DNA-protein interactions and chromosome banding

Insight into magnesium ions effect on chromosome banding and ultrastructure

Magnesium ion (Mg²⁺ ) plays a fundamental role in chromosome condensation which is important for genetic material segregation. Studies about the effects of Mg²⁺ on the overall chromosome structure have been reported. Nevertheless, its effects on the distribution of heterochromatin and euchromatin region have yet to be investigated. The aim of this study was to evaluate the effects of Mg²⁺ on the banding pattern and ultrastructure of the chromosome. Chromosome analysis was performed using the synchronized HeLa cells. The effect of Mg²⁺ was evaluated by subjecting the chromosomes to three different solutions, namely XBE5 (containing 5 mM Mg²⁺ ) as a control, XBE (0 mM Mg²⁺ ), and 1 mM EDTA as cations-chelator. Chromosome banding was carried out using the GTL-banding technique. The ultrastructure of the chromosomes treated with and without Mg²⁺ was further obtained using SEM. The results showed a condensed chromosome structure with a clear banding pattern when the chromosomes were treated with a buffer containing 5 mM Mg²⁺ . In contrast, chromosomes treated with a buffer containing no Mg²⁺ and those treated with a cations-chelator showed an expanded and fibrous structure with the lower intensity of the banding pattern. Elongation of the chromosome caused by decondensation resulted in the band splitting. The different ultrastructure of the chromosomes treated with and without Mg²⁺ was obvious under SEM. The results of this study further emphasized the role of Mg²⁺ on chromosome structure and gave insights into Mg²⁺ effects on the banding distribution and ultrastructure of the chromosome.

Poly(ADP-ribose)-dependent chromatin unfolding facilitates the association of DNA-binding proteins with DNA at sites of damage

The addition of poly(ADP-ribose) (PAR) chains along the chromatin fiber due to PARP1 activity regulates the recruitment of multiple factors to sites of DNA damage. In this manuscript, we investigated how, besides direct binding to PAR, early chromatin unfolding events controlled by PAR signaling contribute to recruitment to DNA lesions. We observed that different DNA-binding, but not histone-binding, domains accumulate at damaged chromatin in a PAR-dependent manner, and that this recruitment correlates with their affinity for DNA. Our findings indicate that this recruitment is promoted by early PAR-dependent chromatin remodeling rather than direct interaction with PAR. Moreover, recruitment is not the consequence of reduced molecular crowding at unfolded damaged chromatin but instead originates from facilitated binding to more exposed DNA. These findings are further substantiated by the observation that PAR-dependent chromatin remodeling at DNA lesions underlies increased DNAse hypersensitivity. Finally, the relevance of this new mode of PAR-dependent recruitment to DNA lesions is demonstrated by the observation that reducing the affinity for DNA of both CHD4 and HP1α, two proteins shown to be involved in the DNA-damage response, strongly impairs their recruitment to DNA lesions.

Activation-induced cytidine deaminase targets SUV4-20-mediated histone H4K20 trimethylation to class-switch recombination sites

Activation-induced cytidine deaminase (AID) triggers antibody diversification in B cells by catalysing deamination and subsequently mutating immunoglobulin (Ig) genes. Association of AID with RNA Pol II and occurrence of epigenetic changes during Ig gene diversification suggest participation of AID in epigenetic regulation. AID is mutated in hyper-IgM type 2 (HIGM2) syndrome. Here, we investigated the potential role of AID in the acquisition of epigenetic changes. We discovered that AID binding to the IgH locus promotes an increase in H4K20me3. In 293F cells, we demonstrate interaction between co-transfected AID and the three SUV4-20 histone H4K20 methyltransferases, and that SUV4-20H1.2, bound to the IgH switch (S) mu site, is replaced by SUV4-20H2 upon AID binding. Analysis of HIGM2 mutants shows that the AID truncated form W68X is impaired to interact with SUV4-20H1.2 and SUV4-20H2 and is unable to bind and target H4K20me3 to the Smu site. We finally show in mouse primary B cells undergoing class-switch recombination (CSR) that AID deficiency associates with decreased H4K20me3 levels at the Smu site. Our results provide a novel link between SUV4-20 enzymes and CSR and offer a new aspect of the interplay between AID and histone modifications in setting the epigenetic status of CSR sites.

