Heterochromatin and the phenomenon of chromosome banding

Cytogenetic characterization of solitary wasp Ancistrocerus flavomarginatus (Brèthes, 1906) (Hymenoptera, Vespidae) with insights into the chromosomal evolution in the genus

Cytogenetic studies have enabled the characterization of the chromosomal macrostructure and microstructure and have contributed to the understanding of the evolution of wasp karyotypes. However, studies on Eumeninae solitary wasps are scarce. In this study, we characterized the karyotype of Ancistrocerus flavomarginatus (Brèthes, 1906) and compared it with previous data from other Ancistrocerus (Wesmael, 1836) species to shed light on the chromosomal diversity of the genus. A chromosome number of 2n = 24 in females and n = 12 in males was observed. Comparing the A. flavomarginatus karyotype with that of another Ancistrocerus species showed variations in the morphology of some chromosomal pairs. The presence of two larger chromosome pairs, almost entirely heterochromatic, and the predominance of subtelocentric chromosomes with heterochromatic short arms in A. flavomarginatus support the occurrence of fissions in Ancistrocerus. A single site of ribosomal genes was observed in A. flavomarginatus, in addition to a size polymorphism of these rDNA clusters between the homologues of some analyzed females. This polymorphism may originate from duplications/deletions due to unequal crossing-over or amplification via transposable elements. The (GA)₁₅ microsatellite is located exclusively in euchromatic regions. Our data show that different rearrangements seem to shape chromosomal evolution in Ancistrocerus species.

Infrared nanospectroscopic mapping of a single metaphase chromosome

The integrity of the chromatin structure is essential to every process occurring within eukaryotic nuclei. However, there are no reliable tools to decipher the molecular composition of metaphase chromosomes. Here, we have applied infrared nanospectroscopy (AFM-IR) to demonstrate molecular difference between eu- and heterochromatin and generate infrared maps of single metaphase chromosomes revealing detailed information on their molecular composition, with nanometric lateral spatial resolution. AFM-IR coupled with principal component analysis has confirmed that chromosome areas containing euchromatin and heterochromatin are distinguishable based on differences in the degree of methylation. AFM-IR distribution of eu- and heterochromatin was compared to standard fluorescent staining. We demonstrate the ability of our methodology to locate spatially the presence of anticancer drug sites in metaphase chromosomes and cellular nuclei. We show that the anticancer 'rule breaker' platinum compound [Pt[N(p-HC6F4)CH2]2py2] preferentially binds to heterochromatin, forming localized discrete foci due to condensation of DNA interacting with the drug. Given the importance of DNA methylation in the development of nearly all types of cancer, there is potential for infrared nanospectroscopy to be used to detect gene expression/suppression sites in the whole genome and to become an early screening tool for malignancy.

Three-dimensional structured illumination microscopy and its application to chromosome structure

This review discusses the exploration of chromosome structure with a recently developed high-resolution microscopy technique, three-dimensional structured illumination microscopy (3dSIM). 3dSIM surpasses the diffraction limit of conventional widefield optical microscopy, increasing the level of detail in images by a factor of 2, while retaining the sample preparation methods, ease of use and flexibility of conventional microscopy. Special attention will be given to the ways in which imaging beyond the diffraction limit can shed light on the structural organization of meiotic chromosomes.

Chromosome plasticity in Ctenomys (Rodentia Octodontidae): chromosome 1 evolution and heterochromatin variation

