Integrated cytogenetic map of chromosome arm 4S of A. thaliana: structural organization of heterochromatic knob and centromere region

We have constructed an integrated cytogenetic map of chromosome arm 4S of Arabidopsis thaliana. The map shows the detailed positions of various multicopy and unique sequences relative to euchromatin and heterochromatin segments. A quantitative analysis of the map positions at subsequent meiotic stages revealed a striking pattern of spatial and temporal variation in chromatin condensation for euchromatin and heterochromatin. For example, the centromere region consists of three domains with distinguishable structural, molecular, and functional properties. We also characterized a conspicuous heterochromatic knob of approximately 700 kb that accommodates a tandem repeat and several dispersed pericentromere-specific repeats. Moreover, our data provide evidence for an inversion event that relocated pericentromeric sequences to an interstitial position, resulting in the heterochromatic knob.     

Heterochromatic regions in corn A- and B- chromosomes

A collection of maize forms from the Vavilov All-Russia Institute of Plant Breeding (VIR) was studied. We compared variation in the following traits: the number and size of heterochromatic knob regions (HKRs) of chromosomes of mother pollen cells at pachytene depending on the presence (B+) or absence (B0) of B-chromosomes; size of B-chromosomes (general, of heterochromatic part); and the frequency of B+ plants in groups of forms contrasting in the HKR number (10-15, 4-10, 2-7, 1-4). It was shown that B chromosomes had statistically significantly different effects on HKR polymorphism, relative heterochromatin "content" in the cell of multiknob and knobless forms, selection of plants for early ear flowering in these forms. The combination of maximum (and minimum) sizes of heterochromatic regions of A- and B-chromosomes was established; the genomic level of control of the trait is suggested. The role of the relationship of polymorphism at heterochromatic regions of A- and B-chromosomes between them and with the systems of maize reproduction is considered as a mechanism of maintenance of optimum plant heterozygosity via adaptive ontogenetic redistribution of heterochromatin among loci, chromosomes, and gametes.     

Heterochromatic Regions of Maize A- and B-Chromosomes

A collection of maize forms from the Vavilov All-Russia Institute of Plant Breeding (VIR) was studied. We compared variation in the following traits: the number and size of heterochromatic knob regions (HKs) of chromosomes of mother pollen cells at pachytene depending on the presence (B⁺) or absence (B⁰) of B-chromosomes; size of B-chromosomes (general, of heterochromatic part); and the frequency of B⁺ plants in groups of forms contrasting in the HK number (10–15, 4–10, 2–7, 1–4). It was shown that B chromosomes had statistically significantly different effects on HK polymorphism, relative heterochromatin content in the cell of multiknob and knobless forms, selection of plants for early ear flowering in these forms. The combination of maximum (and minimum) sizes of heterochromatic regions of A- and B-chromosomes was established; the genomic level of control of the trait is suggested. The role of the relationship of polymorphism at heterochromatic regions of A- and B-chromosomes between them and with the systems of maize reproduction is considered as a mechanism of maintenance of optimum plant heterozygosity via adaptive ontogenetic redistribution of heterochromatin among loci, chromosomes, and gametes.     

Involvement of knob heterochromatin in mitotic abnormalities in germinating aged seeds of maize.

Seeds of three inbred lines of maize, with contrasting numbers of heterochromatic knobs and stored under two different ageing treatments, were analyzed for the occurrence of abnormalities at mitotic anaphase in root meristems 3, 7, 21,42, and 56 days after germination, and in root meristems of their freshly harvested selfed progeny. The largest category of detectable aberrations involved breakage of knobbed chromosome arms. We have obtained evidence that knob heterochromatin plays a central role in the origin of primary chromosome bridges. The initial event responsible for the occurrence of breakages and lagging chromosomes was characterized by the nondisjunction of newly replicated sister chromatids, which was observed to occur preferentially at the knob level. Such configurations, and all the other types of abnormalities (as for example, lagging chromosomes, typical chromosome bridges, fragments, and micronuclei), were observed at decreasing frequencies throughout root growth. Nevertheless, we have detected the occurrence of breakage-fusion-bridge cycles that were initiated by broken chromosomes. The relationship between late-replicating DNA in maize knob heterochromatin and the vulnerability of such regions to breakage is discussed. Our observations suggest a similarity between the mechanisms involved or associated with the origin of the described abnormalities and those reported to occur in cultured maize cells.     