Heterochromatin heterogeneity in Hypostomus prope unae (Steindachner, 1878) (Siluriformes, Loricariidae)from Northeastern Brazil

Cytogenetic analyses using C-banding and chromosomal digestion by several restriction enzymes were carried out in four populations (named A, B, C and D) of Hypostomus prope unae (Loricariidae, Hypostominae) from Contas river basin, northeastern Brazil. These populations share 2n=76 and single NORs on the second metacentric pair but exclusive karyotype forms for each locality. Populations A and B presented conspicuous terminal and interstitial heterochromatic blocks on most of acrocentric chromosomes and equivalent to NORs with differences in both position and bearing pair. Population D showed evident marks at interstitial regions and interspersed with nucleolar region while population C presented interstitial and terminal heterochromatin segments, non-coincident with NORs. The banding pattern after digestion with the endonucleases Alu I, Bam HI, Hae III and Dde I revealed a remarkable heterogeneity within heterochromatin, allowing the identification of distinctive clusters of repeated DNA in the studied populations, besides specific patterns along euchromatic regions. The analysis using restriction enzymes has proved to be highly informative, characterizing population differences and peculiarities in the genome organization of Hypostomus prope unae.

Identification of distinct evolutionary units in allopatric populations of Hypostomus cf. wuchereri Günther, 1864 (Siluriformes: Loricariidae): karyotypic evidence

Few chromosomal reports are available for the endemic fish fauna from coastal basins in northeastern Brazil, and regional biodiversity remains partially or completely unknown. This is particularly true for Loricariidae, the most diverse family of armored catfishes. In the present work, allopatric populations of Hypostomus cf. wuchereri (Siluriformes: Loricariidae) from two basins in Bahia (northeastern Brazil) were cytogenetically analyzed. Both populations shared 2n = 76 chromosomes, a karyotype formula of 10m+18sm+48st/a (FN = 104) and single terminal GC-rich NORs on the second metacentric pair. Nevertheless, microstructural differences were detected by C-banding, fluorochrome staining and chromosomal digestion with restriction enzymes (Alu I, Bam HI, Hae III, and Dde I). The population from Una River (Recôncavo Sul basin) showed conspicuous heterochromatin blocks and a remarkable heterogeneity of base composition (presence of interspersed AT/GC-rich and exclusively AT- or GC-rich sites), while the population from Mutum river (Contas River basin) presented interstitial AT-rich C-bands and terminal GC/AT-rich heterochromatin. Each enzyme yielded a specific band profile per population which allowed us characterizing up to five heterochromatin families in each population. Based on the present data, we infer that these populations have been evolving independently, as favored by their geographic isolation, probably representing cryptic species.

The structure of human metaphase chromosomes: its histological perspective and new horizons by atomic force microscopy

Studies on the structure of the human chromosome were reviewed from the histological perspective and discussed in connection with our recent findings obtained mainly by atomic force microscopy (AFM). In this paper, we introduce several hitherto known models of the high-order structure of the metaphase chromosome and discuss the actual structure of chromosomes in relation to such structures as spiral chromatids, chromosome bands, and chromosome scaffolds. In chromosomes treated with Ohnuki's hypotonic solution, the chromosome arms were elongated and showed a characteristic spiral pattern of chromatid fibers. On the other hand, alternating transverse ridges and grooves were clearly observed on the surface of chromosomes treated with 0.025% trypsin for G-banding, and these ridges and grooves corresponded to the dark and pale bands of G-banded chromosomes. Similar findings were also found in chromosomes treated with quinacrine mastards for Q-banding. Fibers bridging the gap between the sister chromatids were often observed in G/Q-banded chromosomes; these fibers tended to be restricted within the G/Q-positive portions, suggesting the presence of chromatin fibers bridging these regions. Based on these findings in conjunction with previous studies, we outlined the high-order structure of the human chromosome. Recent advances in nanotechnology have provided new AFM techniques for the imaging and handling of materials at nano-scale resolution. Application of these techniques to chromosome research is expected to provide valuable information on the chromosome structure in relation to its function.

