Intra individual variation in the number of B chromosomes in the yellow-necked mouse, Apodemus flavicollis (Mammalia, Rodentia)

The yellow-necked mouse, Apodemus flavicollis, is characterized by a frequent occurrence of B chromosomes. The frequency of intra individual mosaicism of Bs was studied in 995 animals collected at six localities in Serbia. It was found that 329 (33.06%) possessed B chromosomes. Among these, 87 animals (26.44%) were mosaics. A total of 32 mosaic animals with more than one B chromosome were analyzed for distribution of Bs which was found to be quite different between groups of animals with different numbers of Bs and increases with their number. The frequency of mosaics differs between localities and ranges from 0.22 to 0.55.     

Characterization of AFLP sequences from regions of maize B chromosome defined by 12 B-10L translocations

Maize B chromosome sequences have been previously cloned by microdissection, and all are proven to be highly repetitive, to be homologous to the normal complement, and to show no similarity to any published gene other than mobile elements. In this study, we isolated sequences from defined B regions. The strategy involved identification and then mapping of AFLP-derived B fragments before cloning. Of 14 B AFLPs, 13 were mapped by 12 B-10L translocations: 3 around the centromeric knob region, 3 in the proximal euchromatic, 1 around the border of proximal euchromatic and distal heterochromatic, and 6 in the distal heterochromatic region of the B long arm. The AFLP fragments were cloned and sequenced. Analogous to the microdissected sequences, all sequences were repetitive, and all but two were highly homologous to the A chromosomes. FISH signals of all but three clones appeared in pachytene B as well as in somatic A and B chromosomes. None of these clones exhibits identity to any published gene. Six clones displayed homology to two centromeric BACs, four to sequences of chromosomes 3, 4, 7, and 10, four to retrotransposons, and three to no sequence deposited in GenBank. Furthermore, flanking regions of two highly B-specific clones were characterized, showing extension of a B-exclusive nature. The possibility of the presence of novel B repeat(s) is discussed.     

Ribosomal DNA deletions modulate genome-wide gene expression: "rDNA-sensitive" genes and natural variation

The ribosomal rDNA gene array is an epigenetically-regulated repeated gene locus. While rDNA copy number varies widely between and within species, the functional consequences of subtle copy number polymorphisms have been largely unknown. Deletions in the Drosophila Y-linked rDNA modifies heterochromatin-induced position effect variegation (PEV), but it has been unknown if the euchromatic component of the genome is affected by rDNA copy number. Polymorphisms of naturally occurring Y chromosomes affect both euchromatin and heterochromatin, although the elements responsible for these effects are unknown. Here we show that copy number of the Y-linked rDNA array is a source of genome-wide variation in gene expression. Induced deletions in the rDNA affect the expression of hundreds to thousands of euchromatic genes throughout the genome of males and females. Although the affected genes are not physically clustered, we observed functional enrichments for genes whose protein products are located in the mitochondria and are involved in electron transport. The affected genes significantly overlap with genes affected by natural polymorphisms on Y chromosomes, suggesting that polymorphic rDNA copy number is an important determinant of gene expression diversity in natural populations. Altogether, our results indicate that subtle changes to rDNA copy number between individuals may contribute to biologically relevant phenotypic variation.     

The 1.688 repetitive DNA of Drosophila: concerted evolution at different genomic scales and association with genes

Concerted evolution leading to homogenization of tandemly repeated DNA arrays is widespread and important for genome evolution. We investigated the range and nature of the process at chromosomal and array levels using the 1.688 tandem repeats of Drosophila melanogaster where large arrays are present in the heterochromatin of chromosomes 2, 3, and X, and short arrays are found in the euchromatin of the same chromosomes. Analysis of 326 euchromatic and heterochromatic repeats from 52 arrays showed that the homogenization of 1.688 repeats occurred differentially for distinct genomic regions, from euchromatin to heterochromatin and from local arrays to chromosomes. We further found that most euchromatic arrays are either close to, or are within introns of, genes. The short size of euchromatic arrays (one to five repeats) could be selectively constrained by their role as gene regulators, a situation similar to the so-called "tuning knobs."     

