genome of M. guentheri. Our data also suggest that the mechanism of heterochromatin amplification operating on the sex chromosomes could have been different in each species since the repeated sequences of the gonosomal heterochromatic blocks in M. cabrerae and M. agrestis are different. The absence of this sequence in the mouse genome indicates that its evolutionary origin could be recent. Future analysis of the species distribution, localization and sequence of this repeat DNA family in arvicolid rodent species could help to establish the unsolved phylogenetic relationships in this rodent group.
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Affiliation(s)
- J A Marchal
- Departamento de Biología Experimental, Facultad de Ciencias Experimentales y de la Salud, Universidad de Jaén, E-23071, Jaén, Spain
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Abstract
The human Y chromosome contains over 60 million nucleotides, but least number of genes compared to any other chromosome and acts as a genetic determinant of the male characteristic features. The male specific region, MSY, comprising 95% of the Y chromosome represents a mosaic of heterochromatic and three classes of euchromatic (X-transposed, X-degenerate and ampliconic) sequences. Thus far, 156 transcription units, 78 protein-coding genes and 27 distinct proteins of the Y chromosome have been identified. The MSY euchromatic sequences show frequent gene conversion. Of the eight massive palindromes identified on the human Y chromosome, six harbor vital testis specific genes. The human male infertility has been attributed to mutations in the genes on Y chromosome and autosomes and failures of several physical and physiological attributes including paracrine controls. In addition, deletion of any one or all the three azoospermia (AZFa, AZFb or AZFc) factor(s) and some still unidentified regulatory elements located elsewhere in the genome result in infertility. Characterization of palindromic complexes on the long arm of Y chromosome encompassing AZFb and AZFc regions and identification of HERV15 class of endogenous retroviruses close to AZFa region have facilitated our understanding on the organization of azoospermia factors. Considerable overlap of the AZFb and AZFc regions encompassing a number of genes and transcripts has been shown to exist. However, barring details on AZF, information on the exact number of genes or the types of mutations prevalent in the infertile male is not available. Similarly, roles of sizable body of repetitive DNA present in close association with transcribing sequences on the Y chromosome are yet not clear. In a clinical setting with known cases of infertility, systematic search for loss or gain of these repeat elements would help understand their biological role(s). We present a brief overview on the genetic complexity of the human Y chromosome in the context of human male infertility.
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Affiliation(s)
- Sher Ali
- National Institute of Immunology, Molecular Genetics Laboratory, Aruna Asaf Ali Marg, New Delhi 110 067, India.
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de la Torre J, Martínez-Ramírez A, Fernández JL, Díez-Martín JL, Gómez-Pineda A, Gosálvez J, López-Fernández C. A PCR product derived from female DNA with regional localization on the Y chromosome. Genome 2000; 43:580-3. [PMID: 10902724 DOI: 10.1139/g99-123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A 154-bp PCR product amplified from human female DNA mapped onto the Y chromosome under high-stringency in situ hybridization conditions. The female DNA sequence revealed an 89% homology with the HSDYZ1 sequence. When the same primers were used to amplify male DNA, a 154-bp DNA fragment was also obtained, showing a 98% homology with HSDYZ1. However, although the HSDYZ1 sequence is widely distributed along the long arm of the Y chromosome, both of these particular PCR products are di-regionally localized within this distal block of constitutive heterochromatin. In situ hybridization under lower stringency showed that these 154-bp sequences map both onto the autosomes and the Y chromosome. Overall, this paper shows (i) a new class of DNA sequences shared by the autosomes and the Y chromosome; and (ii) a substructured organization of some DNA repeats within the DYZ1 family that forms a large part of the constitutive heterochromatin of the Y chromosome.
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Affiliation(s)
- J de la Torre
- Departamento de Biología, Universidad Autónoma de Madrid, Spain.