Minichromosomes derived from the B chromosome of maize

Fourteen minichromosomes derived from the B chromosome of maize are described. The centromeric region of the B chromosome contains a specific repetitive DNA element called the B repeat. This sequence was used to determine the transmission frequency of the different types of minichromosomes over several generations via Southern blot analysis at each generation. In general, the minichromosomes have transmission rates below the theoretical 50% frequency of a univalent chromosome. The gross structure of each minichromosome was determined using fluorescence in situ hybridization (FISH) on root tip chromosome spreads. The presence of the B centromeric repeat and of the adjacent heterochromatic knob sequences was determined for each minichromosome. In two cases, the amount of the centromeric knob repeat is increased relative to the progenitor chromosome. Other isolates have reduced or undetectable levels of the knob sequence. Potential uses of the minichromosomes are discussed.     

The heterochromatic B chromosome of maize: the segments affecting recombination

The B chromosome of maize is known to increase recombination in specific regions of the genome. In an attempt to determine the portion of the B responsible for crossover enhancement, translocations between the B and A chromosomes were used to dissect the B into four distinct segments. The effects of the segments on crossing over were studied in a sensitive region composed of chromatin from chromosomes 3 and 9. The relatively euchromatic chromomeres terminating the B lacked enhancement activity, but the remaining segments, all of which possess large amounts of heterochromatin, were capable of elevating recombination. There was no localization of activity to a specific heterochromatic region, however.     

The desynaptic mutant of maize as a combined defect of synaptonemal complex and chiasma maintenance.

The phenotype of the desynaptic (dy) mutant of maize in microsporocytes at meiotic prophase was compared with normal microsporocytes of a closely related strain and with microsporocytes of a maize inbred line (KYS) assumed to be normal. Strikingly more univalents and open arms of bivalents were found in the mutant cells than in normal cells at diakinesis, and where there was heterozygosity for a distal knob (heterochromatic region), separation was usually equational, indicating the occurrence of normal crossing-over followed by failure of chiasma maintenance in the mutant. Differences found in the mutant by electron microscopy were a statistically significant wider dimension of the synaptonemal complex central region and also less twisting of synapsed configurations at pachytene. It is suggested that these are side-effect symptoms of a defect in the synaptonemal complex (or associated substance), which is expressed later as sporadic loss of chiasma maintenance.     

Meiotic drive of chromosomal knobs reshaped the maize genome.

Meiotic drive is the subversion of meiosis so that particular genes are preferentially transmitted to the progeny. Meiotic drive generally causes the preferential segregation of small regions of the genome; however, in maize we propose that meiotic drive is responsible for the evolution of large repetitive DNA arrays on all chromosomes. A maize meiotic drive locus found on an uncommon form of chromosome 10 [abnormal 10 (Ab10)] may be largely responsible for the evolution of heterochromatic chromosomal knobs, which can confer meiotic drive potential to every maize chromosome. Simulations were used to illustrate the dynamics of this meiotic drive model and suggest knobs might be deleterious in the absence of Ab10. Chromosomal knob data from maize's wild relatives (Zea mays ssp. parviglumis and mexicana) and phylogenetic comparisons demonstrated that the evolution of knob size, frequency, and chromosomal position agreed with the meiotic drive hypothesis. Knob chromosomal position was incompatible with the hypothesis that knob repetitive DNA is neutral or slightly deleterious to the genome. We also show that environmental factors and transposition may play a role in the evolution of knobs. Because knobs occur at multiple locations on all maize chromosomes, the combined effects of meiotic drive and genetic linkage may have reshaped genetic diversity throughout the maize genome in response to the presence of Ab10. Meiotic drive may be a major force of genome evolution, allowing revolutionary changes in genome structure and diversity over short evolutionary periods.     

