Non-uniform distribution of methylatable CCGG sequences on human chromosomes as shown by in situ methylation

Altered patterns of DNA methylation on chromosomes from leukemia cell lines: identification of 5-methylcytosines by indirect immunodetection

An immunodetection technique has been developed to map with high resolution the methylated sites of human chromosomes. We have used this method to define the methylated areas of chromosomes from normal donors and from leukemia cell lines. The chromosomes were exposed for a short time to UV light to induce mild denaturation. The methylated sites were detected in situ by using monoclonal antibodies against 5-methylcytosine (prepared in mouse), and fluorescein-conjugated antimouse immunoglobulins. The chromosomes from normal cells exhibited a fluorescent pattern with RCT banding, although some differences from previously reported patterns could be detected. With this method we have been able to show the presence of two types of R-bands: High fluorescence R-band (HFR) and low fluorescence R-band (LFR). Chromosomes from leukemia cell lines exhibited low global staining with disrupted RCT banding of the chromosomes. The decreased level of the methylation status of the chromosomes from leukemia cells was confirmed by detection of 5-methylcytosines on total immobilized DNA. Thus, we have shown that this method can be used to determine the methylated status of chromosomes and, in turn, to map not only the structural (banding) but also the functional (methylation status) properties of the different chromosome domains in normal and pathologic human cells.

Identification of the gene-richest bands in human chromosomes

The human genome is a mosaic of isochores, long DNA segments which are compositionally homogeneous and which can be partitioned into five families, L1, L2, H1, H2 and H3, characterized by increasing GC levels and by increasing gene concentrations. Previous investigations showed that in situ hybridization with a DNA fraction derived from the GC-richest and gene-richest isochores of the H3 family produced the highest concentration of signals on 25 R(everse) bands that include the 22 most thermal-denaturation-resistant T(elomeric) bands, a subset of R bands. Using an improved protocol for in situ hybridization and cloned H3 isochore DNA, we have now shown (i) that the number of bands which are characterized by strong hybridization signals, and which are here called T or H3+, is 28; (ii) that 31 additional R bands, here called T'or H3* bands, also contain H3 isochores, although at a lower concentration than H3+ bands; and (iii) that the remaining R bands (about 140 out of 200, at a resolution of 400 bands), here called R" or H3- bands, do not contain any detectable H3 isochores. H3+ and H3* bands contain all the gene-richest isochores of the human genome. The existence of three distinct sets of R bands is further supported (i) by the different compositional features of genes located in them; (ii) by the very low gene density of chromosomes 13 and 18, in which all R bands are H3- bands; (iii) by the compositional map of a H3* band, Xq28; (iv) by the overwhelming presence of GC-rich and GC-poor long (> 50 kb) DNA sequences in H3+/H3* and in H3-/G bands, respectively; and (v) by the large degree of coincidence of H3+ and H3* bands with CpG island-positive bands. These observations have implications for our understanding of the causes of chromosome banding and provide a classification of chromosomal bands that is related to GC level (and to gene concentration).

Selective inhibition of cytosine-DNA methylases by polyamines

We have advanced the hypothesis that polyamines affect DNA methylation and thus promote the expression of developmentally controlled genes. We demonstrate that the activity of cytosine-DNA methyltransferases HpaII, HhaI, HaeIII and SssI is inhibited by physiological concentrations of polyamines. On the other hand, activity of the adenine-DNA methyltransferase EcoRI, and restriction enzymes HpaII, HhaI, HaeIII and EcoRI, is insensitive to polyamine concentrations up to 40 mM. Our results indicate that the effect of polyamines on cytosine-DNA methyltransferases is rather selective and suggest a possible mode of action in vivo.

New sites of methylcytosine-rich DNA detected on metaphase chromosomes

In situ immunofluorescence detection of antibodies against 5-methylcytosine on metaphase chromosomes prepared by a new procedure allows the display of new 5-methylcytosine-rich sites as compared to previously published methods. In short-term culture lymphocytes, the immunofluorescent signals give a recurrent pattern in which four types of binding sites can be distinguished. Type I sites are the secondary constrictions and a few juxtacentromeric regions, type II sites correspond to T-bands. Both types I and II sites emit a strong fluorescence. Type III sites form an R-band pattern and emit a weaker fluorescence. Type IV sites are the short arms of acrocentrics, they emit strong but polymorphic signals. The results obtained from control experiments suggest that the pattern observed is rather the expression of an uneven distribution of 5-methylcytosine-rich sites than a consequence of the various treatments used. In a lymphoblastoid cell line known to have a reduced 5-methylcytosine content, it was possible to demonstrate a heterogeneous hypomethylation among chromosome structures, principally involving type I sites. The method opens the possibility of studying in situ on chromosomes, regional variations of methylation in pathological conditions.

Detection of methylcytosine-rich heterochromatin on banded chromosomes. Application to cells with various status of DNA methylation

A procedure including incorporation of 5-bromodeoxyuridine (BrdU) in DNA and a thermal denaturation step was developed to obtain both R-banding and efficient binding of anti-5-methylcytosine antibodies on metaphase chromosomes. BrdU incorporation improved the efficiency of antibody binding disclosed by immunofluorescence staining. This method allowed semiquantitative analysis of the antibody binding sites on straightforward characterized metaphase chromosomes and was applied to normal human lymphocytes and lymphoblastoid cell lines for which DNA methylation status had been previously analyzed. A correlation was established between level of DNA methylation and the semiquantitative estimate of antibody fixation. This procedure can be used to study DNA methylation on metaphase chromosomes in transformed and cancerous cell lines.

The distribution of CpG islands in mammalian chromosomes

Using fluorescent in situ suppression hybridization to metaphase chromosomes, we have directly shown that CpG islands are predominantly found in the early replicating (R band) regions of the genome. Conversely, late replicating (G band) DNA is sparsely populated with islands. The very highest concentration of CpG islands is in a subset of R bands, most of which are known as T bands. We suggest that there is an interdependence between the differences in island density and the behaviour of chromosomal domains. Our findings indicate which regions of the genome will yield the highest density of coding sequence information. An awareness of local island density may influence the choice of method for identifying exons in genomic DNA.

In human chromosomes telomeric regions are enriched in CpGs relative to R-bands

Human chromosomes were in situ nick-translated using as nicking agents the endonucleases MspI (CCGG), its methyl-sensitive isoschizomer HpaII, HaeIII (GGCC), SacII (CCGCGG), EcoRI (GAATTC) and DNaseI. We show that in metaphase chromosomes R-bands are enriched, as compared with G-bands, in the dinucleotide CpG but no more than what is expected on the basis of their relative G+C content. The telomeric regions, on the contrary, besides having a chromatin conformation that is particularly relaxed and accessible to endonucleases, also show an enrichment in CpGs.