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Watson KR. Man's Closeness to the Apes Argues for a Soul. Linacre Q 1999. [DOI: 10.1080/20508549.1999.11877557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Affiliation(s)
- Kathryn R. Watson
- Loyola University of Los Angeles in 1973, with a B.S. degree in biology
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Kim HS, Hirai H, Takenaka O. Molecular features of the TSPY gene of gibbons and Old World monkeys. Chromosome Res 1996; 4:500-6. [PMID: 8939361 DOI: 10.1007/bf02261777] [Citation(s) in RCA: 48] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Restriction pattern, chromosome localization and the sequence of the testis-specific gene, TSPY, were investigated in the white-handed gibbon, agile gibbon, siamang, hamadryas baboon and Japanese monkey. Southern blot analysis showed the TSPY gene to be male specific in the primates used and disclosed variability of restriction pattern in gibbons. Fluorescence in situ hybridization demonstrated that the probe ppTSPY2372, biotinylated using polymerase chain reaction, is located as a slight signal in the proximal long arm of the Y chromosome of the white-handed gibbon, hamadryas baboon and Japanese monkey and in the middle long arm of the Y chromosome of the siamang, while a faint signal and an intense signal were detected in the proximal long arm of the Y chromosome of the aglle gibbon. These findings allow us to speculate that the gibbons might have evolved some structural differentiation in the TSPY gene. The first introns of the TSPY genes were sequenced and compared. One hundred thirty-seven of 606 sites were found to be variable, and 10 deletions/insertions were noted among these gibbons, two species of Old World monkeys and human. Sequence similarity ranged from 81.7% between humans and hamadryas baboons to 98.7% between Japanese monkeys and hamadryas baboons. These sequences may be of great use in future studies for resolving the phylogeny of gibbons and Old World monkeys.
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Affiliation(s)
- H S Kim
- Department of Cellular and Molecular Biology, Kyoto University, Aichi, Japan
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Pravtcheva DD, Wise TL, Ensor NJ, Ruddle FH. Mosaic expression of an Hprt transgene integrated in a region of Y heterochromatin. THE JOURNAL OF EXPERIMENTAL ZOOLOGY 1994; 268:452-68. [PMID: 8176360 DOI: 10.1002/jez.1402680606] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The sensitivity of small transgenes to position effects on their expression suggests that they could serve as indicators of the chromatin properties at their integration site. In particular, they might be expected to provide information on the functional properties of mammalian heterochromatin. We have produced a transgenic line that carries a mouse Hprt minigene on the Y chromosome. In situ hybridization localized the transgene to the heterochromatic portion of the Y. Analysis of transgene expression by isoelectric focusing indicated that the transgene is expressed in a mosaic pattern, and expressing cells have different levels of transgene activity. These findings can be explained as a position effect variegation induced by Y heterochromatin. However, two other transgenes, located at autosomal sites, also showed mosaic activity. If the mosaic transgene expression is attributed to the influence of the chromatin at the insertion site, the Y heterochromatin would appear less potent than some autosomal regions at inducing variegation. An alternative explanation consistent with our results is that the mosaic expression is a semi-autonomous characteristic of these transgene loci. Transgene-expressing and non-expressing cells differed in their ability to grow and be cloned in vitro, indicating that cellular differentiation affected the chromatin structure of the transgene locus on the Y. Karyotype analysis of male mice with the Y-linked transgene and from control male mice carrying the human HPRT transgene, or the mouse Pgk-1 gene at autosomal sites, indicated that the transgene-carrying Y is prone to non-disjunction, generating cells with two (or more) or no Y chromosomes in equal proportion. Further studies will determine if the propensity of this Y chromosome to mitotic errors is also observed in vivo.
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Affiliation(s)
- D D Pravtcheva
- Pediatric Research Institute, St. Louis University School of Medicine, Missouri 63110
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Affiliation(s)
- P K Tucker
- Museum of Zoology, University of Michigan, Ann Arbor 48109
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Abstract
A 307-bp Sau3AI fragment previously cloned by deletion enrichment from the bovine Y chromosome was used to isolate a larger lambda EMBL3A genomic cattle clone. The whole 13-kb insert did not give a sex-specific pattern of hybridization to Southern blots of cattle DNA. Subclones from this phage, however, did show that this fragment had a Y-chromosomal origin. It was estimated that at least 40% of the cattle Y chromosome is composed of repeated sequences related to those within these subcloned fragments. Sequences within these subclones are male-specific or male-enriched also in sheep, goats, and deer. Comparison of cattle and sheep homologues of these sequences reveals that much greater amplification and rearrangement have occurred on the cattle Y chromosome than on the sheep Y. The apparent insertion of sequences into cattle Y-specific sequences relative to the sheep homologues suggests possible mechanisms for the evolution of the artiodactyl Y chromosome.
