A Y-chromosomal DNA fragment is conserved in human and chimpanzee.

A human male-specific Y-chromosomal DNA fragment (lambda YH2D6) has been isolated. By deletion-mapping analysis, 2D6 has been localized to the euchromatic portion of the long arm (Yq11) of the human Y chromosome. Among great apes, this fragment was found to be conserved in male chimpanzee but was lacking in male gorilla and male orangutan. No homologous fragments were detected in females of orangutan, gorilla, chimpanzee, or human. Nucleotide sequence analysis indicated the presence of partial-Alu-elements and of sequences similar to the GATA repeats of the snake Bkm sequence.     

Fluorescent (F) bodies in the spermatozoa of man and the great apes

Mature spermatozoa of the chimpanzee (Pan troglodytes), the gorilla (Gorilla gorilla), and the orangutan (Pongo pygmaeus) were stained with quinacrine dihydrochloride. Fluorescent (F) bodies were visualized in the spermatozoa of the chimpanzee and gorilla but were absent in the orangutan, in which there is no brilliant fluorescence in any chromosome. The F bodies appeared to be randomly located in the sperm heads of these two species, as they usually are in human spermatozoa. However, the proportion of sperm showing one or more F bodies in the chimpanzee and gorilla was not comparable to what is usually found in man. The F bodies in the chimpanzee presumably represent brilliant regions in the autosomes, since the Y chromosome has no brilliant fluorescence in this species. This is contrary to man, in which the F body is an useful indicator of the Y chromosome. In the gorilla, the F bodies probably correspond to both the Y chromosome and to some brilliant regions in the autosomes.     

Nucleotide sequence comparison of a chromosome rearrangement on human chromosome 12 and the corresponding ape chromosomes

Chromosome rearrangement has been considered to be important in the evolutionary process. Here, we demonstrate the evolutionary relationship of the rearranged human chromosome 12 and the corresponding chromosome XII in apes (chimpanzee, bonobo, gorilla, orangutan, and gibbon) by examining PCR products derived from the breakpoints of inversions and by conducting shotgun sequencing of a gorilla fosmid clone containing the breakpoint and a "duplicated segment" (duplicon). We confirmed that a pair of 23-kb duplicons flank the breakpoints of inversions on the long and short arms of chimpanzee chromosome XII. Although only the 23-kb duplicon on the long arm of chimpanzee chromosome XII and its telomeric flanking sequence are found to be conserved among the hominoids (human, great apes, and gibbons), the duplicon on the short arm of chimpanzee chromosome XII is suggested to be the result of a duplication from that on the long arm. Furthermore, the shotgun sequencing of a gorilla fosmid indicated that the breakpoint on the long arm of the gorilla is located at a different position 1.9 kb from that of chimpanzee. The region is flanked by a sequence homologous to that of human chromosome 6q22. Our findings and sequence analysis suggest a close relationship between segmental duplication and chromosome rearrangement (or breakpoint of inversion) in Hominoidea. The role of the chromosome rearrangement in speciation is also discussed based on our new results.     

Evolution of four human Y chromosomal unique sequences

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.     

Panels of somatic cell hybrids specific for chimpanzee, gorilla, orangutan, and baboon

The generation of panels of somatic cell hybrids specific for chimpanzee, gorilla, orangutan, and olive baboon is reported. The chromosome content of each hybrid clone was characterized using reverse painting on human normal metaphases and by the use of appropriate sequence tag sites (STSs), one for each chromosome arm. These resources can be advantageously exploited in the characterization of chromosome architecture of different primate species, with special reference to the discrimination of inter- and intra-chromosomal arrangement of segmental duplications.     

Characterization and evolution of a single-copy sequence from the human Y chromosome.

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.     

