CpG islands: features and distribution in the genomes of vertebrates

The major compositional transitions in the vertebrate genome

The vertebrate genome underwent two major compositional transitions, between therapsids and mammals and between dinosaurs and birds. These transitions concerned a sizable part (roughly one-third) of the genome, the gene-richest part of it, and consisted in an increase in GC levels (GC is the molar fraction of guanine + cytosine in DNA) which affected both coding sequences (especially third codon positions) and noncoding sequences. These major transitions were studied here by comparing GC3 levels (GC3 is the GC of third codon positions) of orthologous genes from Xenopus, chicken, calf, and man.

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).

The gene distribution of the human genome

Linear correlations exist between the GC levels of third codon positions (GC3) of individual human genes and the GC levels of long genomic sequences and DNA molecules (50-100 kb in size) embedding the genes. These linear relationships allow the positioning of the GC3 histogram of cDNA sequences from the databases relative to the CsCl profile of human DNA. In turn, this allows an estimate of the relative concentrations of genes in genomic regions of different GC content. An estimate obtained by using current sequence data and Gaussian decompositions of the GC3 histogram and of the CsCl profile indicates that the GC-richest (non-ribosomal) component of the human genome is at least 17 times as gene-rich as the GC-poor regions. Moreover, our results suggest that the most recent physical maps of the human genome consisting of overlapping YACs cover less than 50% of the genes.

Quality not quantity: the pufferfish genome

The genome of the pufferfish, Fugu rubripes (Fugu) is compact. With a similar gene complement to mammals and a genome size of just 400 Mb, gene density is high averaging one every 6-7 kb. Initial characterization of this genome has shown that although genes are much smaller and more densely spaced, their intron/exon structure is conserved with the resulting introns being small. There is little repetitive DNA in the genome and this greatly facilitates comparative genomic studies. The coding content of genes is highly conserved as are critical regulatory elements of some genes. Other DNA is not, however, and this allows the identification of homologous coding sequence between Fugu and mammalian genes. Although the genome of Fugu is 7.5 times smaller than the human genome, not all genes are reduced proportionately. Some regions of the genome show conserved synteny with mammalian genomes, although at the present time only short physical distances have been examined. The structure of the genome is also being studied. Initial data suggest that this may be different to that found in mammals. It is not clear that the same kind of isochore structure is present in this early vertebrate genome. Patterns of methylation may be different resulting in a different distribution of CpG islands. An attempt is being made to centralize both resources and data from the genome of Fugu so that everything may be integrated into a single, publicly accessible database which in turn, may be integrated with databases from other organisms.

Transcriptional repression by methylation: cooperativity between a CpG cluster in the promoter and remote CpG-rich regions

Cytosine methylation of binding sites for transcription factors is a straightforward mechanism to prevent transcription, while data on an indirect mechanism, by methylation outside of the factor binding sites, are still scarce. We have studied the latter effect using a model promoter construct. For this, a 69 bp G + C rich DNA segment with a cluster of 14 CpG sites was inserted between upstream lexA sites and the TATA box. Transcription was measured in transient transfection assays with lexA-VP16 as an activating factor. When the entire plasmid was methylated at all CpGs before transfection, transcription was blocked (to 3% residual activity), whereas transcription was only mildly inhibited (to 60%) by methylation of a control plasmid that lacked the 69 bp CpG cluster. However, the effect could not simply be attributed to methylation of the CpG cluster: neither a methylated CpG cluster in an otherwise methylation-free reporter gene plasmid, nor the methylated plasmid with an unmethylated CpG cluster, inhibited transcription considerably (69% and 44% remaining activity, respectively). The data presented here suggest that a minimal length of methylated DNA in the promoter is required for repression, and imply that concomitant methylation of CpGs in the promoter region and in remote sequences can cooperatively block transcription, without the need to methylate any binding sites for transcription factors. We also note that the cooperation for a negative effect described here bears an analogy to transcriptional activation, where a promoter often cooperates with a remote enhancer.

Periodicity of eight nucleotides in purine distribution around human genomic CpG dinucleotides

Mammalian genomes, unlike the genomes of Drosophila and yeast, are characterized by CpG methylation and concomitant CpG depletion, which is caused by the enhanced mutation rate of 5-methylcytosine. To find out whether local nucleotide sequences around existing methylated CpG dinucleotides have common patterns, we analyzed a large population of CpG-poor regions in human DNA, which are typically methylated. We detected a novel periodic variation in the numbers of purine bases around CpGs in the noncoding parts of these sequences. This periodicity of eight nucleotides gradually diminished over 64 nucleotides on each side of the central CpG. Furthermore, the frequencies of the 5' and 3' nearest neighbors of CpGs in CpG-poor regions were biased towards cytosine and guanine, respectively. Such biased sequence contexts may have helped to stabilize CpGs against depletion during mammalian evolution.