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Affiliation(s)
- M E Matthews
- Victorian Institute of Animal Science, Department of Agriculture, Australia
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Guttenbach M, Müller U, Schmid M. A human moderately repeated Y-specific DNA sequence is evolutionarily conserved in the Y chromosome of the great apes. Genomics 1992; 13:363-7. [PMID: 1612595 DOI: 10.1016/0888-7543(92)90254-p] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Evolutionary conservation of the human-derived moderately repeated Y-specific DNA sequence Y-190 (DYZ5) was investigated in the chimpanzee, orangutan, and gorilla. Southern blot analysis showed the presence of the sequence in the Y chromosome of all great apes. Pulsed-field gel electrophoresis and in situ hybridization revealed that the repeat is organized in one major block and confined to a small region of the Y chromosome of the three species. DYZ5 was assigned to the proximal short arm of the Y chromosome of the chimpanzee and orangutan and to the long arm of the Y chromosome of the gorilla. In light of its evolutionary conservation, DYZ5 may have an as yet undetermined structural function in the Y chromosome.
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Affiliation(s)
- M Guttenbach
- Department of Human Genetics, University of Würzburg, Germany
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Griffiths R, Holland PW. A novel avian W chromosome DNA repeat sequence in the lesser black-backed gull (Larus fuscus). Chromosoma 1990; 99:243-50. [PMID: 2170084 DOI: 10.1007/bf01731699] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The phenol emulsion reassociation technique was used to isolate and clone a female specific, repetitive DNA sequence from Larus fuscus. The repeat, designated P2000-17, is restricted to the W chromosome, although related sequences occur elsewhere in the genome of L. fuscus. Similar sequences were detected in the genome of six other bird species from outside the genus Laridae, but the sequence occurs less frequently and to a similar extent in both sexes. The 298 bp DNA sequence of P2000-17 was determined and found to have extensive sequence identity to the rabbit dihydropyridine (DHP) receptor calcium channel. P2000-17 is represented once within a larger 8.6 kb tandem repeat (LfW-1), which has a complex internal DNA sequence. LfW-1 is highly conserved between repeat motifs and may comprise 3% of the female genome. The possible evolutionary origin of LfW-1 is discussed in relation to the repeat types found on the W and Y chromosomes of other species.
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15
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Vogt P. Potential genetic functions of tandem repeated DNA sequence blocks in the human genome are based on a highly conserved "chromatin folding code". Hum Genet 1990; 84:301-36. [PMID: 2407640 DOI: 10.1007/bf00196228] [Citation(s) in RCA: 99] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This review is based on a thorough description of the structure and sequence organization of tandemly organized repetitive DNA sequence families in the human genome; it is aimed at revealing the locus-specific sequence organization of tandemly repetitive sequence structures as a highly conserved DNA sequence code. These repetitive so-called "super-structures" or "higher-order" structures are able to attract specific nuclear proteins. I shall define this code therefore as a "chromatin folding code". Since locus-specific superstructures of tandemly repetitive sequence units are present not only in the chromosome centromere or telomere region but also on the arms of the chromosomes, I assume that their chromatin folding code may contribute to, or even organize, the folding pathway of the chromatin chain in the nucleus. The "chromatin folding code" is based on its specific "chromatin code", which describes the sequence dependence of the helical pathway of the DNA primary sequence (i.e., secondary structure) entrapping the histone octamers in preferential positions. There is no periodicity in the distribution of the nucleosomes along the DNA chain. The folding pathway of the nucleosomal chromatin chain is however still flexible and determined by e.g., the length of the DNA chain between the nucleosomes. The fixation and stabilization of the chromatin chain in the space of the nucleus (i.e., its "functional state") may be mediated by additionally unique DNA protein interactions that are dictated by the "chromatin folding code". The unique DNA-protein interactions around the centromeres of human chromosomes are revealed for example by their "C-banding". I wish to stress that it is not my aim to relate each block of repetitive DNA sequences to a specific "chromatin folding code", but I shall demonstrate that there is an inherent potential for tandem repeated sequence units to develop a locus-specific repetitive higher order structure; this potential may create a specific chromatin folding code whenever a selection force exists at the position of this repetitive DNA structure in the genome.
