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Synteny mapping in the bovine: genes from human chromosome 4.

Genes homologous to those located on human chromosome 4 (HSA4) were mapped in the bovine to determine regions of syntenic conservation among humans, mice, and cattle. Previous studies have shown that two homologs of genes on HSA4, PGM2 and PEPS, are located in bovine syntenic group U15 (chromosome 6). The homologous mouse genes, Pgm-1 and Pep-7, are on MMU5. Using a panel of bovine x hamster hybrid somatic cells, we have assigned homologs of 11 additional HSA4 loci to their respective bovine syntenic groups. D4S43, D4S10, QDPR, IGJ, ADH2, KIT, and IF were assigned to syntenic group U15. This syntenic arrangement is not conserved in the mouse, where D4s43, D4s10, Qdpr, and Igj are on MMU5 while Adh-2 is on MMU3. IL-2, FGB, FGG, and F11, which also reside on MMU3, were assigned to bovine syntenic group U23. These data suggest that breaks and/or fusions of ancestral chromosomes carrying these genes occurred at different places during the evolution of humans, cattle, and mice.

Animals↗

Hotspots of mammalian chromosomal evolution.

BACKGROUND: Chromosomal evolution is thought to occur through a random process of breakage and rearrangement that leads to karyotype differences and disruption of gene order. With the availability of both the human and mouse genomic sequences, detailed analysis of the sequence properties underlying these breakpoints is now possible. RESULTS: We report an abundance of primate-specific segmental duplications at the breakpoints of syntenic blocks in the human genome. Using conservative criteria, we find that 25% (122/461) of all breakpoints contain > or = 10 kb of duplicated sequence. This association is highly significant (p < 0.0001) when compared to a simulated random-breakage model. The significance is robust under a variety of parameters, multiple sets of conserved synteny data, and for orthologous breakpoints between and within chromosomes. A comparison of mouse lineage-specific breakpoints since the divergence of rat and mouse showed a similar association with regions associated with segmental duplications in the primate genome. CONCLUSION: These results indicate that segmental duplications are associated with syntenic rearrangements, even when pericentromeric and subtelomeric regions are excluded. However, segmental duplications are not necessarily the cause of the rearrangements. Rather, our analysis supports a nonrandom model of chromosomal evolution that implicates specific regions within the mammalian genome as having been predisposed to both recurrent small-scale duplication and large-scale evolutionary rearrangements.

Animals↗

Molecular cloning of the breakpoints of a complex Philadelphia chromosome translocation: identification of a repeated region on chromosome 17.

Complex translocations in chronic myelogenous leukemia involve various chromosomes, in addition to chromosomes 9 and 22, in a nonrandom fashion. We have analyzed the DNA from leukemia cells characterized by a complex translocation, t(9;22;10;17)(q34;q11;p13;q21), by using the techniques of Southern blot hybridization, in situ hybridization, and molecular cloning; one of the breakpoints is at 17q21, a band that is frequently involved in complex 9;22 translocations. All of the breakpoint junctions and the corresponding normal sequences from the four involved chromosomes have been molecularly cloned. Restriction mapping is consistent with a simple concerted exchange of chromosomal material among the four chromosomes, except that additional changes appeared to have occurred within the chromosome 17 sequences. The cloned sequences on chromosome 17 at band q21 were found to be repeated in normal cells. By fluorescence in situ hybridization, a strong signal is seen at 17q21, but a weaker signal is also present at 17q23. By comparison with other primate species, an inversion in chromosome 17 during evolution appears to be responsible for the splitting of the cluster of repeat units in normal human cells.

Animals↗

Assignment of the beta subunit of the muscle nicotinic acetylcholine receptor gene (CHRNB1) to sheep chromosome 11.

The chromosomal assignment of the gene for the beta subunit of the sheep muscle nicotinic acetylcholine receptor (CHRNB1) was determined by isotopic in situ hybridization. CHRNB1 was mapped to sheep chromosome 11, with a hybridization peak at 11q14-->q22. This result is further evidence that the chromosomal segment that comprises human chromosome 17 has been highly conserved during evolution.

Animals↗

Clonal analysis of gliomas.