A chromosome 1 (Cr1) pericentric inversion is described in six of seven species in the genus Ctenomys (tuco-tucos) from Uruguay. The inversion was inferred from G-band analyses of subtelocentric Cr1 hypothesised to be derived from the ancestral metacentric condition. Cr1 varies across species in heterochromatin amount and localisation including a metacentric chromosome without positive C-bands in C. torquatus, a subtelocentric chromosome with heterochromatic short arms in C. rionegrensis, and a subtelocentric chromosome negative after C-banding in five of the species analysed here. Pachytene chromosomes from C. rionegrensis, a species with the highest heterochromatin content, and C. torquatus, one of the species with the lowest heterochromatin content, were analysed in order to assess possible mechanisms of heterochromatin evolution. This analysis revealed the presence of three heterochromatic chromocenters in C. rionegrensis where bivalents converge, while in C. torquatus only one chromocenter was observed. In both species, highly repetitive DNA was observed, localised in chromocenters after "in situ" hybridisation. Heterochromatin associated protein M31 was localised in chromocenters of both species after immuno-detection. The spread of heterochromatin in Ctenomys chromosomes could be produced by chromatin exchanges at the chromocenter level. We propose the exchange of this DNA associated proteins between non-homologous chromosomes in pachytene to be the responsible for the spread of heterochromatin through the karyotypes of species like C. rionegrensis.

Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana

Arabidopsis thaliana (Arabidopsis) is unique among plant model organisms in having a small genome (130-140 Mb), excellent physical and genetic maps, and little repetitive DNA. Here we report the sequence of chromosome 2 from the Columbia ecotype in two gap-free assemblies (contigs) of 3.6 and 16 megabases (Mb). The latter represents the longest published stretch of uninterrupted DNA sequence assembled from any organism to date. Chromosome 2 represents 15% of the genome and encodes 4,037 genes, 49% of which have no predicted function. Roughly 250 tandem gene duplications were found in addition to large-scale duplications of about 0.5 and 4.5 Mb between chromosomes 2 and 1 and between chromosomes 2 and 4, respectively. Sequencing of nearly 2 Mb within the genetically defined centromere revealed a low density of recognizable genes, and a high density and diverse range of vestigial and presumably inactive mobile elements. More unexpected is what appears to be a recent insertion of a continuous stretch of 75% of the mitochondrial genome into chromosome 2.

Isolation of a species-specific satellite DNA with a novel CENP-B-like box from the North African rodent Lemniscomys barbarus

A species-specific satellite DNA (Lb-MspISAT) was isolated from the North African rodent Lemniscomys barbarus. This DNA is highly homogeneous in the sequence of different repeats and shows no internal repetitions. Filter and in situ hybridizations demonstrated that it is tandemly repeated at the centromeres of all chromosomes of the complement. A 19-bp CENP-B-like motif was found in Lb-MspISAT which conserves 12 of the 17-bp of the human CENP-B box, but only 5 of the 9-bp of the canonical sequence that is necessary to bind the CENP-B protein. Compared with the human CENP-B box, nucleotide substitutions and insertions increase the palindromic structure of this motif. The possibilities that it may be involved in centromeric function or in homogenization of the Lb-MspISAT sequence are discussed.

Equilocality and heterogeneity of constitutive heterochromatin: in situ localization of two families of highly repetitive DNA in Dociostaurus genei (Orthoptera)

The chromosome complement of the grasshopper Dociostaurus genei is characterized by the presence of constitutive heterochromatin (C-bands) located in the centromeric regions of all the chromosomes and in the distal regions of some autosomes in the form of supernumerary segments. A sequence analysis was carried out to obtain information about the molecular characteristics of both heterochromatic regions. Two families of tandemly repetitive DNA (DgT2 and DgA3) from D. genei were cloned and characterized. Data obtained from in situ hybridization indicate that these families are located solely in the regions of constitutive heterochromatin. The DgT2 clone is representative of a family of sequences which mainly forms the centromeric C-bands in each chromosome of the complement. The DgA3 family is the major component of the distal C-bands (supernumerary segments) present in most of the autosomal pairs. These results show the existence in D. genei of two different families of repetitive DNA restricted to different chromosomal domains. We discuss these results in the light of the possible role of chromosomal disposition in the maintenance of the differences between heterochromatic DNA from different chromosomal regions and the homogenization of DNA sequences from equilocal chromosomal domains.