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Affiliation(s)
- P Vogt
- Institut für Humangenetik und Anthropologie der Universität, Heidelberg, Federal Republic of Germany
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Arnemann J, Gradl G, Casper J, Schmoll HJ, Schmidtke J, Fonatsch C. Characterization of rearranged Y chromosomes in human testicular tumor cell lines. CANCER GENETICS AND CYTOGENETICS 1989; 37:141-51. [PMID: 2539248 DOI: 10.1016/0165-4608(89)90042-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Cytogenetic analysis of four cell lines established from two different human testicular tumors revealed rearranged or missing Y chromosomes. Southern blot analysis and in situ hybridization with different Y-derived human DNA sequences revealed the existence of Y chromosomal material even in a line without a cytogenetically visible Y chromosome and clarified the composition of Y marker chromosomes.
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Affiliation(s)
- J Arnemann
- Institut für Humangenetik, Universitätskliniken, Göttingen, West Germany
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Harata M, Ouchi K, Ohata S, Kikuchi A, Mizuno S. Purification and characterization of W-protein. A DNA-binding protein showing high affinity for the W chromosome-specific repetitive DNA sequences of chicken. J Biol Chem 1988. [DOI: 10.1016/s0021-9258(18)68336-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
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Abstract
Four cloned unique sequences from the human Y chromosome, two of which are found only on the Y chromosome and two of which are on both the X and Y chromosomes, were hybridized to restriction enzyme-treated DNA samples of a male and a female chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla), and pig-tailed macaque (Macaca nemestrina); and a male orangutan (Pongo pygmaeus) and gibbon (Hylobates lar). One of the human Y-specific probes hybridized only to male DNA among the humans and great apes, and thus its Y linkage and sequence similarities are conserved. The other human Y-specific clone hybridized to male and female DNA from the humans, great apes, and gibbon, indicating its presence on the X chromosome or autosomes. Two human sequences present on both the X and Y chromosomes also demonstrated conservation as indicated by hybridization to genomic DNAs of distantly related species and by partial conservation of restriction enzyme sites. Although conservation of Y linkage can only be demonstrated for one of these four sequences, these results suggest that Y-chromosomal unique sequence genes do not diverge markedly more rapidly than unique sequences located on other chromosomes. However, this sequence conservation may in part be due to evolution while part of other chromosomes.
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Affiliation(s)
- R P Erickson
- Laboratory of Human Molecular Genetics, Imperial Cancer Research Fund, London, UK
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Nishioka Y, Lamothe E. Isolation of human Y chromosomal major repetitive sequences from a flow-sorted Y chromosomal library. AMERICAN JOURNAL OF MEDICAL GENETICS 1987; 27:711-7. [PMID: 3631141 DOI: 10.1002/ajmg.1320270327] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The human Y chromosome is highly heterochromatic and consists mainly of repetitive sequences, of which 3.4 kb HaeIII or EcoR1 fragments represent the most abundant species. From a flow-sorted human Y chromosomal library, we isolated 15 clones containing sequences highly homologous to this major repetitive sequence. Although the size of inserts varied from 0.7 to 3.8 kb, their hybridization patterns to human genomic DNA were indistinguishable from each other. These repetitive sequences unambiguously detected the presence of the Y chromosome in a male-female DNA mixture of which 5% was derived from male cells. Thus, these clones would be useful molecular tools to detect contaminating male cells in clinical materials.
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Characterization and evolution of a single-copy sequence from the human Y chromosome. Mol Cell Biol 1985. [PMID: 3990685 DOI: 10.1128/mcb.5.3.576] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To study the evolution and organization of DNA from the human Y chromosome, we constructed a recombinant library of human Y DNA by using a somatic cell hybrid in which the only cytologically detectable human chromosome is the Y. One recombinant (4B2) contained a 3.3-kilobase EcoRI single-copy fragment which was localized to the proximal portion of the Y long arm. Sequences homologous to this human DNA are present in male gorilla, chimpanzee, and orangutan DNAs but not in female ape DNAs. Under stringent hybridization conditions, the homologous sequence is either a single-copy or a low-order repeat in humans and in the apes. With relaxed hybridization conditions, this human Y probe detected several homologous DNA fragments which are all derived from the Y in that they occur in male DNAs from humans and the apes but not in female DNAs. In contrast, this probe hybridized to highly repeated sequences in both male and female DNAs from old world monkeys. Thus, sequences homologous to this probe underwent a change in copy number and chromosomal distribution during primate evolution.
