Differential digestion of the centromeric heterochromatic regions of the 5-azacytidine-decondensed human chromosomes 1, 9, 15, and 16 by NdeII and Sau3AI restriction endonucleases

A study on the factors involved in chromosome digestion by restriction endonuclease was carried out on 5-azacytidine treated and untreated human chromosomes 1, 9, 15 and 16 by using NdeII and Sau3AI isoschizomers. After treatment with 5-azacytidine, chromosomes 1, 9, 15, and 16 showed two differentiated areas at the centromeric regions: the centromere, fully condensed, and the pericentromeric heterochromatin, decondensed. Chromosomes not treated with 5-azacytidine after digestion with Sau3AI and NdeII showed all the centromeric regions undigested, except pair number 1, digested at the pericentromeric area. Digestion of the 5-azacytidine decondensed chromosomes with Sau3AI and NdeII showed the centromeres undigested in the four chromosome pairs while the pericentromeric heterochromatin appeared largely digested. Other factors, different to target distribution, are necessary to explain the pattern of restriction endonuclease digestion observed in this communication.     

Genetic regulation of the centromere division in rye and wheat univalent chromosomes in dimonosomics during meiotic anaphase I

Cytogenetic analysis of meiosis in the wheat--rye dimonosomics 1Rv-1A, 1Ron-1A, 2R-2D, 5R-5A, and 6R-6A was conducted. C-banding was used to study the segregation pattern of each of two univalent chromosomes during the first meiotic division. It has been shown that the division frequency of the centromeric regions of all rye chromosomes in the pair studied is significantly higher than in the wheat chromosomes. The ANOVA performed suggest that the plant genotype contributes significantly (at P = 0.05) to the behavior pattern of univalent chromosomes in meiosis. The data obtained demonstrate that the rye and wheat chromosomes studied are involved in genetic regulation of centromere division in meiotic anaphase I (AI). The presence of rye chromosome 2R and wheat chromosome 2D suppresses the division of centromeres of the sister chromatids in AI. Rye chromosomes 1Rv, 1Ron, 5R, and 6R induce equational division; however, rye chromosome 1Rv increases to a greater degree the frequency of equational division of wheat chromosome 1A as compared with chromosome 1Ron.     

Genetic regulation of the centromere division in rye and wheat univalent chromosomes in dimonosomics during the meiotic anaphase I

Cytogenetic analysis of meiosis in the wheat-rye dimonosomics 1Rv-1A, 1Ron-1A, 2R-2D, 5R-5A, and 6R-6A was conducted. C-banding was used to study the segregation pattern of each of two univalent chromosomes during the first meiotic division. It has been shown that the division frequency of the centromeric regions of all rye chromosomes in the pair studied is significantly higher than in the wheat chromosomes. The ANOVA performed suggest that the plant genotype contributes significantly (at P = 0.05) to the behavior pattern of univalent chromosomes in meiosis. The data obtained demonstrate that the rye and wheat chromosomes studied are involved in genetic regulation of centromere division in meiotic anaphase I (AI). The presence of rye chromosome 2R and wheat chromosome 2D suppresses the division of centromeres of the sister chromatids in AI. Rye chromosomes 1Rv, 1Ron, 5R, and 6R induce equational division; however, rye chromosome 1Rv increases to a greater degree the frequency of equational division of wheat chromosome 1A as compared with chromosome 1Ron.     

Role of rye chromosome 2R from wheat-rye substitution line 2R(2D)1 (Triticum aestivum L. cv. Saratovskaya 29-Secale cereale L. cv. Onokhoiskaya) in genetic regulation of meiotic restitution in wheat-rye polyhaploids

A study was made of the role of rye chromosome 2R from the wheat-rye substitution line 2R(2D)1 (Triticum aestivum L. cv. Saratovskaya 29-Secale cereale L. cv. Onokhoiskaya) in genetic regulation of meiotic restitution in wheat-rye polyhaploids 2R(2D)1 x S. cereale L. cv. Onokhoiskaya. Rye chromosome 2R proved to affect the completeness of the meiotic program, suppressing the formation of restitution gametes. This was evident from the reductional division of univalent chromosomes in AI and the occurrence of the second meiotic division. The interrelationships between the type of chromosome division in AI and the two-step character of meiosis are discussed. The structural and functional organization of the centromeric regions of chromosomes undergoing reductional division is assumed to determine the two-step character of division.     