Electron microscope mapping of the pericentric and intercalary heterochromatic regions of the polytene chromosomes of the mutant Suppressor of underreplication in Drosophila melanogaster

Breaks and ectopic contacts in the heterochromatic regions of Drosophila melanogaster polytene chromosomes are the manifestations of the cytological effects of DNA underreplication. Their appearance makes these regions difficult to map. The Su(UR)ES gene, which controls the phenomenon, has been described recently. Mutation of this locus gives rise to new blocks of material in the pericentric heterochromatic regions and causes the disappearance of breaks and ectopic contacts in the intercalary heterochromatic regions, thereby making the banding pattern distinct and providing better opportunities for mapping of the heterochromatic regions in polytene chromosomes. Here, we present the results of an electron microscope study of the heterochromatic regions. In the wild-type salivary glands, the pericentric regions correspond to the beta-heterochromatin and do not show the banding pattern. The most conspicuous cytological effect of the Su(UR)ES mutation is the formation of a large banded chromosome fragment comprising at least 25 bands at the site where the 3L and 3R proximal arms connect. In the other pericentric regions, 20CF, 40BF and 41BC, 15, 12 and 9 new bands were revealed, respectively. A large block of densely packed material appears in the most proximal part of the fourth chromosome. An electron microscope analysis of 26 polytene chromosome regions showing the characteristic features of intercalary heterochromatin was also performed. Suppression of DNA underreplication in the mutant transforms the bands with weak spots into large single bands.     

Molecular characterization of a family of tandemly repeated DNA sequences,TR-1, in heterochromatic knobs of maize and its relatives

Two families of tandem repeats, 180-bp and TR-1, have been found in the knobs of maize. In this study, we isolated 59 clones belonging to the TR-1 family from maize and teosinte. Southern hybridization and sequence analysis revealed that members of this family are composed of three basic sequences, A (67 bp); B (184 bp) or its variants B' (184 bp), 2/3B (115 bp), 2/3B' (115 bp); and C (108 bp), which are arranged in various combinations to produce repeat units that are multiples of approximately 180 bp. The molecular structure of TR-1 elements suggests that: (1) the B component may evolve from the 180-bp knob repeat as a result of mutations during evolution; (2) B' may originate from B through lateral amplification accompanied by base-pair changes; (3) C plus A may be a single sequence that is added to B and B', probably via nonhomologous recombination; and (4) 69 bp at the 3' end of B or B', and the entire sequence of C can be removed from the elements by an unknown mechanism. Sequence comparisons showed partial homologies between TR-1 elements and two centromeric sequences (B repeats) of the supernumerary B chromosome. This result, together with the finding of other investigators that the B repeat is also fragmentarily homologous to the 180-bp repeat, suggests that the B repeat is derived from knob repeats in A chromosomes, which subsequently become structurally modified. Fluorescence in situ hybridization localized the B repeat to the B centromere and the 180-bp and TR-1 repeats to the proximal heterochromatin knob on the B chromosome.     

Epigenetic profiling of heterochromatic satellite DNA

Sugar beet (Beta vulgaris) chromosomes consist of large heterochromatic blocks in pericentromeric, centromeric, and intercalary regions comprised of two different highly abundant DNA satellite families. To investigate DNA methylation at single base resolution at heterochromatic regions, we applied a method for strand-specific bisulfite sequencing of more than 1,000 satellite monomers followed by statistical analyses. As a result, we uncovered diversity in the distribution of different methylation patterns in both satellite families. Heavily methylated CG and CHG (H=A, T, or C) sites occur more frequently in intercalary heterochromatin, while CHH sites, with the exception of CAA, are only sparsely methylated, in both intercalary and pericentromeric/centromeric heterochromatin. We show that the difference in DNA methylation intensity is correlated to unequal distribution of heterochromatic histone H3 methylation marks. While clusters of H3K9me2 were absent from pericentromeric heterochromatin and restricted only to intercalary heterochromatic regions, H3K9me1 and H3K27me1 were observed in all types of heterochromatin. By sequencing of a small RNA library consisting of 6.76 million small RNAs, we identified small interfering RNAs (siRNAs) of 24 nucleotides in size which originated from both strands of the satellite DNAs. We hypothesize an involvement of these siRNAs in the regulation of DNA and histone methylation for maintaining heterochromatin.     

Direct FISH of 5S rDNA on tomato pachytene chromosomes places the gene at the heterochromatic knob immediately adjacent to the centromere of chromosome 1.

