Sex chromosomes, sex determination, and sex-linked sequences in Microtidae

The Arvicolidae is a widely distributed rodent group with several interesting characteristics in their sex chromosomes. Here, we summarize the actual knowledge of some of these characteristics. This mammalian group has species with abnormal sex determination systems. In fact, some species present the same karyotype in both males and females, with total absence of a Y chromosome, and hence of SRY and ZFY genes. Other species present fertile, sex-reversed XY females, generally due to mutations affecting X chromosomes. Furthermore, in Microtus oregoni males and females are gonosomic mosaic (the females are XO in the soma and XX in the germ cells, while the males are XY in the soma and OY in the germ cells). Regarding sex chromosomes, some species present enlarged (giant) sex chromosomes because of the presence of large blocks of constitutive heterochromatin, which have been demonstrated to be highly heterogeneous. Furthermore, we also consider the alterations affecting composition and localization of sex-linked genes or repeated sequences. Finally, this rodent group includes species with synaptic and asynaptic sex chromosomes. In fact, several species with asynaptic sex chromosomes have been described. It is interesting to note that within the genus Microtus both types of sex chromosomes are present.     

Interstrand crosslink-induced radials form between non-homologous chromosomes, but are absent in sex chromosomes

Fanconi anemia (FA) and cells lacking functional BRCA1 and BRCA2 proteins are hypersensitive to interstrand crosslinking (ICL) agents and show increased numbers of chromosomal breaks and radials. Although radial formation has been used to diagnose FA for more than 30 years, there has been little analysis of these characteristic formations. In this study, radials were analyzed from FA-A and FA-G fibroblasts as well as normal and retrovirally-corrected FA-A fibroblasts treated with high doses of ICLs. Radials were found to only involve non-homologous chromosome interactions and to be distributed nearly randomly along the length of chromosomes. Sites on chromosomes that did show increased frequency of radial involvement did not correlate with known fragile sites or pericentric regions. Hybrid radials were observed between mouse and human chromosomes in human-mouse hybrid cells produced by microcell-mediated chromosome transfer of mouse chromosomes into human FA-A fibroblasts. Both X and Y chromosomes were notably not involved in radials. These observations suggest that ICL repair may involve short stretches of homology, resulting in aberrant radial formation in the absence of FA proteins.     

Molecular cytogenetic characterization of Ciona intestinalis chromosomes

The compact genome of the ascidian Ciona intestinalis has been sequenced. Chromosome karyotype and mapping of the genome sequence information on each of the 14 pairs of chromosomes are essential for genome-wide studies of gene expression and function in this basal chordate. Although the small chromosome size (most pairs measuring less than 2 mum) complicates accurate chromosome pairing based on morphology alone, the present results suggest that 20 chromosomes are metacentric and 8 are submetacentric or subtelocentric, and two pairs of large chromosomes (#1 and #2) were defined. The characterization of chromosomes by FISH and staining with propidium iodide indicated that 18S/28S ribosomal gene repeats are present in the short arms of three pairs of chromosomes and that the short arms of these pairs show remarkable size polymorphism. In addition, each chromosome was characterized molecular cytogenetically by mapping representative BAC clones with FISH. The present study is therefore a first step in expanding the karyotype analysis and entire physical mapping of the genome sequence of Ciona intestinalis.     

Localization of translocation breakpoints in somatic metaphase chromosomes of barley

Karyotype analyses based on staining by acetocarmine followed by Giemsa N-banding of somatic metaphase chromosomes of Hordeum vulgare L. were carried out on 61 reciprocal translocations induced by X-irradiation. By means of computer-based karyotype analyses all of the 122 breakpoints could be localized to defined sites or segments distributed over the seven barley chromosomes. The pre-definition of translocations with respect to their rearranged chromosome arms from other studies rendered it possible to define the break positions even in translocations having exchanged segments equal in size and the breakpoints located distally to any Giemsa band or other cytological marker. The breakpoints were found to be non-randomly spaced along the chromosomes and their arms. All breaks but one occurred in interband regions of the chromosomes, and none of the breaks was located directly within a centromere. However, short and long chromosome arms recombined at random. An improved tester set of translocations depicting the known break positions of most distal location is presented.     