Examination of hominid evolution by DNA sequence homology

Hominoid phylogeny was investigated in terms of unique DNA sequence homologies. In comparisons from the human standpoint the ΔTe₅₀ DNA values were Man 0, chimpanzee 0·7, gorilla 1·4, gibbon 2·7, orangutan 2·9, and African green monkey 5·7. In comparisons from the orangutan standpoint the ΔTe₅₀ DNA values were orangutan 0, chimpanzee 1·8, Man 1·9, gorilla 2·3, gibbon 2·4 and African green monkey 4·3. These results indicate that chimpanzee and gorilla are cladistically closer to Man than to orangutan and other primates, and that gorilla DNA may have diverged slightly more from the ancestral state than chimpanzee or human DNA. Comparisons from chimpanzee and gorilla DNA standpoints are needed to achieve a more definitive picture of hominoid phylogeny.     

Evolution of homologous sequences on the human X and Y chromosomes, outside of the meiotic pairing segment.

A sequence isolated from the long arm of the human Y chromosome detects a highly homologous locus on the X. This homology extends over at least 50 kb of DNA and is postulated to be the result of a transposition event between the X and Y chromosomes during recent human evolution, since homologous sequences are shown to be present on the X chromosome alone in the chimpanzee and gorilla.     

Gorilla and orangutan c-myc nucleotide sequences: Inference on hominoid phylogeny

The nucleotide sequences of the gorilla and orangutan myc loci have been determined by the dideoxy nucleotide method. As previously observed in the human and chimpanzee sequences, an open reading frame (ORF) of 188 codons overlapping exon 1 could be deduced from the gorilla sequence. However, no such ORF appeared in the orangutan sequence.The two sequences were aligned with those of human and chimpanzee as hominoids and of gibbon and marmoset as outgroups of hominoids. The branching order in the evolution of primates was inferred from these data by different methods: maximum parsimony and neighborjoining.Our results support the view that the gorilla lineage branched off before the human and chimpanzee diverged and strengthen the hypothesis that chimpanzee and gorilla are more related to human than is orangutan. Correspondence to: F. Galibert     

A human-derived probe,p82H,hybridizes to the centromeres of gorilla,chimpanzee, and orangutan

A human-derived centromeric sequence, p82H, hybridizes to DNA from gorilla, chimpanzee, pygmy chimpanzee, and orangutan. On DNA blots, multimeric ladders based on 170 or 340 bp repeat units are seen. In metaphase chromosome preparations from these species, p82H hybridizes to the centromeric region of every chromosome. p82H forms less stable hybrids with DNA from the lion-tailed macaque and does not hybridize to DNA or chromosomes of the owl monkey or the mouse.     

An evolutionary conserved early replicating segment on the sex chromosomes of man and the great apes

Replication studies on prometaphase chromosomes of man, the chimpanzee, the pygmy chimpanzee, the gorilla, and the orangutan reveal great interspecific homologies between the autosomes. The early replicating X chromosomes clearly show a high degree of conservation of both the pattern and the time course of replication. An early replicating segment on the short arm of the X chromosomes of man (Xp22.3) which escapes inactivation can be found on the X chromosomes of the great apes as well. Furthermore, the most early replicating segment on the Y chromosomes of all species tested appears to be homologous to this segment on the X chromosomes. Therefore, these early replicating segments in the great apes may correspond to the pseudoautosomal segment proposed to exist in man. From further cytogenetic characterization of the Y chromosomes it is evident that structural alterations have resulted in an extreme divergence in both the euchromatic and heterochromatic parts. It is assumed, therefore, that, in contrast to the X chromosomes, the Y chromosomes have undergone a rapid evolution within the higher primates.     

Isolation and characterization of an alphoid centromeric repeat family from the human Y chromosome

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.     

5-Methylcytosine in heterochromatic regions of chromosomes: chimpanzee and gorilla compared to the human

Fixed metaphase chromosomes of gorilla and chimpanzee were UV-irradiated to produce regions of single-stranded DNA and then treated with antibodies specific for the minor DNA base 5-methylcytosine (5 MeC). An indirect immunofluorescence technique was used to visualize sites of antibody binding. In the gorilla six pairs of autosomes contained major fluorescent regions, indicating localized regions of highly methylated DNA. These corresponded, with the exception of chromosome 19, to the major regions of constitutive heterochromatin as seen by C-banding. The Y chromosome also contained a highly fluorescent region which was located just proximal to the intense Q-band region. In the chimpanzee no comparable concentrations of highly methylated DNA were seen. Smaller regions of intense 5 MeC binding were present on perhaps six chimpanzee chromosomes, including the Y. Five of these corresponded to chromosomes which were highly methylated in the gorilla.--There is diversity among the human, gorilla and chimpanzee in both the size and location of concentrations of 5 MeC, supporting the idea that satellite DNA evolves more rapidly than DNA in the remainder of the chromosome.     