C-banding visualized by atomic force microscopy

C-banding is a method used for studying chromosome rearrangements near centromeres and for investigating polymorphisms. In human chromosomes, the C-bands are located at the centromere of all the chromosomes and the distal long arm of the Y chromosome. In this study, we aimed to detect the structural changes in chromosomes during the stages of C-banding by atomic force microscopy. We observed crater-like structures in the chromosomes after 2xSSC (saline sodium citrate) treatment and measured the relative difference between the heights of chromatid and centromere of the chromosomes. Results showed that the relative difference was 3 nm in chromosomes 1, 9, 16, and Y, whereas in the other chromosomes this value was 11.6 nm. After Giemsa staining, the relative difference increased by a factor of 16 in chromosomes 1, 9, 16, and Y. The other chromosomes showed no such increase, which is in accordance with our suggestion that nonhiston proteins associated with DNA in constitutive heterochromatin can make the constitutive heterochromatin resistant to C-banding.

The mechanism of G-banding detected by atomic force microscopy

The morphologic changes occurring in human chromosomes during G-banding by trypsin treatment on the same metaphase were followed with the aid of an atomic force microscope (AFM). It was found that trypsin treatment alone caused a pattern of collapse in the chromosomes that was clearly dependent on the duration of trypsinization. The progressive pattern of collapse first indicated the loss of internal differentiation between chromatids, then bands, and finally all internal structures, except for edges running around the chromosomes' perimeter. When stained with Giemsa, the collapsed chromosomes partly regained their original form, and transverse ridges appeared that correspond to G-positive band regions. However, the treatment of fixed chromosomes with trypsin for 42 s diminished the chromosomal edges, and the z-dimensions could not be measured even with the subsequent application of Giemsa.

Characterization of Dasypyrum villosum (L.) candargy chromosomal chromatin by means of in situ restriction endonucleases, fluorochromes, silver staining and C-banding

The distribution of C-banded heterochromatin was determined in an inbred line of Dasypyrum villosum. Practically no difference in chromosome morphology or band distribution could be observed within the chromosomes of the same pair. Heterochromatin bands, revealed by Giemsa banding, were characterized by means of their differential reaction to fluorochromes, silver staining and in situ digestion with different restriction endonucleases. The results clearly indicate that in D. villosum two different classes of heterochromatin with different chromosomal local-ization exist: one is evidenced by both C-banding and DAPI staining and has mainly telomeric distribution, the other is evidenced only by C-banding and has mainly centromeric distribution.

Banding human chromosomes using a combined C-banding-fluorochrome staining technique

Slides pretreated for C-banding and stained with DAPI or CMA3 show different banding patterns in human metaphase chromosomes compared to those obtained with either standard Giemsa C-banding or fluorochrome staining alone. Human chromosomes show C-plus DA-DAPI banding after C-banding plus DAPI and enhanced R-banding after C-banding plus Chromomycin A3 staining. If C-banding preferentially removes certain classes of DNA and proteins from different chromosome domains, C-banding pretreatment may cause a differential DNA extraction from G- and R-bands in human chromosomes, resulting in a preferential extraction of DNA included in G-bands. This hypothesis is partially supported by the selective cleavage and removal of DNA from R-bands of restriction endonuclease HaeIII with C-banding combined with DAPI or Chromomycin A3 staining. Structural factors relating to regional differences in DNA and/or proteins could also explain these results.

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.

Morphological and biochemical effects of endonucleases on isolated mammalian chromosomes in vitro

Endonuclease digestion of isolated and unfixed mammalian metaphase chromosomes in vitro was examined as a means to study the higher-order regional organization of chromosomes related to banding patterns and the mechanisms of endonuclease-induced banding. Isolated mouse LM cell chromosomes, digested with the restriction enzymes AluI, HaeIII, EcoRI, BstNI, AvaII, or Sau96I, demonstrated reproducible G- and/or C-banding at the cytological level depending on the enzyme and digestion conditions. At the molecular level, specific DNA alterations were induced that correlated with the banding patterns produced. The results indicate that: (1) chromatin extraction is intimately involved in the mechanism of endonuclease-induced chromosome banding. (2) The extracted DNA fragments are variable in size, ranging from 200 bp to more than 4 kb in length. (3) For HaeIII, there appears to be variation in the rate of restriction site cleavage in G- and R-bands; HaeIII sites appear to be more rapidly cleaved in R-bands than in G-bands. (4) AluI and HaeIII ultimately produce banding patterns that reflect regional differences in the distribution of restriction sites along the chromosome. (5) BstNI restriction sites in the satellite DNA of constitutive heterochromatin are not cleaved intrachromosomally, probably reflecting an inaccessibility of the BstNI sites to enzyme due to the condensed nature of this chromatin or specific DNA-protein interactions. This implies that some enzymes may induce banding related to regional differences in the accessibility of restriction sites along the chromosome. (6) Several specific nonhistone protein differences were noted in the extracted and residual chromatin following an AluI digestion.(ABSTRACT TRUNCATED AT 250 WORDS)