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Wolfe J, Darling SM, Erickson RP, Craig IW, Buckle VJ, Rigby PW, Willard HF, Goodfellow PN. Isolation and characterization of an alphoid centromeric repeat family from the human Y chromosome. J Mol Biol 1985; 182:477-85. [PMID: 4040175 DOI: 10.1016/0022-2836(85)90234-7] [Citation(s) in RCA: 195] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
A collection of human Y-derived cosmid clones was screened with a plasmid insert containing a member of the human X chromosome alphoid repeat family, DXZ1. Two positive cosmids were isolated and the repeats they contained were investigated by Southern blotting, in situ hybridization and sequence analysis. On hybridization to human genomic DNAs, the expected cross-hybridization characteristic of all alphoid sequences was seen and, in addition, a 5500 base EcoRI fragment was found to be characteristic of a Y-specific alphoid repeat. Dosage experiments demonstrated that there are about 100 copies of this 5500 base EcoRI alphoid fragment on the Y chromosome. Studies utilizing DNA from human-mouse hybrids containing only portions of the Y chromosome and in situ hybridizations to chromosome spreads demonstrated the Y centromeric localization of the 5500 base repeat. Cross-hybridization to autosomes 13, 14 and 15 was also seen; however, these chromosomes lacked detectable copies of the 5500 base EcoRI repeat sequence arrangement. Sequence analysis of portions of the Y repeat and portions of the DXZ1 repeat demonstrated about 70% homology to each other and of each to the human consensus alphoid sequence. The 5500 base EcoRI fragment was not seen in gorilla, orangutan or chimpanzee male DNA.
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Cremer C, Rappold G, Gray JW, Müller CR, Ropers HH. Preparative dual-beam sorting of the human Y chromosome and in situ hybridization of cloned DNA probes. ACTA ACUST UNITED AC 1985; 5:572-9. [PMID: 6549159 DOI: 10.1002/cyto.990050604] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Bivariate Hoechst/chromomycin flow karyotypes for chromosomes from a Chinese hamster-human hybrid cell line (CH-Y-VII) were established that have retained a human Y chromosome. These bivariate flow karyotypes showed the human Y chromosome to be completely separated from the peaks for the Chinese hamster chromosomes. In preparative dual-beam sorting experiments, 3 X 10(6) chromosomes were sorted from the Y peak into frozen petri dishes. An examination of Q-banded samples of sorted chromosomes revealed that 82% +/- 5% of them were human Y chromosomes. The DNA from the sorted chromosomes (approximately 250 ng) was isolated and used to establish a genomic library (vector lambda gt WES. lambda B). Three clones (YACG 45, 52, 54) of this library containing inserts of repetitive human DNA were used for chromosomal localization by means of in situ hybridization to metaphase spreads of male human lymphocytes and of CH-Y-VII cells. In all three cases, a significant binding to the human Y chromosome was observed. A more detailed study of the chromosomal distribution of sequences homologous to the insert of YACG 45 suggested the existence of minor binding sites on several human autosomes. Southern blot analysis revealed the existence of other human specific sequences without Y chromosome specificity.
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Burk RD, Ma P, Smith KD. Characterization and evolution of a single-copy sequence from the human Y chromosome. Mol Cell Biol 1985; 5:576-81. [PMID: 3990685 PMCID: PMC366751 DOI: 10.1128/mcb.5.3.576-581.1985] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
To study the evolution and organization of DNA from the human Y chromosome, we constructed a recombinant library of human Y DNA by using a somatic cell hybrid in which the only cytologically detectable human chromosome is the Y. One recombinant (4B2) contained a 3.3-kilobase EcoRI single-copy fragment which was localized to the proximal portion of the Y long arm. Sequences homologous to this human DNA are present in male gorilla, chimpanzee, and orangutan DNAs but not in female ape DNAs. Under stringent hybridization conditions, the homologous sequence is either a single-copy or a low-order repeat in humans and in the apes. With relaxed hybridization conditions, this human Y probe detected several homologous DNA fragments which are all derived from the Y in that they occur in male DNAs from humans and the apes but not in female DNAs. In contrast, this probe hybridized to highly repeated sequences in both male and female DNAs from old world monkeys. Thus, sequences homologous to this probe underwent a change in copy number and chromosomal distribution during primate evolution.