C-banded chromosomes of the genus Bembidion Latr. (Coleoptera, Carabidae)

The C-banding pattern of Bembidion punctulatum, B. varium, B. varicolor, B. ascedens, B. tibiale, B. ustulatum, B. decorum, and B. modestum are presented. All examined species have a symmetrical karyotype with meta- and submentacentric chromosomes and meioformula n=11+XY. All of them have an achiasmatic spermatogenesis in common. The present data confirm earlier studies indicating a considerable morphological and numerical stability of the Bembidiini karyotype. The C-banding showed the existence of heterochromatin in the paracentric regions of chromosomes, and also 2-3 intercalar C-positive segments were observed. The Y chromosome is entrely euchromatic. The C-banded karyotype of the analysed species in genus Bembidion has large heterochromatin segments on chromosomes, an exception in Coleoptera.     

Bends in human mitotic metaphase chromosomes, including a bend marking the X-inactivation center.

Bends in mitotic metaphase chromosomes are not distributed randomly throughout the karyotype. The frequency of bends at centromeres is positively correlated with the relative length of the chromosomes and negatively correlated with the centromere index (more bends in metacentrics, fewer in acrocentrics). The frequency of bends in the noncentromeric regions (except at Xq13-Xq21) is positively correlated with the relative length of chromosome arms. A bend at Xq13.3 to Xq21.1 was more frequent than a bend in any other region of the karyotype, centromeric or noncentromeric. It was observed in one member of the X-chromosome pair in 63% of 46,XX cells. In contrast, it was observed in only 2% of 46,XY cells. RBG-staining showed that this specific bend is confined to the lyonized X chromosome. These observations in cells from normal subjects were confirmed using G-banding and RBG-staining on cells from nine subjects with different X-chromosome abnormalities and on metaphases from amniotic fluid cell and lymphocyte cultures. The "center for Barr body condensation" has been localized to the region between Xq11.2 and Xq21.1. The functional and structural relationship is unclear, but we believe this highly specific bend may represent a visible manifestation of the condensation process; it could represent the first folded (and last unfolded) position, upon or around which the rest of the chromosome condenses. The late replication of this region may also be a factor. The smallest region of overlap (SRO) for the X-chromosome inactivation center and the specific chromosome bend is Xq13.3 to Xq21.1.     

Theoretical study of inversions affecting human chromosomes

A theoretical study of inversions affecting human chromosomes is proposed. Taking into consideration the number of bands and the fact that breaks occur at interfaces between bands, it is concluded that: 7.659 different pericentric inversions might be detected in a prometaphasic 802-band karyotype; this number decreases to 917 in a metaphasic 273-band karyotype; 8.607 and 862 different paracentric inversions might be detected in the same karyotypes respectively, but these results are likely to be overestimated. These theoretical data are used for showing that the pericentric inversions detected in human cytogenetic laboratories, are too frequently recurrent and are not distributed at random.     

Variation in the relative length of chromosomes in mammalian karyotypes. Hypothesis of equalizing selection

A hypothesis on the selective neutrality of relative lengths of karyotype chromosomes was tested. Idiograms expected based on an assumption of selective neutrality of chromosome lengths were compared with actual idiograms in more than a hundred mammalian species. The observed idiograms differed from those expected in a similar manner: in the observed idiograms, the longest chromosomes were shorter, and the shortest were longer than expected. It is suggested that karyotype chromosome variation is limited by selection against chromosome rearrangements that produce very long or very short chromosomes. An analysis of reciprocal translocations in the mouse and Drosophila showed that translocations generating chromosomes of extreme lengths were more deleterious than those generating normal-sized chromosomes. A working hypothesis was advanced stating that within-karyotype variation of chromosome lengths is accounted for by two factors: chromosome rearrangements and natural selection. Chromosome rearrangements tend to randomize relative chromosome lengths in a karyotype, whereas natural selection acts to equalize them.     