Regional localization of human M-BCR gene to chromosome 23 band q11 in the great apes

We hybridized a human M-BCR DNA probe to the chromosomes of chimpanzee (Pan troglodytes), gorilla (Gorilla gorilld) and orangutan (Pongo pygmaeus) by FISH-technique. The human M-BCR gene was localized to chromosome 23 band q11 (23q11), which is equivalent to the human chromosome 22 band q11 in all three species. The conservation of M-BCR gene in higher primates at the corresponding human chromosome locus provides phylogenetic clues concerning the evolution of genes.     

Characterisation of a human Y chromosome repeated sequence and related sequences in higher primates

The human Y chromosome carries 2000 copies of a tandemly repeated sequence, 2.47 kb long, which constitutes about 20% of the DNA of this chromosome. These sequences are localised on the tip of the long arm of the Y chromosome. Related sequences are present in DNA of females with a related but distinguishable restriction pattern. These autosomal sequences are distributed in tandem arrays on a number of autosomes. Related sequences are also present in gorilla and chimpanzee. In gorilla they resemble the human sequences in their restriction map but are not found on the Y chromosome whereas in chimpanzee the related sequences behave as a dispersed repeat. Changes in the level of methylation of this sequence in different tissues of human males can be detected with the lowest levels found in sperm and placental DNA.     

Evolution of DNA on Y-chromosome in hominoid primates as examined by PCR

Every species of non-human primates, especially those of hominoids, has a variety of reproductive structures and accompanying male traits, such as sexual dimorphism and relative size of testis to body weight, which may be at least partly triggered by DNA on the Y-chromosome. Recently, a panel of PCR (Polymerase Chain Reaction) primer sets were designed to amplify various DNA segments spread over the human Y-chromosome. We applied these primer sets for amplification of DNA segments on the Y-chromosome of hominoid species: chimpanzee, bonobo (Pygmy chimpanzee), gorilla, orangutan, whitehanded gibbon, agile gibbon, and Japanese monkey as an out group. The DNA segments including SRY, testis determining factor, and ZFX/ZFY could be amplified clearly in males of all species examined. These highly conserved genes may serve important biological functions. However, as the phylogenic distance from humans increased, some of the DNA segments could not be amplified. For example, DYZ1 (SY160) could be amplified only using human DNA as a template, and DYF60S1 (SY61), DYZ217 (SY126) and DYS233 (SY148) could be amplified only using human and African great ape DNA. It is interesting to note that locus DYS250 (SY17) could not be amplified in chimpanzee and bonobo but amplified in gorilla and orangutan. Locus DYS251 (SY18) was amplified in all species except the white-handed gibbon. These results indicate that a variety of evolutionary events including mutation, deletion, insertion, and rearrangement occurred in Y-chromosome DNA during primate evolution.     

Origin of human chromosome 2 revisited

Similarities in chromosome banding patterns and hornologies in DNA sequence between chromosomes of the great apes and humans have suggested that human chromosome 2 originated through the fusion of two ancestral ape chromosomes. A lot of work has been directed at understanding the nature and mechanism of this fusion. The recent availability of the human chrornosome-2-specific alpha satellite DNA probe D2Z and the human chromosome-2p-specific subtelomeric DNA probe D2S445 prompted us to attempt cross-hybridization with chromosomes of the chimpanzee (Pan troglodytes), gorilla (Gorilla gorilla) and orangutan (Pongo pygmaeus) to search for equivalent locations in the great apes and to comment on the origin of human chromosome 2. The probes gave different results. No hybridization to the chromosome-2-specific alpha satellite DNA probe was observed on the presumed homologous great ape chromosomes using both high-stringency and low-stringency post-hybridization washes, whereas the subtelomeric-DNA probe specific for chromosome 2p hybridized to telomeric sites of the short arm of chromosome 12 of all three great apes. These observations suggest an evolutionary difference in the number of alpha satellite DNA repeat units in the equivalent ape chromosomes presumably involved in the chromosome fusion. Nevertheless, complete conservation of DNA sequence of the subtelomeric repeat sequence D2S445 in the ape chromosomes is demonstrated.     