Cryptic variants of acrocentric human chromosomes as analysed by restriction endonucleases

Ten phenotypically normal human individuals have been analysed by in situ treatments with restriction endonucleases in order to obtain a better characterization of some cryptic variants of acrocentric chromosomes. Treatments with AluI, NdeII and Sau 3AI confirm the existence of two cryptic amplified regions on the short arms of both one chromosome 15 and one chromosome 22, in one female. These amplifications seem to be of different origin involving the nucleolar organizer region of chromosome 15 and the satellite of chromosome 22.     

The genetic significance of accessory bisatellited marker chromosomes

Ten new cases of accessory bisatellited marker chromosomes examined in different laboratories are reported. As a basis for genetic counseling in the context of prenatal diagnosis a cytogenetic categorization of such marker chromosomes is proposed and an estimation of the genetic risk associated with each category is carried out. The results are as follows: There is no increased risk for offspring with abnormal phenotype born to a healthy carrier of an accessory bisatellited marker chromosome with either a single or two closely adjacent C-bands (Category AI or AII). The unbiased sample of cases with de novo accessory bisatellited marker chromosomes of categories AI and AII is too small to allow a satisfactory estimation of the actual risk that, in case of such a prenatal finding, the foetus may not show a normal phenotype as a consequence of the marker chromosome. There is, however, evidence that this risk may be lower than 10%. Accessory bisatellited marker chromosomes showing a discrete pattern of G- and R-bands situated between two distant C-bands (Category AIII) usually indicate a chromosomal imbalance giving rise to an abnormal phenotype. Mosaic carriers of such dicentric marker chromosomes may, however, present a normal phenotype.     

Allelic imbalance in primary breast carcinomas and metastatic tumors of the axillary lymph nodes

Axillary lymph node status is the most important prognostic factor in predicting disease outcome in women with breast cancer. A number of chromosomal aberrations in primary breast tumors have been correlated with lymph node status and clinical outcome, but chromosomal changes particular to metastatic lymph node tumors have not been well studied. DNA samples isolated from laser-microdissected primary breast and metastatic axillary lymph node tumors from 25 women with invasive breast cancer were amplified using 52 microsatellite markers defining 26 chromosomal regions commonly deleted in breast cancer. Levels and patterns of allelic imbalance (AI) within and between breast and lymph node tumors were assessed to identify chromosomal alterations unique to primary or metastatic tumors and to examine the timing of metastatic potential. The overall frequency of AI in primary breast tumors (0.24) was significantly greater (P < 0.001) than that in lymph node tumors (0.10), and congruent AI events were observed for < 20% of informative markers. AI at chromosomes 11q23.3 and 17p13.3 occurred significantly more frequently (P < 0.05) in primary breast tumors alone; no chromosomal regions showed a significantly higher AI frequency in lymph nodes. Higher rates of AI in primary versus metastatic lymph node tumors suggest that acquisition of metastatic potential may be an early event in carcinogenesis, occurring before significant levels of AI accumulate in the primary tumor. In addition, patterns of AI were highly discordant between tumor types, suggesting that additional genetic alterations accumulated independently in the two cell populations.     

Impact of the diagnosis definition on linkage detection

Previous genome scan linkage analyses of the disease Kofendrerd Personality Disorder (KPD) with microsatellites led to detect some regions on chromosomes 1, 3, 5, and 9 that were identical for the three populations AI, KA, and DA but with large differences in significance levels. These differences in results may be explained by the different diagnosis definitions depending on the presence/absence of 12 traits that were used in the 3 populations AI, KA, and DA. Heterogeneity of linkage was thus investigated here according to the absence/presence of each of the 12 traits in the 3 populations. For this purpose, two methods, the triangle test statistic and the predivided sample test were applied to search for genetic heterogeneity. Three regions with a strong heterogeneity of linkage were detected: the region on chromosome 1 according to the presence/absence of the traits a and b, the region on chromosome 3 for the trait b, and the region on chromosome 9 for the traits k and l. These 3 regions were the same as those detected by linkage analyses. No novel region was detected by the heterogeneity tests. Concerning chromosome 1, linkage analyses showed a much stronger evidence of linkage for traits a and b and for a combination of these traits than for KPD. Moreover, there was no indication of linkage to any of the other traits used to define the diagnosis of KPD. A genetic factor located on the chromosome 1 may have been detected here which would be involved specifically in traits a and b or in a combination of these traits.     