Distribution of radiation induced lesions in human chromosomes and dose-effect relation analysed with G-banding

Summary Human female lymphocytes were exposed to X-rays in vitro at 7 different doses between 40–280 R. In 830 metaphases chromosome analyses were carried out with either conventional staining or G-banding, respectively. 486 breakpoints are non-randomly distributed between chromosomes and chromosome arms. An excess of lesions was present in chromosomes 1 and 5 or in lp. 85% of the lesions were located in G-negative bands (pale G-bands). 29% of all lesions appeared in either the last terminal pale band (21%) or in the centromere region (8%).With regard to an application of G-banding for a biological dose-estimation, the dose-response relations of dic and ace were analysed. Although G-banding enables detailed analysis of the whole karyotype it cannot be recommended for cytogenetic routine analyses in medical radioprotection monitoring, without suitable automated scoring techniques. Dose estimations based on the frequency of dic and carried out with conventional staining cannot be essentially improved at present with banding. Nevertheless, by banding criteria for a correct evaluation of other aberration types, e.g. ace, can be provided. This is a prerequisite for the calculation of representative dose-effect curves.     

Higher levels of organization in chromosomes.

On the basis of recent results a unified view of different aspects of the higher levels in the organization of chromatin in chromosomes is presented. Basic to these forms of organization is the arrangement of DNA in the complex with nucleosomes and recent studies suggest that at least some species of satellite DNA may maintain a fixed DNA sequence relationship to the phasing of nucleosomes. Special proteins such as the high-mobility group (HMG) proteins or other non-histone proteins could serve specific functions in the recognition of satellite DNA sequences.In the presence of histone H1 the 110 Å nucleosome fiber formed from the basic string of nucleosomes can be further condensed into a thicker 250–300 Å fiber formed by a solenoidal coiling of the 110 Å fiber with about 6–8 nucleosomes per turn and the available evidence suggests that these structures are found in mitotic chromosomes as well as other forms of inactive chromatin. A further level of coiling of the 250–300 Å solenoid has been suggested by our recent studies of disintegrated mitotic chromosomes consisting of a thin-walled tube with an outer diameter of 4000 Å referred to as the unit fiber. This structure would account for a factor of 1400 × contraction of DNA in mitotic chromosomes which in their intact state are only 5-fold more contracted. The recently described “scaffold” proteins could be responsible for this final coiling of the unit fibers in intact chromosomes.Meiotic chromosomes are generally less contracted than mitotic chromosomes. An extreme example of this are lampbrush chromosomes that apart from the axial segments which might contain some structural proteins appear to consist of naked DNA arranged in lateral loops. In the later stages of meiosis more condensed structures arise as exemplified by the synaptonemal complex during the pachytene stage in many organisms. The characteristic features of this structure are interpreted to suggest that the structure consists of lateral components containing two parallel 110 Å nucleosome fibers each representing the axial segments of two sister chromatids. From these paired regions loops protrude laterally in a manner which closely resembles the less condensed lampbrush chromosomes. The implication of this structure in the process of crossingover is discussed.Less is known about the organization of chromatin in interphase nuclei, but structures analogous to the loop-like structures in meiotic chromosomes are suggested on the basis of the isolation of supercoiled DNA loops constrained by RNA-DNA and protein-DNA interactions. The position of these loops is suggested to be fixed by specific repeated DNA sequences that could be associated with specific tenacious non-histone or HMG proteins.     

The majority of the marker chromosomes in Japanese patients with stigmata of turner syndrome are derived from Y chromosomes

Summary DNA analyses of 41 individuals with stigmata of Turner syndrome and a 45,X/46,X+mar or 46,X+mar karyotype were carried out. Southern-blot analysis employing 17 Y-specific probes was used to determine whether the marker chromosome was Y-chromosomal in origin. Of the 41 DNA samples from these patients, 23 contained detectable Y-chromosomal DNA. Points of chromosome breakage were distributed over the entire length of the Y long arm. Three individuals, who carry different portions of the Y chromosome, had developed gonadoblastoma. GBY (the gonadoblastoma locus on the Y chromosome) is mapped proximal to DYS132, midway between the 13 Yq loci that we have studied. We also used a polymerase chain reaction technique that could detect 7 loci over the length of the Y chromosome. This technique may be useful for the rapid assessment of marker chromosomes, especially for evaluating the risk of gonadoblastoma.     