We describe a molecular cytogenetic procedure for high resolution physical mapping of DNA markers, an essential step toward construction of an integrated molecular-classical-cytological map. Tomato was selected as material because its pachytene chromosomes are amenable for study and because detailed molecular, classical, and cytological maps are available. Karyotyping of acetocarmine-stained pachytene chromosomes showing detailed cytogenetic landmarks was combined with direct FISH of the 5S rDNA gene. This enabled us to pinpoint the 5S rDNA gene to the first heterochromatic knob immediately adjacent to the centromere in the short arm of chromosome 1. Thus the position of the 5S rDNA gene on the molecular map was related to the position of the 5S rDNA on the cytogenetic map. The results also provide conclusive evidence of the location of a functional gene in the pericentric heterochromatic region, a rare event to date in plants. We conclude that karyotyping of pachytene chromosomes can be combined with FISH to map a DNA sequence to a cytogenetically defined region and to determine the chromatin origin of an expressed gene. Key words : direct fluorescence in situ hybridization, 5S rDNA, pachytene chromosomes, heterochromatic gene.     

Structural organization of the heterochromatic region of human chromosome 9

Giemsa-11, G-banding and Lateral Asymmetry staining techniques were used to define the substructure of the C-band heterochromatin of human chromosome 9, in a sample of 108 different chromosomes 9, from 54 individuals. In this sample, the juxtacentromeric portion of the C-band region stained positive by the G-banding technique while Giemsa-11 delineated a more distally located block. Examination of the pericentric inversions generally revealed that the entire C-band region is changed with the substructural organization left intact; i.e. the G-band is proximal, the G-11 distal to the centromere. The partial pericentric inversions were found to have larger than average amounts of G-band heterochromatin on the short arm. The G-11 staining was in its usual position on the long arm with none on the short arm. Such apparent inversions therefore may not represent true inversions. — Long heterochromatic regions frequently had a segmented appearance when stained with G-11; there was a dark G-band within the pale heterochromatic region when stained with the G-banding technique which corresponded in location to the achromatic gap produced by G-11. This extra G-band may have been derived from the juxtacentromeric G-band by processes analogous to unequal crossing over. — Simple lateral asymmetry was consistently present only in the G-band heterochromatin of those chromosomes 9 containing large blocks of G-band positive material. Examination of the portion of the C-band which would correspond to the G-11 positive material revealed no consistent patterns of asymmetry. Usually both strands were heavily stained and symmetrical but occasionally there were light areas present on one strand suggestive of compound lateral asymmetry.     

The interaction of knobs and B chromosomes of maize in determining the level of recombination

Enhancement of recombination by B chromosomes is influenced by the kind of heterochromatic knob present in or near the tested region of the A chromosomes. In homomorphic chromosome 9 bivalents of K^s/K^s constitution, double exchanges were increased at the expense of singles, but in the K*/K^s heteromorphs there was a gain in both single and double exchanges at the expense of no-exchange tetrads. Modification of the B chromosome enhancement in different knob compounds was observed only in the megasporocytes.—Different frequencies of recombination are found in plants with odd and even numbers of B chromosomes; this effect is especially striking in the megasporocytes. The modification in recombination produced by an odd or even number of B chromosomes is a function of the interaction of a particular region and the knob constitution. Odd numbers of B chromosomes were more effective than even numbers in causing increased recombination.—It is concluded that heterochromatic knobs and the essentially heterochromatic supernumeraries may interact in the process of crossing over, with the level of recombination determined in part by knob constitution.     

A COMPARISON OF CHROMOSOME KNOB FREQUENCIES BETWEEN SYMPATRIC AND ALLOPATRIC POPULATIONS OF TEOSINTE AND MAIZE

Unrestricted gene flow would be expected to lead to similar chromosome knob frequencies in sympatric populations of maize and teosinte. Chi-square tests were therefore used to compare chromosome knob frequencies of 45 collections of Mexican teosinte, grouped according to six geographic regions, with sympatric and allopatric populations of maize. Comparisons of knob frequencies between sympatric and allopatric populations within each region produced an initial classification for each knob-forming position. Further comparisons for each knob position over all regions, led to an interpretation of results for sympatric populations of maize and teosinte in terms of gene flow, selection, differentiation, ancestral similarities, and ancestral differences. Within regions, a high number of knob positions suggesting gene flow was associated with a low number of knob positions suggesting recent differentiation, and vice versa. It is suggested that the teosinte populations most likely to represent unique sources of germplasm are those most susceptible to future genetic erosion by maize. These relationships may represent a general model applicable to a number of crop plants and associated weed races.     

