The Nup2 meiotic-autonomous region relieves inhibition of Nup60 to promote progression of meiosis and sporulation in Saccharomyces cerevisiae

During meiosis, chromosomes undergo dramatic changes in structural organization, nuclear positioning, and motion. Although the nuclear pore complex has been shown to affect genome organization and function in vegetative cells, its role in meiotic chromosome dynamics has remained largely unexplored. Recent work in the budding yeast Saccharomyces cerevisiae demonstrated that the mobile nucleoporin Nup2 is required for normal progression through meiosis I prophase and sporulation in strains where telomere-led chromosome movement has been compromised. The meiotic-autonomous region, a short fragment of Nup2 responsible for its role in meiosis, was shown to localize to the nuclear envelope via Nup60 and to bind to meiotic chromosomes. To understand the relative contribution these 2 activities have on meiotic-autonomous region function, we first carried out a screen for meiotic-autonomous region mutants defective in sporulation and found that all the mutations disrupt interaction with both Nup60 and meiotic chromosomes. Moreover, nup60 mutants phenocopy nup2 mutants, exhibiting similar nuclear division kinetics, sporulation efficiencies, and genetic interactions with mutations that affect the telomere bouquet. Although full-length Nup60 requires Nup2 for function, removal of Nup60’s C-terminus allows Nup60 to bind meiotic chromosomes and promotes sporulation without Nup2. In contrast, binding of the meiotic-autonomous region to meiotic chromosomes is completely dependent on Nup60. Our findings uncover an inhibitory function for the Nup60 C-terminus and suggest that Nup60 mediates recruitment of meiotic chromosomes to the nuclear envelope, while Nup2 plays a secondary role counteracting the inhibitory function in Nup60’s C-terminus.     

Variability of genetic sex determination in poeciliid fishes

Poeciliids are one of the best-studied groups of fishes with respect to sex determination. They present an amazing variety of mechanisms, which span from simple XX-XY or ZZ-ZW systems to polyfactorial sex determination. The gonosomes of poeciliids generally are homomorphic, but very early stages of sex chromosome differentiation have been occasionally detected in some species. In the platyfish Xiphophorus maculatus, gene loci involved in melanoma formation, in different pigmentation patterns and in sexual maturity are closely linked to the sex-determining locus in the subtelomeric region of the X- and Y- chromosomes. The majority of traits encoded by these loci are highly polymorphic. This phenomenon might be explained by the high level of genomic plasticity apparently affecting the sex-determining region, where frequent rearrangements such as duplications, deletions, amplifications, and transpositions frequently occur. We propose that the high plasticity of the sex-determining region might explain the variability of sex determination in Xiphophorus and otherbreak poeciliids.     

Microsatellite variation and evolutionary history of PCDHX/Y gene pair within the Xq21.3/Yp11.2 hominid-specific homology block

To better understand the evolutionary dynamics of repetitive sequences in human sex chromosomes, we have analyzed seven new X/Y homologous microsatellites located within PCDHX/Y, one of the two recently described gene pairs in the Xq21.3/Yp11.2 hominid-specific homology block, in samples from Portugal and Mozambique. Sharp differences were observed on X/Y allele distributions, concerning both the presence of private alleles and a different modal repeat length for X-linked and Y-linked markers, and this difference was statistically significant. Higher diversity was found in X-linked microsatellites than in their Y chromosome counterparts; when comparing populations, Mozambicans showed more allele diversity for the X chromosome, but the contrary was true for the Y chromosome microsatellites. Evolutionary patterns, relying on intragenic PCDHX/Y SNPs, also revealed distinct scenarios for X and Y chromosomes. Greater microsatellite diversity was displayed by African X chromosomes within the most common haplotypes shared by both populations, whereas higher microsatellite diversity was found in Portugal for the ancestral Y chromosome haplotype. The most frequent PCDHY haplotype in Portuguese was the derived one, and it was not found in Mozambicans. TMRCA estimated by the rho parameter resulted in 13,700 years (7,500-20,000 years), which is consistent with a recent, post-Out-of-Africa origin for this haplotype. In conclusion, the newly described microsatellite loci generally displayed greater X-linked to Y-linked diversity and this pattern was also detected with slower evolving markers, with a remarkable differentiation between populations observed for Y chromosome haplotypes and, thus, greater divergence among Y chromosomes in human populations.     