Chromosome painting using chromosome-specific probes from flow-sorted pig chromosomes.

Biotinylated chromosome-specific probes were prepared from flow-sorted pig chromosomes 1, 13, 18, X, and Y using the degenerate oligonucleotide-primed polymerase chain reaction. Probes prepared in this way can be used to confirm the identity of chromosomes in the bivariate pig flow karyotype and in pig x mouse somatic cell hybrids.     

Flow microfluorometric analysis of isolated Chinese hamster chromosomes

Isolated Chinese hamster chromosomes were analysed by flow microfluorometry after staining with ethidium bromide. Peaks corresponding to the expected DNA content of each of the autosomes were observed. Examination of chromosomes partially fractionated by zonal centrifugation on sucrose gradients verified the identity of the chromosomes in the various peaks of the whole karyotype. The significance of these observations to karyotype analysis is discussed.     

Two-dimensional analysis of proteins sedimenting with simian virus 40 chromosomes.

The nonhistone proteins sedimenting in low-salt glycerol gradients with simian virus 40 chromosomes were analyzed by two-dimensional gel electrophoresis, utilizing nonequilibrium pH gradients as the first dimension and sodium dodecyl sulfate-gel electrophoresis as the second dimension. By densitometric quantitation of the radiolabeled proteins present in each fraction of the gradients, it was possible to identify sedimenting with all or a fraction of the simian virus 40 chromosomes. VP-1 sedimented with simian virus 40 chromosomes; additional evidence for its binding to chromosomes was obtained by immunochemical techniques. Four proteins (Mr 25,000, pI 6.0; Mr 32,000, pI 7.2; Mr 35,000, pI 8.5; and Mr 80,000, pI 7.2) sedimented with specific subsets of chromosomes.     

Heterochromatin and rDNA sites distribution in the holocentric chromosomes of Cuscuta approximata Bab. (Convolvulaceae).

Cuscuta is a widely distributed genus of holoparasitic plants. Holocentric chromosomes have been reported only in species of one of its subgenera (Cuscuta subg. Cuscuta). In this work, a representative of this subgenus, Cuscuta approximata, was investigated looking for its mitotic and meiotic chromosome behaviour and the heterochromatin distribution. The mitotic chromosomes showed neither primary constriction nor Rabl orientation whereas the meiotic ones exhibited the typical quadripartite structure characteristic of holocentrics, supporting the assumption of holocentric chromosomes as a synapomorphy of Cuscuta subg. Cuscuta. Chromosomes and interphase nuclei displayed many heterochromatic blocks that stained deeply with hematoxylin, 4',6-diamidino-2-phenylindole (DAPI), or after C banding. The banded karyotype showed terminal or subterminal bands in all chromosomes and central bands in some of them. The single pair of 45S rDNA sites was observed at the end of the largest chromosome pair, close to a DAPI band and a 5S rDNA site. Two other 5S rDNA site pairs were found, both closely associated with DAPI bands. The noteworthy giant nuclei of glandular cells of petals and ovary wall exhibited large chromocentres typical of polytenic nuclei. The chromosomal location of heterochromatin and rDNA sites and the structure of the endoreplicated nuclei of C. approximata seemed to be similar to those known in monocentric nuclei, suggesting that centromeric organization has little or no effect on chromatin organization.     

Studies on rodent chromosomes

The karyotype ofTatera indica cuverii consists of 68 chromosomes with two X chromosomes in the female and an X and a Y chromosome in the male. The X chromosomes are the largest and can be distinguished from each other morphologically. Autoradiographic studies indicate that the two morphologically distinguishable X chromosomes are out-of-phase in DNA replication in approximately equal proportion and thus substantiate the random inactivation hypothesis.     