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Lau YF, Ying KL, Donnell GN. Identification of a case of Y:18 translocation using a Y-specific repetitive DNA probe. Hum Genet 1985; 69:102-5. [PMID: 2982722 DOI: 10.1007/bf00293276] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We have used a recombinant DNA clone derived from the Y-specific 3.4-kb repeats for in situ chromosome hybridization and Southern blotting analysis to identify a case of de novo Y;18 translocation. The proband has a chromosome complement of 46,XY and a variant chromosome 18 with a Q-bright and C-positive short arm. The father has a normal male karyotype of 46,XY. The mother has a female karyotype of 46,XX and an unusually large Q-bright satellite on one chromosome 22. In situ hybridization with the 3.4-kb probe to the metaphase preparations of family members indicated that the additional Q-bright material in the proband's variant chromosome 18 derived from the Y chromosome of his father, and not from the variant chromosome 22 of his mother. On Southern hybridization, the proband had approximately twice the amount of 3.4-kb repeats per cell as his father. These observations suggest a de novo genetic rearrangement in the proband which probably occurred during the father's spermatogenesis.
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Fitch N, Richer CL, Pinsky L, Kahn A. Deletion of the long arm of the Y chromosome and review of Y chromosome abnormalities. AMERICAN JOURNAL OF MEDICAL GENETICS 1985; 20:31-42. [PMID: 3881955 DOI: 10.1002/ajmg.1320200106] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We report on a patient whose karyotype is 45,X/46,X,del(Y) (pter----q11.212). We also present a review of literature on the Y chromosome in which evidence is presented that there are genes on the Y chromosome that prevent Ullrich-Turner syndrome manifestations; aid in testes maturation and spermatogenesis; and affect height, tooth size, and bone maturation.
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Burk RD, Szabo P, O'Brien S, Nash WG, Yu L, Smith KD. Organization and chromosomal specificity of autosomal homologs of human Y chromosome repeated DNA. Chromosoma 1985; 92:225-33. [PMID: 2990828 DOI: 10.1007/bf00348698] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The human Y chromosome contains a group of repeated DNA elements, identified as 3.4-kilobase pair (kb) fragments in Hae III digests of male genomic DNA, which contain both Y-specific and non-Y-specific sequences. We have used these 3.4-kb Hae III Y fragments to explore the organizational properties and chromosomal distribution of the autosomal homologs of the non-Y-specific (NYS) 3.4-kb Hae III Y elements. Three distinct organizations, termed domains, have been identified and shown to have major concentrations on separate chromosomes. We have established that domain K is located on chromosome 15 and domain D on chromosome 16 and suggested that domain R is on chromosome 1. Our findings suggest that each domain is composed of a tandemly arrayed cluster of a regularly repeating unit containing two sets of repeated sequences: one that is homologous to the NYS 3.4-kb Hae III Y sequences and one that does not cross-react with the 3.4-kb Hae III Y repeats. Thus, these autosomal repeated DNA domains, like their Y chromosome counterparts, consist of a complex mixture of repeated DNA elements interspersed among each other in ways that lead to defined periodicities. Although each of the three identified autosomal domains cross-reacts with 3.4-kb Hae III Y fragments purified from genomic DNA, the length periodicities and sequence content of the autosomal domains are chromosome specific. The organizational properties and chromosomal distribution of these NYS 3.4-kb Hae III homologs seem inconsistent with stochastic mechanisms of sequence diffusion between chromosomes.
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Wolfe J, Erickson RP, Rigby PW, Goodfellow PN. Regional localization of 3 Y-derived sequences on the human X and Y chromosomes. Ann Hum Genet 1984; 48:253-9. [PMID: 6465842 DOI: 10.1111/j.1469-1809.1984.tb01022.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The structure of the Y chromosome and the relationship between the human sex chromosomes have been studied using Y-derived sequences cloned in cosmids. Two probes recognize different unique sequences which map to the heterochromatic part of the long arm of the Y chromosome. A third sequence is shared by the long arm of the X chromosome and the euchromatic part of the Y chromosome. Thus homology between the sex chromosomes occurs outside the pairing region.