Molecular analysis of chromosomal polymorphism in the South American cricetid, Graomys griseoflavus

Graomys griseoflavus is a South American phyllotine rodent widespread in Argentina that shows a high frequency of Robertsonian fusions (RFs). DNA restriction with EcoRI produced a 250-bp repeated family (EG250) specific for the genus. Southern hybridization and sequencing analysis indicate that the EG250 family is heterogeneous, comprising at least two subfamilies. In situ hybridized EG250 probe showed a centromere location in almost all chromosomes. In all karyomorphs C-banding was negative, but restriction enzyme banding (Re-banding) with Alul and Mbol showed centromeric blocks in the autosomes that will generate Robertsonian fusions. Thus, we found three groups of chromosomes: (a) EG250 and Re-banding negative; (b) EG250 positive and Re-banding negative; and (c) EG250 and Re-banding positive. We consider that group (b) is more the result of chromatin condensation state than that of the frequency of recognition sites for the enzymes used. Restriction enzyme blocks would appear in regions with heterochromatic EG250 subfamilies, while lack of banding would be due to decondensed EG250 subfamilies becoming an easier target for chromosomal restriction. It is suggested that heterochromatic EG250 DNA provides a favourable molecular environment for Robertsonian fusion occurrence.

Chromosomal variation in the northwestern American newts of the genus Taricha (Caudata: Salamandridae)

Chromosomal variation was analysed in 22 populations of newts of the salmandrid genus Taricha of western North America, and compared with that of the eastern North American newts of the genus Notophthalmus. The karyotypes of the species Taricha and Notophthalmus were very similar. However, there was considerable variation in the distribution patterns of heterochromatins (revealed by C-banding) and in the sites of the nucleolar organizing region (NOR) (revealed by fluorochrome chromomycin A3 banding) within and between species of these two genera. Chromosomal variation patterns were interpreted in relation to a phylogenetic hypothesis derived from data on mitochondrial DNA sequences and allozyme variation. This study suggests that the pattern distributions of heterochromatins in chromosomes of Taricha are more derived than those of its sister taxon Notophthalmus. Furthermore, the chromosomal NOR types found in the southernmost and northernmost populations of T. granulosa, in the northernmost populations of T. t. sierrae, and in the southern populations of T. t. torosa are recently derived. The implications of this chromosomal variation for phylogeny and biogeography are discussed.

Genome size variation and its phenotypic consequences in Phyllotis rodents

Constitutive heterochromatin and genome size were studied in Phyllotis darwini, three Phyllotis xanthopygus subspecies, and their interspecific laboratory hybrids. P. darwini, with no or only small C-bands, had the smallest genome size; P. xanthopygus rupestris and P. x. vaccarum, with large C-bands in all the chromosomes, had the largest; and P. x. xanthopygus, with heterochromatin only in a few chromosomes, showed intermediate genome size. To examine some phenotypic consequences of nuclear DNA content, we measured nuclear and cellular surfaces and volumes. Linear regression analyses showed that all these cellular characters had a highly significant direct relationship with genome size. Hybrids had always the expected intermediate parental characteristics. Previous results indicate that P. x. vaccarum should have longer mitotic cycles and lower reproductive capacity than P. darwini. Our findings suggest that the "nucleotypic DNA" hypothesis, which considers genome size as an adaptive feature in higher plants and lower vertebrates, could be extended to these mammals. The analysis of heterochromatin and nuclear DNA amounts of other phyllotine and akodontine rodents supports the idea that small C-bands and genomes are ancestral conditions, from which independent and parallel events occurred until large genomes were produced.

C-banding with specific fluorescent DNA-ligands: a new approach to constitutive heterochromatin heterogeneity

The employment of certain DNA-specific fluorescent stains on unbanded and C-banded chromosomes of two species of grasshoppers shows remarkable differences among C-heterochromatic regions supposed to be similar in their base pair composition, according to their response to the standard fluorescence techniques. The possible interspersion of the opposite DNA base pairs in these regions as well as the role played by proteins in chromosome banding are discussed.