Linkage and association analyses of microsatellites and single-nucleotide polymorphisms in nuclear families

Several simulation studies have suggested that a high-density single-nucleotide polymorphisms (SNPs) marker set may be as useful as a traditional microsatellites (MS) marker set in performing whole-genome linkage analysis. However, very few studies have directly tested the SNPs-based genome-wide scan. In the present study, we compared the linkage results from the SNPs-based scan with a map density of 3-cM spacing with those from the MS scan using a 10-cM marker set among 300 nuclear families each from the Aipotu (AI), Danacaa (DA), and Karangar (KA) populations from the simulated Genetic Analysis Workshop 14 Problem 2 data. We found that information contents obtained from the SNPs scan were somewhat lower than those from the MS scan. However, the linkage results obtained from the two scans showed a high degree of similarity. Both scans identified a similar number of chromosomal regions attaining nominal significance (p < 0.05). Specifically, both scans detected confirmed evidence for linkage (NPL >or= 4.07, p = 2 x 10(-5)) to chromosome 1 in the AI families, chromosomes 1 and 3 in the DA families, and chromosomes 3, 5, and 9 in the KA families. An additional confirmed linkage to chromosome 5 in the AI families was detected only by the MS scan. We also observed slightly wider 1-LOD intervals for more of the SNP peaks than for the MS peaks, which is likely due to lower information contents for the SNPs. Subsequent fine-mapping association analysis further identified 2 to 3 markers significantly associated with disease status in each population; B03T3056, B03T3058, and B05T4139 in the AI population, B03T3056 and B03T3058 in the KA population, and B03T3056, B03T3057, and B03T3058 in the DA population. Among the four markers, three were chosen based on results obtained from the two scans, but one was solely from the SNP scan. In summary, our finding suggests that the SNP-based genome scan has the potential to be as powerful as the traditional MS-based scan and offers good identification of peak location for further fine-mapped association analysis.     

Wheat chromosome instability in the selfed progeny of the double monosomics 1Rv-1A

Structural alterations of chromosomes are often found in wheat-rye hybrids. In the majority of cases modifications are observed for rye chromosomes, yet chromosome aberration cases are described for wheat, including the progeny of Triticum aestivum disomic and monosomic addition lines. Since wheat-rye substitution and translocation lines are the source of rye chromatin in wheat breeding programs, the information on possible chromosome changes in the genomes of introgressive forms is important. Chromosome behavior in F₁ meiosis and chromosomal composition of F₂ karyotypes for double monosomics 1Rv-1A were studied by applying C-banding, genomic in situ hybridisation (GISH) using rye genomic DNA, and sequential in situ hybridization using repetitive sequences pAs1, pSc119.2 and centromere specific pAet-06 as probes. The double monosomics 1Rv-1A were obtained by crossing of disomic substitution line with chromosome 1A replaced by Secale cereale 1Rv in the bread wheat Saratovskaya 29 (S29) background with S29. The results indicated a high frequency of bipolar chromosome 1Rv orientation, as compared to 1A, at metaphase I (MI) (58.6 and 34.7 % of meiocytes, respectively), and, at anaphase I (AI), chromatid segregation of 1Rv compared to 1A (70.53 and 32.14 % of meiocytes, respectively). In few cases desynapsis of wheat homologues was observed, at AI, the chromosomes randomly distributed between the poles or underwent chromatid segregation. At AI, the two wheat homologues separated onto sister chromatids in 10.89 % of cells.The plants F2 karyotypes were marked with aneuploidy not only of chromosomes 1A and 1Rv, but also of 1D, 2D, 3D, 3B, 3A, 4A, 6D, 6B, 6A, and 7D. Structural changes were observed for the chromosomes of the first homoeologous group (1Rv, 1A, 1D, 1B), as well as for 2B, 5D, 6B, and 7B. The chromosomes 1Rv and 6B often demonstrated aberrations. The types of aberrations were centromeric break, deletions of various sizes, and a changed repeat pSc119.2 localization pattern.     

Relocation of genes generates non-conserved chromosomal segments in Fusarium graminearum that show distinct and co-regulated gene expression patterns

Background

Genome comparisons between closely related species often show non-conserved regions across chromosomes. Some of them are located in specific regions of chromosomes and some are even confined to one or more entire chromosomes. The origin and biological relevance of these non-conserved regions are still largely unknown. Here we used the genome of Fusarium graminearum to elucidate the significance of non-conserved regions.