Chromosomal aberrations induced in human cultured cells by liposome-encapsulated deoxyribonuclease I

Experiments of incorporation of a nucleolytic enzyme into human cells cultured in vitro have been carried out with the aim of inducing structural chromosome variations. Human heteroploid cells, either as asynchronous populations or enriched in mitoses, and PHA-stimulated lymphocytes were used as recipients. We found that all these cells when exposed to pancreatic DNAase I encapsulated in liposomes, either of multilamellar (MLV) or of small unilamellar (SUV) type, show an incidence of chromosome damage higher than that induced by the enzyme free in the incubation buffer. Our results indicate that liposomes are suitable vehicles for the transfer of an exogenous nuclease into human cultured cells. The enzyme remains functionally active and interacts with nuclear DNA, giving rise to chromosome lesions.

Some factors affecting the action of restriction endonucleases on human metaphase chromosomes

We have investigated whether restriction endonucleases produce bands on human chromosomes by extracting DNA, using staining methods which are stoichiometric for DNA. Restriction enzymes that produce C-band patterns appear to remove DNA extensively from chromosome arms. In general, however, those restriction enzymes that produce G-bands do not extract DNA from chromosomes, and their effects are believed to be due to conformational change in the chromosomal DNA; in these cases, the chromosomal regions affected appear to be determined by the chromosome structure and not by the specificity of the enzyme. DNA loss from chromosomes due to digestion by restriction enzymes may in some cases be uniform, although a G-banding pattern is visible after Giemsa staining.

The structural basis for C-banding. A scanning electron microscopy study

The same C-banded human polymorphic chromosomes were observed in the light microscope (LM) and then in the scanning electron microscope (SEM) to investigate the structural changes produced by the C-banding technique. C-banded regions, which stained positively in LM, were highly condensed with tightly packed chromatin fibres, resembling non-banded chromosomes. In striking contrast, adjacent non-C-banded regions were represented by loosely arranged fibres, resembling G-banded chromosomes. The significance of these observations in relation to current theories on the effects of C-banding on chromosome structure is discussed.

The effect of chromosome banding techniques on the proteins of isolated chromosomes

Experiments were undertaken to determine the effect of various chromosome banding treatments on the histone and nonhistone proteins of isolated, fixed, air-dried metaphase chromosomes. Chromosome preparations were exposed to G-banding (SSC, urea, NaCl-urea, or trypsin), R-banding (Earle's balanced salt solution), and C-banding (NaOH or Ba(OH)2) treatments, and the extracted and residual proteins were examined by SDS polyacrylamide gel electrophoresis. The results indicate that each of the banding treatments induce characteristic alterations in the chromosomal proteins. The residual proteins left in chromosomes after the diverse G-banding treatments were generally similar to one another, indicating that treatments inducing the same type of banding have similar effects on the chromosomal proteins. This was also true for the two different C-banding treatments. On the other hand, the residual protein patterns seen after the G-banding treatments were strikingly different from those seen after R-banding, which in turn differed from those seen after C-banding. The treatments inducing different types of banding therefore produce markedly different effects on the chromosomal proteins. These protein alterations may have an important influence on the induction of chromosome bands.

Proteins in chromosome banding. II. Effect of R- and C-banding treatments on the proteins of isolated nuclei

SDS polyacrylamide gel electrophoresis was used to study the proteins extracted from, and those remaining in isolated, fixed, air-dried nuclei subjected to a variety of R- and C-banding techniques. The R-banding procedures, involving exposure to hot Earle's BSS or NaH2PO4, had the least effect of any of the banding techniques on the extraction of proteins from isolated nuclei. Only small amounts of 5 nonhistone proteins were detected in the Earle's BSS extract, and no proteins were found in the NaH2PO4 solution after treatment. The residual proteins remaining in the nuclei after either treatment were virtually identical to those in control nuclei. The C-banding techniques, on the other hand, produced substantial changes in the nuclear proteins. These techniques involve several sequential steps, including HCl treatment, exposure to NaOH or Ba(OH)2, and an incubation in hot SSC. The HCl treatment extracted a large variety of nonhistones and some of each of the remaining histones. No proteins were detected in the SSC solution. Some of the proteins extracted by Ba(OH)2 appeared after the two complete C-banding treatments revealed both similarities and differences. The Ba(OH)2 technique appeared to have a more severe effect on the nuclear proteins than the NaOH technique. Fewer residual nuclear proteins were observed after the former technique, but all of these were also represented in nuclei after the NaOH technique. The results indicate that the different treatments producing a common type of banding generally have similar effects on the nuclear proteins, while the treatments producing different types of banding (G-, R-, C-banding) have substantially different effects on these proteins. Such alterations may have implications for chromosome banding.