Genome physical mapping with large-insert bacterial clones by fingerprint analysis: methodologies, source clone genome coverage, and contig map quality

Genome physical mapping with large-insert clones by fingerprint analysis is becoming an active area of genomics research. Here, we report two new capillary electrophoresis-based fingerprinting methods for genome physical mapping and the effects of different fingerprinting methods and source clone genome coverage on quality physical map construction revealed by computer simulations and laboratory experiments. It was shown that the manual sequencing gel-based two-enzyme fingerprinting method consistently generated larger and more accurate contigs, followed by the new capillary electrophoresis-based three-enzyme method, the new capillary electrophoresis-based five-enzyme (SNaPshot) method, the agarose gel-based one-enzyme method, and the automatic sequencing gel-based four-enzyme method, in descending order, when 1% or fewer questionable clones were allowed. Analysis of clones equivalent to 5x, 8x, 10x, and 15x genomes using the fingerprinting methods revealed that as the number of clones increased from 5x to 10x, the contig length rapidly increased for all methods. However, when the number of clones was increased from 10x to 15x coverage, the contig length at best increased at a lower rate or even decreased. The results will provide useful knowledge and strategies for effective construction of quality genome physical maps for advanced genomics research.     

Elongated mouse chromosomes suitable for enhanced molecular cytogenetics

Characterization of genetic disorders in humans and animal models requires identification of chromosomal aberrations. However, identifying fine deletions or insertion in metaphase chromosomes has been always a challenge due to limitations of resolution. In this study we developed a rapid method for chromosome elongation using two different intercalating agents: ethidium bromide and 5-bromo-2′-deoxyuridine (BrdU), together with a short-term mitotic block using colcemid. About 70% of the chromosomes from cells that underwent this elongation procedure reached three times longer than those prepared from control cells. FISH experiments using elongated chromosomes revealed a duplicated region of chromosome 11 that was not visible in cells prepared with conventional methods.     

Clinical and cytogenetic manifestations of subtelomeric aberrations: Report of six cases

BACKGROUND: Fluorescent subtelomeric probes for the 41 different subtelomeric regions (the p arms of the acrocentric chromosomes were excluded) have been developed over the last 10 years. These probes can detect deletions, duplications, and translocations in the gene-rich subtelomeric regions of human chromosomes, regions where crossing over frequently occurs and where a high number of abnormalities have been found. Recently, commercially produced probes have become available, which has led to the detection of subtelomeric abnormalities in 7.4% of patients with moderate to severe mental retardation (Knight et al., 1999). CASES: We evaluated 43 dysmorphic children with developmental delay and/or mental retardation of unknown etiology and/or autism who were previously assessed for chromosome abnormalities, metabolic disorders, or recognizable dysmorphic syndromes, all of which were ruled out. Of the 43 children tested, 6 (14%) were found to have subtelomeric aberrations. CONCLUSIONS: We recommend that patients with dysmorphic features and mental retardation of unknown etiology who also have a normal standard chromosome analysis should have subtelomeric FISH testing performed earlier in their clinical workup.     

Those amazing dinoflagellate chromosomes

Dinoflagellates are a very large and diverse group of eukaryotic algae that play a major role in aquaticfood webs of both fresh water and marine habitats. Moreover, the toxic members of this group posea health threat in the form of red tides. Finally, dinoflagellates are of great evolutionary importance,because of their taxonomic position, and their unusual chromosome structure and composition. While the cytoplasm of dinoflagellates is typically eukaryotic, the nucleus is unique when compared to the nucleusof other eukaryotes. More specifically, while the chromosomes of all other eukaryotes contain histones,dinoflagellate chromosomes lack histones completely. There are no known exceptions to this observation: all dinoflagellates lack histones, and all other eukaryotes contain histones. Nevertheless, dinoflagellates remain a relatively unstudied group of eukaryotes.     