A view of interphase chromosomes

Metaphase chromosomes are dynamically modified in interphase. This review focuses on how these structures can be modified, and explores the functional mechanisms and significance of these changes. Current analyses of genes often focus on relatively short stretches of DNA and consider chromatin conformations that incorporate only a few kilobases of DNA. In interphase nuclei, however, orderly transcription and replication can involve highly folded chromosomal domains containing hundreds of kilobases of DNA. Specific "junk" DNA sequences within selected chromosome domains may participate in more complex levels of chromosome folding, and may index different genetic compartments for orderly transcription and replication. Three-dimensional chromosome positions within the nucleus may also contribute to phenotypic expression. Entire chromosomes are maintained as discrete, reasonably compact entities in the nucleus, and heterochromatic coiled domains of several thousand kilobases can acquire unique three-dimensional positions in differentiated cell types. Some aspects of neoplasia may relate to alterations in chromosome structure at several higher levels of organization.

Intragenomic movement, sequence amplification and concerted evolution in satellite DNA in harvest mice, Reithrodontomys: evidence from in situ hybridization

Three DNA probes isolated from three species of Reithrodontomys (R. montanus, R. megalotis, R. fulvescens) were used to examine within and among species variation in the chromosomal location of satellite DNA and constitutive heterochromatin. These probes hybridized to the centromeric regions on all chromosomes in six species of the subgenus Reithrodontomys. Additionally, nearly all extra-centromeric C-band positive regions (with the exception of some heterochromatic material on the X and Y) hybridized to these probes. Within the subgenus Reithrodontomys both the chromosomal distribution and organization of satellite DNA has changed throughout evolution. The evolutionary transition has been from a totally centromeric position in R. fulvescens to centromeric and non-centromeric regions in other species that have undergone extensive chromosomal rearrangements from the primitive karyotype for peromyscine rodents. In addition, the monomer repeat of the satellite sequence differs between R. fulvescens (monomer defined by PstI) and the remaining species in the subgenus Reithrodontomys (monomer defined by EcoRI). These results suggest at least two amplification events for this satellite DNA sequence. Models and mechanisms concerned with the homogenization and spread of satellite sequences in complex genomes are evaluated in light of the Reithrodontomys data. From a phylogenetic standpoint, the satellite sequences composing heterochromatic regions were restricted to the subgenus Reithrodontomys, which supports morphological differences used to recognize two subgenera, Reithrodontomys and Aporodon. Probes failed to hybridize to any part of the karyotype of R. mexicanus (subgenus Aporodon) or to seven species from other closely related genera (Baiomys, Neotoma, Nyctomys, Ochrotomys, Onychomys, Peromyscus, Xenomys), some of which are considered as potential sister taxa for Reithrodontomys.

Meiotic chromosome behaviour reflects levels of sequence divergence in Sus scrofa domestica satellite DNA

We present a general model for the evolution of chromosome-specific satellite DNA subfamilies. Sus scrofa domestica has a bimodal karyotype with two autosomal subsets of 12 meta-/submetacentric (Mc) and 6 acrocentric (Ac) chromosome types (Mc and Ac "subgenomes"). We show that the centromeric heterochromatin is characterised by two distinct satellite DNA families designed Mc1 and Ac2. Mc1 is a diverse satellite family of the Mc subgenome of which certain members with a 100 bp repeat unit are found to occur at the pericentromeric regions of each Mc autosome, while others are chromosome-specific, e.g. clone Mc pAv1.5, a higher order repeat variant, which hybridises specifically to chromosome 1. Ac2 is a homogeneous satellite occurring at the subterminal pericentromeric regions of all Ac autosomes. DNA sequence analyses showed that all clones investigated are built up from a 14 bp repeat unit which is highly conserved. In situ hybridisation to meiotic pachytene nuclei revealed a distinct spatial arrangement of the Ac2 centromeric satellite.