Results

The genome of F. graminearum harbours thirteen non-conserved regions dispersed over all of the four chromosomes. Using RNA-Seq data from the mycelium of F. graminearum, we found weakly expressed regions on all of the four chromosomes that exactly matched with non-conserved regions. Comparison of gene expression between two different developmental stages (conidia and mycelium) showed that the expression of genes in conserved regions is stable, while gene expression in non-conserved regions is much more influenced by developmental stage. In addition, genes involved in the production of secondary metabolites and secreted proteins are enriched in non-conserved regions, suggesting that these regions could also be important for adaptations to new environments, including adaptation to new hosts. Finally, we found evidence that non-conserved regions are generated by sequestration of genes from multiple locations. Gene relocations may lead to clustering of genes with similar expression patterns or similar biological functions, which was clearly exemplified by the PKS2 gene cluster.

Conclusions

Our results showed that chromosomes can be functionally divided into conserved and non-conserved regions, and both could have specific and distinct roles in genome evolution and regulation of gene expression.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-191) contains supplementary material, which is available to authorized users.     

Characterization of constitutive heterochromatin in Cebus apella (Cebidae, Primates) and Pan troglodytes (Hominidae, Primates): comparison to human chromosomes.

Using G bands, some homologies between the chromosomes of Cebus apella (CAP) and human chromosomes are difficult to establish. To solve this problem, we analyzed these homologies by fluorescence in situ hybridization using human whole chromosome probes (ZOO-FISH). The results indicated that 1) the human probe for chromosome 2 partially hybridizes with CAP chromosomes 13 and 5, 2) the human probe for chromosome 3 partially hybridizes with CAP chromosomes 18 and 20, 3) the human probe for chromosome 9 partially hybridizes with CAP chromosome 19, and 4) the human probe for chromosome 14 hybridizes with the p-terminal and q-terminal regions of CAP chromosome 6. However, none of the human probes employed hybridized with the heterochromatic regions of CAP chromosomes. For this reason, we characterized the heterochromatic regions of CAP chromosomes and of the chromosomes of Pan troglodytes (PTR), to allow comparison between CAP, PTR, and human chromosomes using in situ digestion of fixed chromosomes with the restriction enzymes AluI, HaeIII, and RsaI and by fluorescent staining with DA/DAPI. The results show that 1) centromeric heterochromatin is heterogeneous in the three species studied and 2) noncentromeric heterochromatin is homogeneous within each of the three species, but is different for each species. Thus, centromeric heterochromatin undergoes a higher degree of variability than noncentromeric heterochromatin.     

Genes on Rat Chromosomes 3, 5, 10, and 16 Are Linked With Facets of Metabolic Syndrome

WOKW (Wistar Ottawa Karlsburg W) rats develop metabolic syndrome closely resembling human disorder. In crossing studies between disease‐prone WOKW and disease‐resistant DA (Dark Agouti) rats, several quantitative trait loci (QTLs) were mapped. To prove the in vivo relevance of QTLs, congenic DA.WOKW rats, briefly termed DA.3aW, DA.3bW, DA.5W, DA.10W, and DA.16W, were generated by transferring chromosomal regions of WOKW chromosomes 3, 5, 10, and 16 onto DA genetic background. Male (n = 12) and female (n = 12) rats of each congenic strain and their parental strain DA were characterized for adiposity index (AI), serum leptin, and serum insulin as well as serum cholesterol and serum triglycerides as single facets of metabolic syndrome at the age of 30 weeks. The data showed a significant higher AI for male and female DA.3aW and female DA.16W compared with DA. Serum leptin was significantly elevated in male and female DA.3aW, DA.10W, and DA.16W rats in comparison with DA. Rats of both sexes of DA.10W and female DA.16W showed significantly elevated serum insulin in comparison to DA. Female rats of all congenics had significantly higher serum cholesterol compared with DA, while males did not differ. Finally, triglycerides were only elevated in male DA.16W. The results demonstrate an involvement of WOKW chromosomes 3, 5, 10, and 16 in developing facets of the metabolic syndrome.     

The pachytene chromosomes of maize as revealed by fluorescence in situ hybridization with repetitive DNA sequences