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Friesen H, Nishioka Y. A molecular method for detecting the presence of the human Y chromosome. AMERICAN JOURNAL OF MEDICAL GENETICS 1984; 18:289-94. [PMID: 6087662 DOI: 10.1002/ajmg.1320180213] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The presence of the human Y chromosome can be inferred from the detection of a male-specific 3.4-Kb band generated by digestion with the restriction enzyme Hae III. However, direct visualization of this band is sometimes difficult owing to high background of DNA fragments common to both sexes, and Y chromosome length polymorphism. We have shown that the 3.4-Kb band can be detected by filter hybridization to a large DNA fragment (greater than 20 Kb) also generated by Hae III digestion. Since this large DNA fragment is easily isolated from either sex, it should prove useful to determine sex when chromosome analysis is impractical.
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Abstract
A recombinant DNA probe was used for antenatal sex determination. The probe was isolated from the 3.4 kilobase human repeat sequence derived from heterochromatin of the Y chromosome and had 1000 times more affinity for male DNA than for female DNA. A dot blot hybridisation method with 200 microliter of amniotic fluid yielded accurate results in 2 to 3 days. This test should facilitate antenatal diagnosis of sex-linked genetic disorders.
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Jabs EW, Wolf SF, Migeon BR. Characterization of reiterated human DNA with respect to mammalian X chromosome homology. SOMATIC CELL AND MOLECULAR GENETICS 1984; 10:93-103. [PMID: 6583856 DOI: 10.1007/bf01534476] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Recombinants containing human repetitive DNA sequences were identified by dot hybridization and classified with respect to presence on the X chromosome and homology to mouse DNA. Using genomic probes that differ in number of X chromosomes, we observed extensive homology between human autosomal and X sequences. Hybridization to genomic probes that differ in species of origin indicate that these reiterated sequences have diverged between mouse and man. Eleven recombinants, each containing a different reiterated sequence(s), were hybridized in situ to metaphase chromosomes of mouse and man. These studies indicate that reiterated DNA which is homologous to the human X chromosome is more similar to DNA of human autosomes than to any murine chromosome. Therefore, it seems that reiterated DNA sequences on the human X chromosome have diverged as much during mammalian evolution as sequences on human autosomes. Moreover, the extensive modification of the original mammalian X has not interferred with the X inactivation process.
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Abstract
Six recombinant DNA clones are described, which are derived from the Y chromosome of Drosophila hydei. They reveal characteristic features of Y chromosomal DNA sequences. Three of the cloned inserts are Y-specific and are members of the same family of repeated sequences associated with the lampbrush loop-forming fertility gene "nooses" in the short arm of the Y chromosome. The other three cloned sequences are members of three different families of repeated sequences, but display a small amount of homology to one another and to the family of the nooses sequences. These three cloned sequences are found preferentially in the Y chromosome, but also in other chromosomal positions. The Y chromosomal copies are located in the short arm of the Y chromosome. The other copies are found in autosomal kinetochore-associated heterochromatin or, for one of the cloned sequences, in one band of the giant chromosome 4, in addition to the kinetochore heterochromatin.
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Willard HF, Smith KD, Sutherland J. Isolation and characterization of a major tandem repeat family from the human X chromosome. Nucleic Acids Res 1983; 11:2017-33. [PMID: 6300789 PMCID: PMC325859 DOI: 10.1093/nar/11.7.2017] [Citation(s) in RCA: 220] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We report the identification and characterization of a family of repeated restriction fragments whose molecular organization is apparently specific to the human X chromosome. This fragment, identified as an ethidium bromide-staining 2.0 kilobase (kb) band in BamHI-digested DNA from a Chinese hamster-human somatic cell hybrid containing a human X chromosome, has been cloned into pBR325 and characterized. The 2.0 kb repeated family has been assigned to the Xp11 leads to Xq12 region on the X by Southern blot analysis of somatic cell hybrids and is predominantly arranged in tandem clusters of up to seven 2.0 kb monomers. Homologous DNA sequences, not organized as 2.0 kb BamHI fragments, are found elsewhere on the X chromosome and on at least some autosomes, but are not found on the Y chromosome. From a dosing experiment using various amounts of the cloned repeat, we estimate that there are 5,000-7,500 copies of the 2.0 kb BamHI repeat per haploid genome. Since the vast majority, if not all, of these are confined to the X chromosome, this repeated DNA family must account for 5-10% of all X chromosome DNA and must constitute the major sequence component of the pericentromeric region of the X.
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