The evolution of heteromorphic sex chromosomes

The facts and ideas which have been discussed lead to the following synthesis and model. 1. Heteromorphic sex chromosomes evolved from a pair of homomorphic chromosomes which had an allelic difference at the sex-determining locus. 2. The first step in the evolution of sex-chromosome heteromorphism involved either a conformational or a structural difference between the homologues. A structural difference could have arisen through a rearrangement such as an inversion or a translocation. A conformational difference could have occurred if the sex-determining locus was located in a chromosomal domain which behaved as a single control unit and involved a substantial segment of the chromosome. It is assumed that any conformational difference present in somatic cells would have been maintained in meiotic prophase. 3. Lack of conformational or structural homology between the sex chromosomes led to meiotic pairing failure. Since pairing failure reduced fertility, mechanisms preventing it had a selective advantage. Meiotic inactivation (heterochromatinization) of the differential region of the X chromosome in species with heterogametic males and euchromatinization of the W in species with heterogametic females are such mechanisms, and through them the pairing problems are avoided. 4. Structural and conformational differences between the sex chromosomes in the heterogametic sex reduced recombination. In heterogametic males recombination was reduced still further by the heterochromatinization of the X chromosome, which evolved in response to selection against meiotic pairing failure. 5. Suppression of recombination resulted in an increase in the mutation rate and an increased rate of fixation of deleterious mutations in the recombination-free chromosome regions. Functional degeneration of the genetically isolated regions of the Y and W was the result. In XY males this often led to further meiotic inactivation of the differential region of the X chromosome, and in this way an evolutionary positive-feedback loop may have been established. 6. Structural degeneration (loss of material) followed functional degeneration of Y or W chromosomes either because the functionally degenerate genes had deleterious effects which made their loss a selective advantage, or because shorter chromosomes were selectively neutral and became fixed by chance. 7. The evolutionary routes to sex-chromosome heteromorphism in groups with female heterogamety are more limited than in those with male heterogamety. Oocytes are usually large and long-lived, and are likely to need the products of X- or Z-linked genes. Meiotic inactivation of these chromosomes is therefore unlikely. In the oocytes of ZW females, meiotic pairing failure is avoided through euchromatinization of the W rather than heterochromatinization of the Z chromosome.(ABSTRACT TRUNCATED AT 400 WORDS)

High-mobility group protein HMG-I localizes to G/Q- and C-bands of human and mouse chromosomes

Mammalian metaphase chromosomes can be identified by their characteristic banding pattern when stained with Giemsa dye after brief proteolytic digestion. The resulting G-bands are known to contain regions of DNA enriched in A/T residues and to be the principal location for the L1 (or Kpn 1) family of long interspersed repetitive sequences in human chromosomes. Here we report that antibodies raised against a highly purified and biochemically well characterized nonhistone "High-Mobility Group" protein, HMG-I, specifically localize this protein to the G-bands in mammalian metaphase chromosomes. In some preparations in which chromosomes are highly condensed, HMG-I appears to be located at the centromere and/or telomere regions of mammalian chromosomes as well. To our knowledge, this is the first well-characterized mammalian protein that localizes primarily to G-band regions of chromosomes.