A Cytogenetic Study of the Leaf Beetle Genus Cyrtonus (Coleoptera, Chrysomelidae)

The chromosomes of ten species of Cyrtonus and the genome sizes of six are surveyed. Among the total of 15 chromosomally studied species, 11 have 2n=28 chromosomes and a 13+Xy_p male meioformula, three have 2n=40 and 19+Xy_p and one 2n=46 and 22+Xy_p. All but one species with 28 chromosomes show only metacentric or submetacentric chromosomes, whereas the species with 40 and 46 chromosomes display some telocentrics or subtelocentrics, that are probably derived from the former by centric fissions. However, since the number of major chromosome arms is strikingly higher in these latter species (NF=70 and 78) than in the 28-chromosome species (mostly NF=56), other chromosomal rearrangements such as pericentric inversions or heterochromatin accretions could also be involved. The genome sizes display a narrow range, from 1C=0.6–1.22pg, and they are not significantly correlated with the chromosome numbers. Some possible factors implied in the rough chromosomal evolution of Cyrtonus are discussed in relation to a few other genera of the subfamily Chrysomelinae.     

A comparison of nuclear and mitochondrial cline shapes in a hybrid zone in the Sceloporus grammicus complex (Squamata; Phrynosomatidae)

The F5 and FM2 chromosome races of the Sceloporus grammicus complex form a hybrid zone in the Mexican state of Hidalgo. Previous studies of this zone have assessed genetic structure by averaging estimates of shape and width across three diagnostic chromosome markers. This approach is likely to mask subtle differences in cline shape among loci (e.g. selected vs. neutral), and obscure any displacement of cline centres (if present). Here we use maximum likelihood methods to construct the best fitting individual clines for three chromosomal markers, and also add two new markers; the mitochondrial DNA (mtDNA) locus, and the nuclear ribosomal DNA (rDNA) repeat. For each locus, hybrid zone models were fitted by cline shape and width, and the position and number of segments describing the centre of the zone. Pairwise comparisons between all clines revealed concordance between chromosomes 2 and 6, but significant discordance in cline structure among all other paired combinations. The concordance of chromosomes 2 and 6 suggests that these clines are maintained by genome-wide forces. The discordance of the chromosome 1 cline suggests an influence of asymmetric introgression, while the mtDNA cline is probably influenced by selection and drift. The rDNA locus reveals a pattern best explained by either extreme asymmetric introgression or gene conversion. The structure of zone indicates that genome-wide processes and locus specific selective forces as well as drift, are operating to different degrees on different loci. The locus-by-locus approach used here permits a finer discrimination among possible mechanisms responsible for the maintenance of the individual clines.     

Synaptic pattern of sex complements and sperm head malformation in X-autosome translocation carrier bulls

Testicular activity and semen characteristics of bulls carrying an X-autosome translocation t(Xp +;23q-) revealed all stages of spermatogenesis although their semen consisted of few and, exclusively, of malformed spermatozoa. Chromosome painting on metaphase spreads of their mother and synaptonemal complex analysis on these and normal bulls were carried out to test whether the location and meiotic pairing behaviour of the rearranged segments could have contributed to the sperm head malformation and oligospermia in our X-autosome translocation (X-AT) carrier bulls. Spermatocytes of X-AT carriers displayed the rearranged chromosomes in a univalent-trivalent association, with 23q- always remaining as a univalent and Xp + in synapsis with normal chromosome 23 and the Y chromosome. Chromosome painting studies to test whether the total absence of meiocytes showing a quadrivalent is due to the non-reciprocal nature of this translocation, identified Xp sequence homology with the distal end of 23q- confirming its relocation to the terminal segment of 23q-. Our synaptonemal complex analyses also confirmed that the bovine pseudo-autosomal region (PAR) is at the distal ends of Xq and Yp and further revealed that over 85% of spermatocytes of X-AT carriers (and up to 13% of spermatocytes of normal bulls) sustain a Y-axis break adjacent to the PAR. Although the exact cause of a Y-axis break in bovine spermatocytes is not known at present, we believe that the break and possible loss of Yq in such high proportions of spermatocytes of X-AT carriers could have contributed to the sperm head malformation and oligospermia in our X-AT carrier bulls.