Organization of endoreduplicated chromosomes in the endosperm of Zea mays L

The chromosomes of the maize endosperm proceed through an endoreduplication phase in later stages of development. Endoreduplication is a process in which the cell cycle continues DNA synthesis but does not proceed through cytokinesis. When this occurs, the normally triploid endosperm cell can reach ploidy levels greater than 200× in some lines of maize. In this work, we examined the structure of the endoreduplicated chromosomes. Previous cytological work has indicated that, although the DNA content per cell increases, the number of nucleoli and knobs remains the same. Using fluorescence in situ hybridization and slot blot techniques, we show that the highly repetitive heterochromatic areas both on the A and B chromosomes, as well as several actively transcribed genes, are endoreduplicated. This result suggests that the entire genome follows that same trend. Further evidence shows that the various chromatin strands stay associated throughout the length of the chromosomes after they have been replicated, and that the DNA at the centromeric and knob regions is more tightly associated than the other regions of the chromosomes. Interploidy crosses between diploid and tetraploid derivatives of the same inbred exhibit changes in the chromatin organization of centromeres and heterochromatic knobs.     

Organization and possible origin of the Bari-1 cluster in the heterochromatic h39 region of Drosophila melanogaster

The molecular organization of the heterochromatic h39 region of the Drosophila melanogaster second chromosome has been investigated by studying two BAC clones identified both by Southern blotting and by FISH experiments as containing tandem arrays of Bari1, a transposable element present only in this region. Such BAC clones appear to contain different portions of the h39 region since they differ in the DNA sequences flanking the Bari1 repeats on both sides. Thus, the 80 Bari1 copies estimated to be present in the h39 region are split into at least two separated subregions. On the basis of the analysis of the flanking sequences a possible mechanism depending on an aberrant activity of the Bari1 transposase is proposed for the genesis of the heterochromatic tandem arrays of the element.     

Somatic synapsis of eu- and heterochromatic regions of Drosophila melanogaster chromosomes

Quantitative cytogenetical analysis has been used to study the synapsis of D. melanogaster neuroblast mitotic chromosomes from normal females, flies with heterozygous deletions, duplications or inversions in the heterochromatic regions of chromosome 2 and in triploid females. In all these genotypes chromocentric fusion of heterochromatic regions of heterologous chromosomes is observed. Eu- and heterochromatic regions of homologous chromosomes are intimately paired at the same time during the cell cycle. The structural rearrangements lead to reduced frequencies of chromocentric association as well as of homologous synapsis compared with the frequencies in the wild-type. The results obtained are discussed with respect to the general problem of the homologous interaction of chromosomes and the significance of heterochromatin for these processes.     

Nucleotide variation and molecular structure of the heterochromatic repetitive AluI DNA in the brine shrimp Artemia franciscana

Summary It has been suggested that DNA bending could play a role in the regulation of gene expression, chromosome segregation, specific recombination and/or DNA packaging. We have previously demonstrated that an Alul DNA family of repeats is the major component of constitutive heterochromatin in the brine shrimp A. franciscana. By the analysis of cloned oligomeric (monomer to hexamer) heterochromatic fragments we verified that the repetitive AluI DNA shows a stable curvature that determines a solenoidal geometry to the double helix. This particular structure could be of relevant importance in conferring the characteristic heterochromatic condensation. In this paper we evaluate how the point mutations that occurred during the evolution of the Alul sequence of A. franciscana could influence the sequence-dependent tridimensional conformation. The obtained data underline that, in spite of the high sequence mutation frequency (10%) of the repetitive DNA, the general structure of the heterochromatic DNA is not greatly influenced, but rather there is a substantial variation of the copy number of the repetitive AluI fragment. This variation could be responsible for the hypothetical function of the constitutive heterochromatin.Offprint requests to: N. Landsberger