A repetitive DNA sequence, ZmCR2.6c, was isolated from maize based on centromeric sequence CCS1 of the wild grass Brachypodium sylvaticum. ZmCR2.6c is 309 bp in length and shares 65% homology to bases 421–721 of the sorghum centromeric sequence pSau3A9. Fluorescence in situ hybridization (FISH) localized ZmCR2.6c to the primary constrictions of pachytene bivalents and to the stretched regions of MI/AI chromosomes, indicating that ZmCR2.6c is an important part of the centromere. Based on measurements of chromosome lengths and the positions of FISH signals of several cells, a pachytene karyotype was constructed for maize inbred line KYS. The karyotype agrees well with those derived from traditional analyses. Four classes of tandemly repeated sequences were mapped to the karyotype by FISH. Repeats 180 bp long are present in cytologically detectable knobs on 5L, 6S, 6L, 7L, and 9S, as well as at the termini and in the interstitial regions of many chromosomes not reported previously. A most interesting finding is the presence of 180-bp repeats in the NOR-secondary constriction. TR-1 elements co-exist with 180-bp repeats in the knob on 6S and form alone a small cluster in 4L. 26S and 5S rRNA genes are located in the NOR and at 2L.88, respectively. The combination of chromosome length, centromere position, and distribution of the tandem repeats allows all chromosomes to be identified unambiguously. The results presented form an important basis for using FISH for physical mapping and for investigating genome organization in maize. Received: 29 June 1999 / Accepted: 10 November 1999     

Mapping the anther culture response genes in maize (Zea mays L.).

In order to map the genes conditioning the induction of embryos during our anther culture process, we evaluated F2 plants from three different crosses for their anther culture ability and also performed RFLP analysis on these plants. The results showed that six chromosomal regions appear to be associated with the ability to induce embryo-like structures from maize microspores. These regions are located on chromosomes 1 (two regions), 3, 5, 7, and 8. Some of these chromosomes are identical to those found in previous studies and we have localized the regions more precisely. Notably, all chromosome regions identified, except one, are near viviparous mutant loci. Since the viviparous mutations are known to involve the plant hormone abscisic acid (ABA), these results suggest that ABA or its antagonist, gibberellic acid (GA3), might somehow be related to anther culture ability. We also propose some combinations of probes to screen for anther culture ability in the three genotypes studied.     

RING-POSITION AND FREQUENCY OF ADJACENT DISTRIBUTION OF MEIOTIC CHROMOSOMES IN RHOEO SPATHACEA

The morphological sequence of the twelve chromosomes around the ring as worked out by Sax is reaffirmed with slight corrections of the centromere position on three chromosomes: Aa, fA, and Dd. Adjacent distribution was found in 53/120 MI PMC (44.2%). Ring-position analysis was achieved in 34 of the 53. There were 127 chromosomes and 66 arm-pairs involved in adjacent distribution in these 34 MI PMC. Adjacent distributions occurred at random among the twelve chromosome positions and among the twelve arm-pair positions. There were eleven instances among the 66 arm-pairs (16.7%) of adjacent distribution despite free ends due to chiasma failure. Up to four consecutive chromosomes may pass to the same pole. Not all cells with 6–6 distribution are genetically balanced. Distribution of 7–5 occurred in 24/120 AI PMC (20.0%). Another nine (7.5%) in the same sample had one or more lagging chromosomes. At MI, three PMC had 8–4 distribution, but none such were seen at AI.     

Transposable Element Numbers in Cosmopolitan Inversions from a Natural Population of Drosophila Melanogaster

Population studies of the distribution of transposable elements (TEs) on the chromosomes of Drosophila melanogaster have suggested that their copy number increase due to transposition is balanced by some form of natural selection. Theory suggests that, as a consequence of deleterious ectopic meiotic exchange between TEs, selection can favor genomes with lower TE copy numbers. This predicts that TEs should be less deleterious, and hence more abundant, in chromosomal regions in which recombination is reduced. To test this, we surveyed the abundance and locations of 10 families of TEs in recombination-suppressing chromosomal inversions from a natural population. The sample of 49 chromosomes included multiple independent isolates of seven different inversions and a corresponding set of standard chromosomes. For all 10 TE families pooled, copy numbers were significantly higher overall within low frequency inversions than within corresponding regions of standard chromosomes. TEs occupied chromosomal sites at significantly higher frequencies within the In(3R)M0 and In(3R)K inversions than within the corresponding regions of standard 3R chromosomes. These results are consistent with the predictions of the ectopic exchange model.     

SuUR protein binds to the boundary regions separating forum domains in Drosophila melanogaster

Forum domains are 50-150 kb DNA fragments that are released during spontaneous fragmentation of chromosomes. They are separated by islands of putative heterochromatin boundary regions. The SuUR protein, which is involved in the control of chromosome organization, is localized exclusively in heterochromatin and often colocalizes on chromosomes with Polycomb group proteins. To test whether the SuUR protein is associated with boundary regions, we used gel retardation assays and found that the SuUR protein binds specifically to boundary regions and that boundary regions are under-replicated. These results suggest that the regular distribution of boundary regions in chromosomes may represent the dispersion of sites designed for chromosomal silencing.