Sex reversal caused by Mus musculus domesticus Y chromosomes linked to variant expression of the testis-determining gene Sry

When the Y chromosomes from certain populations of Mus musculus domesticus are introduced into the mouse strain C57BL/6 (B6), testis determination can fail, resulting in gonads developing either as ovotestes (with both ovarian and testicular components) or as ovaries. Not all Y(DOM) chromosomes cause sex reversal. Y(DOM) chromosomes are divided into three classes based upon their ability to induce testes in B6. The molecular basis underlying the three Y(DOM) classes is an enigma. The simplest explanation is that they harbor different alleles of the testis-determining gene, Sry. Sequencing of Sry(DOM) genes has indeed identified polymorphisms. However, none were unequivocally linked to the sex-reversal trait. It was concluded that all SRY(DOM) proteins are functionally equivalent. Using a semiquantitative RT-PCR assay, we now show that representatives of the three Y(DOM) classes have variant Sry expression patterns, that severity of sex reversal correlates with Sry mRNA titers, and that genetic correction of the sex reversal results in the upregulation of Sry expression. We propose that the variant Sry expression patterns result from polymorphisms at the site of a putative Sry enhancer.     

Differential expression of signaling pathways in odontogenic differentiation of ectomesenchymal cells isolated from the first branchial arch

The aim of this study was to screen for differential expression of signaling pathways in odontogenic differentiation of ectomesenchymal cells isolated from the first branchial arch of embryonic day 10 (E10) mice by real time RT-PCR microarray. Observations of cellular morphology, immunocytochemistry, and RT-PCR were used to identify the cell source. A real time RT-PCR microarray was then used to detect the differential expression of signaling pathways in cells dissected from animals at two different developmental stages. These assays identified 25 up-regulated genes and 16 down-regulated genes involved in odontogenic differentiation of the ectomesenchymal cells of the first branchial arch. They represented the main members of Wnt, Hedgehog, TGF-β, NF-κB, and LDL signaling pathways. This study determined that these signaling pathways are important for odontogenic differentiation of ectomesenchymal cells of the first branchial arch.     

Genomic Instability in Wheat Induced by Chromosome 6b(s) of Triticum Speltoides

A massive restructuring of chromosomes was observed during the production of a substitution of chromosome 6B(s) from Triticum speltoides (Tausch) Gren. ex Richter for chromosome 6B of Chinese Spring wheat (Triticum aestivum L.). Deletions, translocations, ring chromosomes, dicentric chromosomes and a paracentric inversion were observed. Chromosome rearrangements occurred in both euchromatic and heterochromatic regions. Chromosome rearrangements were not observed either in the amphiploid between Chinese Spring and T. speltoides or in Chinese Spring. No chromosome rearrangements were observed in the backcross derivatives; however, after self-pollination of a monosomic substitution (2n = 41) of chromosome 6B(s) for wheat chromosome 6B, 49 of the 138 plants carried chromosome aberrations. Chromosome rearrangements were observed in both wheat and T. speltoides chromosomes. The frequency of chromosome rearrangements was high among the B-genome chromosomes, moderate among the A-genome chromosomes, and low among the D-genome chromosomes. In the B genome, the rearrangements were nonrandom, occurring most frequently in chromosomes 1B and 5B. Chromosome rearrangements were also frequent for the 6B(s) chromosome of T. speltoides. An intriguing aspect of these observations is that they indicate that wheat genomes can be subject to uneven rates of structural chromosome differentiation in spite of being in the same nucleus.     

Genetic and molecular characterization of a variegating hsp70-acZ fusion gene in the euchromatic 31 B region of Drosophila melanogaster.

A hsp70-lacZ fusion gene introduced into Drosophila melanogaster at the euchromatic 31B region by Pelement transformation displayed a variegated expression with respect to the lacZ fusion protein in the salivary gland cells under heat-shock conditions. The variegation is also reflected by the chromosome puffing pattern. Subsequent transposition of the 31B P element to other euchromatic positions restored wild-type activity, that is, a nonvariegated phenotype. A lower developmental temperature reduced the amount of expression under heat-shock conditions, similar to genes undergoing position-effect variegation (PEV). However, other modifiers of PEV did not affect the expression pattern of the gene. These results show a novel euchromatic tissue-specific variegation that is not associated with classical heterochromatic PEV.     