In malignant gliomas, the characteristically heterogeneous features and frequent diffuse spread within the brain have raised the question of whether malignant gliomas arise monoclonally from a single precursor cell or polyclonally from multiple transformed cells forming confluent clones. Although monoclonality has been shown in surgically resected tissues, these may not include the full spectrum of patterns seen on autopsy material. Little is known about the clonality of low-grade gliomas from which malignant gliomas may sometimes arise. We sought to investigate the clonality of low-grade and malignant gliomas by using and comparing surgical and autopsy material with a Polymerase chain reaction (PCR)-based assay for nonrandom X chromosome inactivation. For that, purpose, archival surgical and autopsy material from 15 female patients (group A) (age 4 to 73 years; median, 45) with malignant gliomas (12 glioblastomas, one gliosarcoma, one anaplastic oligoastrocytoma, one gliomatosis cerebri), surgical material only from 21 female patients (group S) (age 6 to 78 years; median, 60) with low-grade and malignant gliomas (four low-grade astrocytomas, three oligoastrocytomas, two anaplastic astrocytomas, one gemistocytic astrocytoma, four oligodendrogliomas, seven glioblastomas) were analyzed. In group A, representative areas (mean = 5/patient; median = 7) were microdissected from tissue sections and assayed by PCR amplification of a highly polymorphic microsatellite marker locus of the human androgen receptor gene (HUMARA) in the presence of alpha32P with and without predigestion with a methylation-sensitive restriction enzyme (HhaI). Products were resolved by denaturing gel electrophoresis and autoradiographed. In group S, selected tumor areas were used for the assay. Each patient's normal brain tissue was used for control. The band intensity of alleles were measured by densitometric scanning. In group A, 13 of 15 cases were informative (heterozygous). The same pattern of nonrandom X chromosome inactivation was present in all areas of solid dense and moderate tumor infiltration in eight including all components of the gliosarcoma. Two of eight also showed focal loss of heterozygosity (LOH). One of 13 presented global LOH. Two of 13 showed microsatellite instability, one of which in a patient with Turcot syndrome, the other in gliomatosis cerebri. Opposite skewing patterns were seen in distant areas of gliomatosis cerebri consistent with oligoclonal derivation. Clonality remained indeterminate in one glioblastoma and in the anaplastic oligoastrocytoma because of skewed lyonization in the normal control. In group S, 19 of 21 cases were informative. Fifteen of 19 were monoclonal (four low-grade astrocytomas, one anaplastic astrocytoma, one gemistocytic astrocytoma, two oligodendrogliomas, one oligoastrocytoma, six glioblastomas). Four of 19 were indeterminate. We conclude that (1) Low-grade and malignant gliomas are usually monoclonal tumors, and extensively infiltrating tumors must result from migration of tumor cells (2) Gliomatosis cerebri may initiate as an oligoclonal process or result from collision gliomas (3) Biphasic gliomas likely arise from a single precursor cell. (4) LOH at the HUMARA locus is probably related to partial or complete deletion of an X-chromosome, which occurs in malignant gliomas during clonal evolution.

Adolescent↗

ZOO-FISH analysis: cat and human karyotypes closely resemble the putative ancestral mammalian karyotype.

DNA in situ hybridization with human chromosome specific DNA libraries was applied to compare the karyotypes of humans (Homo sapiens, 2n = 46) and cats (Felis catus, 2n = 38). For the autosomes alone, 30 segments of conserved synteny were revealed. The arrangement of these segments in the feline karyotype differs by only seven single chromosome breaks and one intrachromosomal inversion from their arrangement in humans. Comparison of these data with those recently obtained for pig and those available from conventional gene mapping studies in mice and cattle has allowed us to develop a model of karyotype evolution in mammals. The cat and human karyotypes, with 36 and 44 autosomes respectively, were found to be very similar to a putative ancient mammalian founder karyotype. It would appear that during evolution to the human karyotype the status quo has been conserved for at least some 100-120 million years. There has been no need to alter the well-balanced gene arrangement of the mammalian founder karyotype.

Animals↗

The Azoospermia region AZFa: an evolutionar y view.

Compared to other regions on the human Y chromosome, the genomic segment encompassing the functionally defined AZFa locus has undergone higher X-Y sequence divergence, which is detectable by fluorescence in-situ hybridisation. This allows an evolutionary definition of an interval enclosing AZFa with a size of about 1.1 Mb. The region includes the genes USP9Y, DBY and UTY and is limited by evolutionary breakpoints within the PAC clones 41L06 and 46M11. These breakpoints restrict an area of possible male specific evolution that may have resulted in the acquisition of male specific functions, including a role in spermatogenesis.

Cells, Cultured↗

CAFE: a computational tool for the study of gene family evolution.

SUMMARY: We present CAFE (Computational Analysis of gene Family Evolution), a tool for the statistical analysis of the evolution of the size of gene families. It uses a stochastic birth and death process to model the evolution of gene family sizes over a phylogeny. For a specified phylogenetic tree, and given the gene family sizes in the extant species, CAFE can estimate the global birth and death rate of gene families, infer the most likely gene family size at all internal nodes, identify gene families that have accelerated rates of gain and loss (quantified by a p-value) and identify which branches cause the p-value to be small for significant families. AVAILABILITY: Software is available from http://www.bio.indiana.edu/~hahnlab/Software.html

Algorithms↗

ZOO-FISH analysis in insectivores: "Evolution extols the virtue of the status quo".