Semi-automated detection of aberrant chromosomes in bivariate flow karyotypes.

A method is described that is designed to compare, in a standardized procedure, bivariate flow karyotypes of Hoechst 33258 (HO)/Chromomycin A3 (CA) stained human chromosomes from cells with aberrations with a reference flow karyotype of normal chromosomes. In addition to uniform normalization of normal and abnormal flow karyotypes, the main purpose is detection of structurally abnormal chromosomes in often complex karyotypes of tumor cells. The method, which has been implemented in a computer program, consists of a comparison of individual chromosome peaks with the positions of peaks in the flow karyotype constituted by normal chromosomes and takes into account the natural variability in base composition of normal chromosomes among healthy individuals. Flow-karyotypes are normalized using an iterative fitting procedure, using corrections for (1) amplification of HO and CA fluorescence, (2) cross-talk between the fluorescence signals of HO and CA, and (3) offset of the HO and CA origin. Flow karyotypes of two cell lines, one with a simple deletion and the other with more complex karyotypic changes, were analyzed. The results of flow analysis were found to be in general agreement with the cytogenetic analysis of quinacrine banded karyotypes.     

Assignment of cloned genes to the seven electrophoretically separated Candida albicans chromosomes.

By using orthogonal-field alternating gel electrophoresis (OFAGE), field-inversion gel electrophoresis (FIGE), and contour-clamped homogeneous field gel electrophoresis (CHEF), we have clearly resolved 11 chromosomal bands from various Candida albicans strains. OFAGE resolves the smaller chromosomes better, while FIGE, which under our conditions causes the chromosomes to run in the reverse order of OFAGE, is more effective in separating the larger chromosomes. CHEF separates all chromosomes under some conditions, but these conditions do not often resolve homologs. The strains examined are highly polymorphic for chromosome size. Fourteen cloned Candida genes, isolated on the basis of conferral of new properties to or complementation of auxotrophic deficiencies in Saccharomyces cerevisiae, and three sequences of unknown function have been hybridized to Southern transfers of CHEF, FIGE, and OFAGE gels. Four sets of resolvable bands have been shown to be homologous chromosomes. On the basis of these data, we suggest that C. albicans has seven chromosomes. Genes have been assigned to the seven chromosomes. Two chromosomes identified genetically have been located on the electrophoretic karyotype.     

Chromosomes tell half of the story: the correlation between karyotype rearrangements and genetic diversity in sedges,a group with holocentric chromosomes

Chromosome rearrangements may affect the rate and patterns of gene flow within species, through reduced fitness of structural heterozygotes or by reducing recombination rates in rearranged areas of the genome. While the effects of chromosome rearrangements on gene flow have been studied in a wide range of organisms with monocentric chromosomes, the effects of rearrangements in holocentric chromosomes—chromosomes in which centromeric activity is distributed along the length of the chromosome—have not. We collected chromosome number and molecular genetic data in Carex scoparia, an eastern North American plant species with holocentric chromosomes and highly variable karyotype (2n = 56–70). There are no deep genetic breaks within C. scoparia that would suggest cryptic species differentiation. However, genetic distance between individuals is positively correlated with chromosome number difference and geographic distance. A positive correlation is also found between chromosome number and genetic distance in the western North American C. pachystachya (2n = 74–81). These findings suggest that geographic distance and the number of karyotype rearrangements separating populations affect the rate of gene flow between those populations. This is the first study to quantify the effects of holocentric chromosome rearrangements on the partitioning of intraspecific genetic variance.     

Isolation of specific human metaphase chromosomes

The human karyotype can be subdivided into seven fractions containing specific chromosomes to provide material for recombinant DNA research. The isolated metaphase chromosomes are sorted according to size by velocity zonal centrifugation, and specific chromosome groups are further purified by electrostatic deflection in a flow microfluorometer. Rapid improvements in technology should soon provide preparations of single chromosomes.