Genome-wide microarray expression analysis of CD4+ T Cells from nonobese diabetic congenic mice identifies Cd55 (Daf1) and Acadl as candidate genes for type 1 diabetes

NOD.Idd3/5 congenic mice have insulin-dependent diabetes (Idd) regions on chromosomes 1 (Idd5) and 3 (Idd3) derived from the nondiabetic strains B10 and B6, respectively. NOD.Idd3/5 mice are almost completely protected from type 1 diabetes (T1D) but the genes within Idd3 and Idd5 responsible for the disease-altering phenotype have been only partially characterized. To test the hypothesis that candidate Idd genes can be identified by differential gene expression between activated CD4+ T cells from the diabetes-susceptible NOD strain and the diabetes-resistant NOD.Idd3/5 congenic strain, genome-wide microarray expression analysis was performed using an empirical Bayes method. Remarkably, 16 of the 20 most differentially expressed genes were located in the introgressed regions on chromosomes 1 and 3, validating our initial hypothesis. The two genes with the greatest differential RNA expression on chromosome 1 were those encoding decay-accelerating factor (DAF, also known as CD55) and acyl-coenzyme A dehydrogenase, long chain, which are located in the Idd5.4 and Idd5.3 regions, respectively. Neither gene has been implicated previously in the pathogenesis of T1D. In the case of DAF, differential expression of mRNA was extended to the protein level; NOD CD4+ T cells expressed higher levels of cell surface DAF compared with NOD.Idd3/5 CD4+ T cells following activation with anti-CD3 and -CD28. DAF up-regulation was IL-4 dependent and blocked under Th1 conditions. These results validate the approach of using congenic mice together with genome-wide analysis of tissue-specific gene expression to identify novel candidate genes in T1D.     

Dosage compensation in birds

The Z and W sex chromosomes of birds have evolved independently from the mammalian X and Y chromosomes [1]. Unlike mammals, female birds are heterogametic (ZW), while males are homogametic (ZZ). Therefore male birds, like female mammals, carry a double dose of sex-linked genes relative to the other sex. Other animals with nonhomologous sex chromosomes possess "dosage compensation" systems to equalize the expression of sex-linked genes. Dosage compensation occurs in animals as diverse as mammals, insects, and nematodes, although the mechanisms involved differ profoundly [2]. In birds, however, it is widely accepted that dosage compensation does not occur [3-5], and the differential expression of Z-linked genes has been suggested to underlie the avian sex-determination mechanism [6]. Here we show equivalent expression of at least six of nine Z chromosome genes in male and female chick embryos by using real-time quantitative PCR [7]. Only the Z-linked ScII gene, whose ortholog in Caenorhabditis elegans plays a crucial role in dosage compensation [8], escapes compensation by this assay. Our results imply that the majority of Z-linked genes in the chicken are dosage compensated.     

Comprehensive molecular cytogenetic analysis of sorghum genome architecture: distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice

Cytogenetic maps of sorghum chromosomes 3-7, 9, and 10 were constructed on the basis of the fluorescence in situ hybridization (FISH) of approximately 18-30 BAC probes mapped across each of these chromosomes. Distal regions of euchromatin and pericentromeric regions of heterochromatin were delimited for all 10 sorghum chromosomes and their DNA content quantified. Euchromatic DNA spans approximately 50% of the sorghum genome, ranging from approximately 60% of chromosome 1 (SBI-01) to approximately 33% of chromosome 7 (SBI-07). This portion of the sorghum genome is predicted to encode approximately 70% of the sorghum genes ( approximately 1 gene model/12.3 kbp), assuming that rice and sorghum encode a similar number of genes. Heterochromatin spans approximately 411 Mbp of the sorghum genome, a region characterized by a approximately 34-fold lower rate of recombination and approximately 3-fold lower gene density compared to euchromatic DNA. The sorghum and rice genomes exhibit a high degree of macrocolinearity; however, the sorghum genome is approximately 2-fold larger than the rice genome. The distal euchromatic regions of sorghum chromosomes 3-7 and 10 are approximately 1.8-fold larger overall and exhibit an approximately 1.5-fold lower average rate of recombination than the colinear regions of the homeologous rice chromosomes. By contrast, the pericentromeric heterochromatic regions of these chromosomes are on average approximately 3.6-fold larger in sorghum and recombination is suppressed approximately 15-fold compared to the colinear regions of rice chromosomes.     