Concerted evolution of alpha satellite DNA: Evidence for species specificity and a general lack of sequence conservation among alphoid sequences of higher primates

We investigated relationships among alpha satellite DNA families in the human, gorilla, chimpanzee, and orangutan genomes by filter hybridization with cloned probes which correspond to chromosome-specific alpha satellite DNAs from at least 12 different human chromosomes. These include representatives of both the dimer-based and pentamer-based subfamilies, the two major subfamilies of human alpha satellite. In addition, we evaluated several high-copy dimer-based probes isolated from gorilla genomic DNA. Under low stringency conditions, all human probes tested hybridized extensively with gorilla and chimpanzee alpha satellite sequences. However, only pentameric and other non-dimeric human alphoid probes hybridized with orangutan alpha satellite sequences; probes belonging to the dimer subfamily did not cross-hybridize detectably with orangutan DNA. Moreover, under high stringency conditions, each of the human probes hybridized extensively only with human genomic DNA; none of the probes cross-hybridized effectively with other primate DNAs. Dimer-based gorilla alpha satellite probes hybridized with human and chimpanzee, but not orangutan, sequences under low stringency hybridization conditions, yet were specific for gorilla DNA under high stringency conditions. These results indicate that the alpha satellite DNA family has evolved in a concerted manner, such that considerable sequence divergence is now evident among the alphoid sequences of closely related primate species.     

Highly conserved segments in mammalian chromosomes

Mammalian chromosomes from seven species for which gene maps exist were studied by high-resolution techniques to identify areas of conserved chromosome banding homology. High-resolution comparisons of human, chimpanzee, gorilla, orangutan, African green monkey, cat, and mouse chromosomes revealed regions of apparently conserved chromosomal banding, which may indicate the likely positions of conserved linkage in the phylogeny of mammals. This analysis indicates that many regions of subbanding homology may have remained intact during the evolution of mammals and reflects a high degree of chromosome conservation in diverse species.     

Organizational variation of DYZ1 repeat sequences on the human Y chromosome and its diagnostic potentials

The long arm of the human Y chromosome is flecked with various fractions of repetitive DNA. DYZ1 is one such fraction, which is organized tandemly as an array of a 3.4-kb repeat ranging from 2000-4000 copies in normal males. We have studied the organizational variation of the DYZ1 fraction on the human Y chromosome using DNA samples from CEPH family members and the random population employing the RFLP approach, fluorescence in situ hybridization (FISH), and conducted a similarity search with GenBank sequences. Typing of genomic DNA using DYZ1 as a probe showed an allele length and copy number variations even between two male siblings. Hybridization of DNA from monochromosome hybrids with this probe showed its presence on chromosome 15 in addition to the Y chromosome. Fluorescence in situ hybridization of metaphase chromosomes from an apparently normal male showed DYZ1 sequences in the proximal region of chromosome 11 in addition to the long arm of the Y chromosome. Typing of sets of semen and blood DNA samples from the same human individuals showed discernible allelic variation between the two samples, indicating tissue-specific programmed sequence modulation. DYZ1 seems to be the first probe having the unique potential to discriminate unequivocally the difference between the DNA originating from semen and blood samples, and may be exploited in forensic cases. This probe may also be used as a diagnostic tool to ascertain Y chromosome mosaicism in patients (e.g., Turner), its aberrant status in somatic cells, and possible sequence modulation/rearrangement in the germline samples. Additionally, this can be used to uncover sequence polymorphism in the human population.