SINEs and LINEs cluster in distinct DNA fragments of Giemsa band size

By in situ hybridization, short interspersed repeated DNA elements (SINEs), exemplified by Alu repeats, are located principally in Giemsa-light human metaphase chromosome bands. In contrast, the L1 family of long interspersed repeats (LINEs) preferentially cluster in Giemsa-dark bands. These SINE/LINE patterns also generally correspond to early and later replication band patterns. In order to provide a molecular link between structurally visible chromosome bands and a framework of interspersed repeats, we investigated patterns of SINE and LINE hybridization using pulse-field gel electrophoresis (PFGE). Interspersed SINEs and LINEs hybridize with high intensity to specific size fragments of 0.2-3 megabase pairs (Mb). Using appropriate restriction enzymes and pulse-field conditions, a number of fragments were delineated that were either SINE or LINE rich, and were mutually exclusive. Control studies with a human endogenous retroviral repeat that is related in sequence to the major LINE family, delineated a subset of fragments of 0.07-0.4 Mb with unequal intensity. Thus these less numerous repeats also appear to cluster selectively in DNA domains that are larger than a chromosome loop (60-120 kb). In summary, PFGE studies independently confirm the clustering of interspersed repeats on contiguous DNA loops. Selective clustering of repeat motifs may contribute to special structural or functional properties of large chromosome domains, such as chromatin extension/condensation or replication characteristics. In some cases the DNA fragments defined by these repeats approach the size of tandem satellite arrays.

Differential decondensation of mitotic chromosomes during hypotonic treatment of living cells as a possible cause of G-banding: an ultrastructural study

The chromosomal ultrastructure of Chinese hamster cells treated with 0.075 M KCl - a solution ordinarily used for making preparations of spread chromosomes - was studied. The hypotonic treatment was shown to result in differential decondensation of chromosomes which consists in the uneven distribution of deoxyribonucleoprotein (DNP) fibrils along chromatids. Fixation of cells with methanol acetic acid causes an abrupt restructuring of chromosomes. However, the DNP preserves its uneven distribution along chromatids. As seen on ultra-thin sections of marker nucleolus organizer chromosomes, the densely packed regions may correspond to G-bands detected in the selfsame chromosomes by standard methods of differential staining. The results suggest that the capacity of chromosomes for differential staining is based on the different resistance of G- and R-bands to the decondensing action of hypotonic solutions on living cells.

Movement of the X chromosome in epilepsy

The position of selected chromosomes was assessed in samples of normal and epileptic human cortex with biotinylated probes specific for individual chromosome domains. Optical sectioning provided a rapid method for three-dimensional resolution of in situ hybridization signals in interphase cells, and solid models were reconstructed from digitized images for detailed rotational studies. There was a dramatic repositioning of the X chromosome in neurons of both males and females in electrophysiologically defined seizure foci. Other chromosomes (1, 9, and Y) showed more subtle positional changes. Specifically altered nuclear patterns involving the X chromosome may become established and create the genetic memory for intractable seizure activity.

Evolutionary diversity of reverse (R) fluorescent chromosome bands in vertebrates

Mitotic chromosomes, interphase cell nuclei, and male meiosis of 41 species representing all vertebrate classes were analyzed with distamycin A/mithramycin counterstaining. The purpose of the study was to recognize differences and common characteristics in the reverse (R) fluorescent banding patterns in the chromosomes of vertebrate species at various stages of evolution. In contrast to the warm-blooded mammals and birds, the euchromatic segments in the chromosomes of most reptiles, amphibians, and fishes contain no multiple fluorescent R-bands. This is thought to be due to the absence of the long homogeneous regions (isochores) in the DNA of the cold-blooded vertebrates. Distamycin A/mithramycin banding specifically reveals the GC-rich constitutive heterochromatin in all vertebrates. In most of the vertebrate chromosomes examined, the heterochromatic regions have opposite staining properties with mithramycin and quinacrine. Mithramycin labels the nucleolus organizer regions very brightly in the karyotypes of fishes, amphibians, reptiles and birds, but not of mammals. The lack of mithramycin fluorescence at the nucleolus organizer regions of mammals is attributed to the relatively low level of redundancy of the GC-rich ribosomal DNA in their genomes. Studies on the various meiotic stages of the cold-blooded vertebrates show that the mithramycin labeling of the nucleolus organizers is independent of their state of activity. This can be confirmed by mithramycin fluorescence at the nucleoli of actinomycin-treated cells.