In evolutionary terms, insectivores are thought to be close to primates. Through ZOO-FISH analysis using human chromosome-specific painting probes, the syntenic relationship between the human and common shrew, Sorex araneus, karyotypes was studied. The human karyotype was found to be conserved in the shrew, with 32 autosomal segments of common synteny. Special arrangements, already known from similar studies on other species, were noted: fusions of HSA 16 and 19, HSA 3 and 21, and HSA 14 and 15. Only 10 breaks are necessary to transform the human karyotype into the karyotype of the common shrew. Together with known ZOO-FISH data from species belonging to other orders, this puts the human karyotype arrangement near the basis of all mammalian karyotypes. Human chromosome 2 was found to be conserved in its entirety as a single chromosome arm in the shrew. Evidence is presented that the same fusion of two original chromosomal segments formed the shrew chromosome ortholog of HSA 2 as the fusion that occurred during primate evolution to form human chromosome 2. This is a remarkable example of chromosomal coevolution.

Animals↗

Comparative mapping of human Chromosome 14q11.2-q13 genes with mouse homologous gene regions.

An examination of the synteny blocks between mouse and human chromosomes aids in understanding the evolution of chromosome divergence between these two species. We comparatively mapped the human (HSA) Chromosome (Chr) 14q11.2-q13 cytogenetic region with the intervals of orthologous genes on mouse (MMU) chromosomes. A lack of conserved gene order was identified between the human cytogenetic region and the interval of orthologs on MMU 12. The evolutionary breakpoint junction was defined within 2.5 Mb, where the conserved synteny of genes on HSA 14 changes from MMU 12 to MMU 14. At the evolutionary breakpoint junction, a human EST (GI: 1114654) with identity to the human and mouse BCL2 interacting gene, BNIP3, was mapped to mouse Chr 3. New gene homologs of LAMB1, MEOX2, NRCAM, and NZTF1 were identified on HSA 7 and on the proximal cytogenetic region of HSA 14 by mapping mouse genes recently reported to be genetically linked within the relevant MMU 12 interval. This study contributes to the identification of homology relationships between the genes of HSA 14q11.2-q13 and mouse Chr 3, 12, and 14.

Animals↗

The Z-chromosome is involved in the regulation of H-W (H-Y) antigen gene expression in Xenopus.

H-W (H-Y) antigen was investigated in diploid, triploid, and tetraploid Xenopus hybrids. These hybrids differ from each other with respect to their sex chromosome constitution-they all have a single W chromosome but one to three Z chromosomes. The H-W antigen concentration is reduced with increasing numbers of Z chromosomes. In the diploid and triploid hybrids the single W chromosome is able to guarantee ovary development, but among the tetraploids both male and female animals occur. However, both sexes have identical H-W antigen titers in the somatic tissues. It can be concluded that in these tetraploid hybrids with a ZZZW sex chromosome complement, the amount of H-W antigen is too low to sustain ovary development in all cases. Our results clearly indicate that in Xenopus a Z-coded gene is involved in the regulation of H-W antigen gene expression. In man and mouse there is evidence that such a regulatory gene is located on the X chromosome. Because of the concordance of man, mouse, and Xenopus we hypothesize that not only was the H-Y (H-W) antigen gene conserved during evolution but also the genes engaged in its regulation.

Animals↗

LTR retrotransposons and the evolution of eukaryotic enhancers.

Since LTR retrotransposons and retroviruses are especially prone to regional duplications and recombination events, these viral-like systems may be especially conducive to the evolution of closely spaced combinatorial regulatory motifs. Using the Drosophila copia LTR retrotransposon as a model, we show that a regulatory region contained within the element's untranslated leader region (ULR) consists of multiple copies of an 8 bp motif (TTGTGAAA) with similarity to the core sequence of the SV40 enhancer. Naturally occurring variation in the number of these motifs is correlated with the enhancer strength of the ULR. Our results indicate that inter-element selection may favor the evolution of more active enhancers within permissive genetic backgrounds. We propose that LTR retroelements and perhaps other retrotransposons constitute drive mechanisms for the evolution of eukaryotic enhancers which can be subsequently distributed throughout host genomes to play a role in regulatory evolution.

Animals↗

Satellite DNA evolution in Tytonidae (Aves: Strigiformes): dynamic repeat landscapes despite conserved karyotypes.