Proteins in chromosome banding. I. Effect of G-banding treatments on the proteins of isolated nuclei

Nuclei were isolated from Chinese hamster cells, treated with hypotonic KCl, fixed in acetic methanol, and either air-dried in glass tubes (in situ) or left in suspension (in vitro). These preparations were then exposed to a variety of G-banding treatments, including the 2 xSSC, urea, NaCl-urea, and trypsin methods. The proteins extracted into the treatment solution and those remaining in the nuclei were analyzed by SDS polyacrylamide gel electrophoresis. The three former treatments extracted specific subsets of the total nuclear nonhistone proteins into the treatment solution. Some of the extracted nonhistones were common to all treatments while others were unique to a particular treatment. Variable amounts and types of the histones were also extracted by these treatments, but significant quantities of all of these proteins still remained in the nuclei afterwards. The trypsin treatment appeared to degrade some of the nonhistones, while other nonhistones, as well as the histones, were relatively resistant to trypsin digestion. Although there were a few differences in the residual proteins found in the nuclei after the various G-band treatments, the overall electrophoretic patterns of these proteins were generally similar. The results indicate that the G-banding techniques induce specific and reproducible changes in the proteins of isolated nuclei. If these banding treatments induce similar changes in the proteins of mitotic chromosomes, such alterations might be involved in mechanisms of chromosome banding.

Effects of acetic acid-alcohol, trypsin, histone 1 and histone fragments on Giemsa staining patterns in chromosomes

In an effort to minimize subjective bias, a classification scheme was devised to assess Giemsa staining patterns obtained with experiments involving acetic acid-alcohol and exogenously applied histone 1 and polypeptides. A single rinse of metaphase preparations with acetic acid-alcohol quantitatively reduced Giemsa dye binding. Acid-alcohol irreversibly changed the conformation of H1 and its ability to interfere with trypsin G-banding. Our results suggest that, in addition to protein extraction, acid-alcohol may alter the conformation of acid-insoluble components of metaphase chromosomes. The carboxy-terminal polypeptide (residues 73--212) from NBS cleavage of H1 was an effective inhibitor of Giemsa staining and trypsin G-banding. However, this polypeptide which is preferential for supercoiled DNA was much less efficient in inhibiting Giemsa staining of trypsinized metaphase chromosomes. The molecular consequences of these experiments are discussed.

The mechanism of C-binding: depurination and beta-elimination

C-banding of chromosomes involves the differential solubilization of fragmented DNA from euchromatin by three sequential treatments: 1. Acid, 2. Mild base, 3. Hot salt. The data indicate solubilization is effected by 1) depurination, 2) DNA denaturation, 3) chain breakage of the depurinated sites respectively in the three treatments. Conditions were found wherein each treatment in proper sequence was necessary for C-banding and the appropriate chemical reactions were measured in these treatment conditions. The acid treatment (0.2 N HCl) depurinates chromosomal DNA at the rate of 0.26 x 10(-6) purines/dalton min to an alkaline molecular weight of 10(5) daltons but does not break the depurinated sites. Bleomycin can substitute for acid as a base removing agent. Sodium borohydride, by reducing the depurinated sugar's aldehyde thereby preventing chain breakage by the beta-elimination reaction, reversibly inhibits DNA-extraction. Chain breakage at the DNA's apurinic sites occurs not in the 2 min mild alkali treatment where the half-life for breakage is 26 min but in the 18 h hot salt treatment where the half-life for chain breakage is 1-2 h. Most of the DNA extraction occurs in the hot salt as 10(5) dalton fragments as measured in formamide gradients. Bleomycin is introduced as a substitute for HCl; it removes nitrogenous bases from DNA in situ while better preserving the morphology of the final C-banded chromosomes.