BRU1 Maintains Configuration of the Euchromatic Subchromosomal Domain in the Nucleus of Arabidopsis

Chromatin states are inseparably associated with regulation of genes. In yeast and animals, chromatin states also correlate with the configuration and spatial localization pattern of chromosomal domains in the nucleus. In plants, however, the dynamics of such domains associated with gene regulation is poorly understood except for heterochromatic domains. We have previously reported several euchromatic regions of Arabidopsis chromosomes where genes are preferentially upregulated by a defect in BRU1—a nuclear factor involved in DNA damage responses and epigenetic gene regulation. In this study, we present a cytogenetic characterization of one of these subchromosomal regions, SCR1. In nuclei of wild-type leaf cells, the 174-kb SCR1 region was moderately condensed near nucleolus organizing region 4 (NOR4). In bru1 mutants, the confined localization pattern of SCR1 was stochastically disrupted. In contrast, bru1 defects did not affect the localization patterns of NOR4 and another 149-kb euchromatic region in which gene activity was not altered in bru1. The degree of confinement of SCR1 in the nucleus varied between leaves, hypocotyls, and undifferentiated calli, but not drastically. These results suggest that BRU1 plays a role in maintaining the configuration of a euchromatic subchromosomal domain that is a potential determinant in the control of gene activity.     

Gene expression profile analysis in human hepatocellular carcinoma by cDNA microarray

We performed gene expression profiling of normal and hepatocellular carcinoma (HCC) liver tissues using a high-density microarray that contained 3,063 human cDNA. The results of a microarray hybridization experiment from eight different HCC tissues were analyzed and classified by the Cluster program. Among these differentially-expressed genes, the galectin-3, serine/threonine kinase SGK, translation factor eIF-4A, -4B, -3, fibroblast growth factor receptor, and ribosomal protein L35A were up-regulated; the mRNAs of Nip3, decorin, and the insulin-like growth factor binding protein-3 were down-regulated in HCC. The differential expression of these genes was further confirmed by an RT-PCR analysis. In addition, our data suggest that the gene expression profile of HCC varies according to the histological types.     

The Role of Heterochromatin in the Expression of a Heterochromatic Gene, the Rolled Locus of Drosophila Melanogaster

Constitutive heterochromatic regions of chromosomes are those that remain condensed through most or all of the cell cycle. In Drosophila melanogaster, the constitutive heterochromatic regions, located around the centromere, contain a number of gene loci, but at a much lower density than euchromatin. In the autosomal heterochromatin, the gene loci appear to be unique sequence genes interspersed among blocks of highly repeated sequences. Euchromatic genes do not function well when brought into the vicinity of heterochromatin (position-effect variegation). We test the possibility that the blocks of centromeric heterochromatin provide an environment essential for heterochromatic gene function. To assay directly the functional requirement of autosomal heterochromatic genes to reside in heterochromatin, the rolled (rl) gene, which is normally located deep in chromosome 2R heterochromatin, was relocated within small blocks of heterochromatin to a variety of euchromatic positions by successive series of chromosomal rearrangements. The function of the rl gene is severely affected in rearrangements in which the rl gene is isolated in a small block of heterochromatin, and these position effects can be reverted by rearrangements which bring the rl gene closer to any large block of autosomal or X chromosome heterochromatin. There is some evidence that five other 2R heterochromatic genes are also affected among these rearrangements. These findings demonstrate that the heterochromatic genes, in contrast to euchromatic genes whose function is inhibited by relocation to heterochromatin, require proximity to heterochromatin to function properly, and they argue strongly that a major function of the highly repeated satellite DNA, which comprises most of the heterochromatin, is to provide this heterochromatic environment.