The elevated chromosome numbers observed in Tytonidae relative to the putative ancestral avian karyotype suggest that lineage-specific chromosomal fissions may have played an important role in the evolutionary history of this family. Here, we provide the first cytogenetic characterization of the American barn owl (Tyto furcata) and performs a comparative repeatome analysis across members of the Tytonidae, including other two species, the Western barn owl (Tyto alba), and the Oriental bay owl (Phodilus badius). The karyotype of T. furcata showed a 2n&#x2009;=&#x2009;92, closely resembling that previously described for T. alba, indicating a high degree of chromosomal conservation within Tytonidae. Although T. furcata and T. alba exhibit similar karyotypic organization, comparative repeatomic analyses revealed differences in their composition, including variation in satellite DNA (satDNA) repertoires and abundance. Eight satDNA families were identified in T. furcata, nine in T. alba, and 28 in P. badius, highlighting the dynamic evolution of repetitive sequences. Several satDNA families were shared between T. furcata and T. alba, whereas some appeared species-specific, supporting the library hypothesis of satDNA evolution. In P. badius, multiple satDNAs exhibited similarity to transposable elements, suggesting that mobile elements contributed to their diversification. Cytogenetic analyses demonstrated centromeric heterochromatin distribution in T. furcata, as well as a large heterochromatic W chromosome enriched in DNA repeats. The localization of satDNAs in centromeric regions and the apparent accumulation of repeats on the W chromosome reinforce the role of repetitive sequences in chromosome organization and sex chromosome differentiation. Together, these findings reveal repeatome diversification despite conserved macrochromosomal structure and provide new insights into genome evolution and chromosomal dynamics in birds.

Animals↗

Recent segmental duplications in the human genome.

Primate-specific segmental duplications are considered important in human disease and evolution. The inability to distinguish between allelic and duplication sequence overlap has hampered their characterization as well as assembly and annotation of our genome. We developed a method whereby each public sequence is analyzed at the clone level for overrepresentation within a whole-genome shotgun sequence. This test has the ability to detect duplications larger than 15 kilobases irrespective of copy number, location, or high sequence similarity. We mapped 169 large regions flanked by highly similar duplications. Twenty-four of these hot spots of genomic instability have been associated with genetic disease. Our analysis indicates a highly nonrandom chromosomal and genic distribution of recent segmental duplications, with a likely role in expanding protein diversity.

Alleles↗

Murine segmental duplications are hot spots for chromosome and gene evolution.

Mouse and rat genomic sequences permit us to obtain a global view of evolutionary rearrangements that have occurred between the two species and to define hallmarks that might underlie these events. We present a comparative study of the sequence assemblies of mouse and rat genomes and report an enrichment of rodent-specific segmental duplications in regions where synteny is not preserved. We show that segmental duplications present higher rates of molecular evolution and that genes in rearranged regions have evolved faster than those located elsewhere. Previous studies have shown that synteny breakpoints between the mouse and the human genomes are enriched in human segmental duplications, suggesting a causative connection between such structures and evolutionary rearrangements. Our work provides further evidence to support the role of segmental duplications in chromosomal rearrangements in the evolution of the architecture of mammalian chromosomes and in the speciation processes that separate the mouse and the rat.

Animals↗

The molecular genetics of C1 utilizing microorganisms. An overview.

The availability of recombinant DNA techniques has enabled the successful genetic analysis and manipulation of a range of C1 utilizing microorganisms. It has resulted in the identification of genes of interest on both plasmids and the chromosome; enabled the linkage of chromosomal genes to be determined; established the function and regulatory patterns of genes essential for utilization of C1 compounds and provided information on the evolution of methanogenic bacteria.

Bacteria↗

Isolation of a new germ line-specific repetitive DNA family in Acricotopus by microdissection of polytenized germ line-limited chromosome sections from a permanent larval salivary gland preparation.

In Acricotopus lucidus (Diptera, Chironomidae) the germ line-limited chromosomes (Ks) have developed from the soma chromosomes (Ss) by endoreduplication, rearrangements and accumulation of germ line-specific repetitive sequences. For molecular analysis of specific small K sections, microdissection of metaphase Ks generally yields very limited amounts of DNA. In this study, K-specific DNA was microdissected from defined polytenized K sections of X-ray induced K-S-rearrangements of permanent salivary gland chromosome preparations and was then amplified by DOP-PCR. A new germ line-specific tandem repetitive DNA family was isolated by this way from a heterochromatic K segment, characterized and localized on the Ks by FISH. The repetitive elements are related to sequences of earlier described K-specific tandem repetitive DNA families in A. lucidus, but are located mainly in terminal heterochromatin bands of the two largest Ks and only to a limited degree in the paracentromeric K heterochromatin. This demonstrates that a collection of permanent preparations of K-S-rearrangements with polytenized heterochromatic and S-homologous K sections of A. lucidus can be used as a source for obtaining K sequences of defined K parts to investigate the molecular evolution of the Ks.

Animals↗