Single-copy sequence homology among the GC-richest isochores of the genomes from warm-blooded vertebrates

We have hybridized a human DNA fraction corresponding to the GC-richest and gene-richest isochore family, H3, on compositional fractions of DNAs from 12 mammalian species and three avian species, representing eight and three orders, respectively. Under conditions in which repetitive sequences are competed out, the H3 isochore probe only or predominantly hybridized on the GC-richest fractions of main-band DNA from all the species investigated. These results indicate that single-copy sequences from the human H3 isochores share homology with sequences located in the compositionally corresponding compartments of the vertebrate genomes tested. These sequences are likely to be essentially formed by conserved coding sequences. The present results add to other lines of evidence indicating that isochore patterns are highly conserved in warm-blooded vertebrate genomes. Moreover, they refine recent reports (Sabeur et al., 1993; Kadi et al., 1993), and correct them in some details and also in demonstrating that the shrew genome does not exhibit the general mammalian pattern, but a special pattern.

Possible implications of CpG avoidance in the flatworm Schistosoma mansoni

We report the analysis of the biases of CpG, TpG, and CpA of all the DNA sequences data from the Trematode Schistosoma mansoni. Our results show CpG avoidance whereas TpG and CpA frequencies are over the expected values. These characteristics are similar to the biases displayed by methylated genomes, but in platyhelminths 5mC has not been detected by biochemical methods. The possible implications of this CpG shortage are discussed.

The isochore organization of the human genome and its evolutionary history--a review

This review will first present some properties (including compositional pattern, correlations between isochores and chromosomal bands, and gene distribution) of the human genome, the most extensively studied among vertebrate genomes. It will then explain how these properties came about during the evolution of the vertebrates.

Evidence for erosion of mouse CpG islands during mammalian evolution

In housekeeping and many tissue-specific genes, the promoter is embedded in a so-called CpG island. We have compared the available human and mouse DNA sequences with respect to their CpG island properties. While mouse sequences showed a simple gradient distribution of G + C content and CpG densities, man had a distinct peak of sequences with typical CpG island characteristics. Pairwise comparison of 23 orthologous genes revealed that mouse almost always had a less pronounced CpG island than man, or none at all. In both species the requirements for a functional CpG island may be similar in that most DNA regions with a density of six or more CpG per 100 bp remain unmethylated. However, the mouse has apparently experienced more accidental CpG island methylation, suggested by local TpG and CpA excess. We propose that: (1) in mouse the CpG islands do not represent the ancestral state but have been eroded during evolution, and (2) this erosion may be related to the mouse's small body mass and short life-span, allowing for a more relaxed control of gene activity.

Construction of a library of bovine genomic fragments enriched in CpG islands

A procedure is described to isolate DNA probes from the bovine genome that are enriched in sites for the so-called rare cutter restriction endonucleases. A collection of SacII (CvCGCGG)-Hin-dIII fragments from bovine sperm was established in the plasmid Bluescript. 180 clones were picked at random and analysed for the presence of inserts with sites for the following rare cutters: EagI, BsshII, NarI, MluI, NruI, NaeI: 70% of the clones contained at least 1 site and 5% contained four different such sites. 22.8% had multiple sites for one or more of the rare cutters tested. Sequence analysis for 16 clones confirmed the cloning of DNA with a G+C content and a proportion of CpG vs GpCs indicative of CpG islands.

Compositional bimodality and evolution of retroviral genomes

The compositional distributions of genomes, genes (and their third codon positions) and long terminal repeats from retroviruses of warm-blooded vertebrates are characterized by a striking bimodality which is accompanied by a remarkable compositional homogeneity within each retroviral genome. A first, major class of retroviral genomes is GC-rich, whereas a second, minor class is GC-poor. Representative expressed viral genomes from the two classes integrate in GC-rich and GC-poor isochores, respectively, of host genomes. The first class comprises all oncoviruses (except B-types and some D-types), the second, lentiviruses, spumaviruses, as well as B-type and some D-type oncoviruses (e.g., mouse mammary tumor virus and simian retroviruses type D, respectively). The compositional bimodal distribution of retroviral genomes and the accompanying compositional homogeneity within each retroviral genome appear to be the result of the compositional evolution of retroviral genomes in their integrated form.

Information contents and dinucleotide compositions of plant intron sequences vary with evolutionary origin

The DNA sequence composition of 526 dicot and 345 monocot intron sequences have been characterized using computational methods. Splice site information content and bulk intron and exon dinucleotide composition were determined. Positions 4 and 5 of 5' splice sites contain different statistically significant levels of information in the two groups. Basal levels of information in introns are higher in dicots than in monocots. Two dinucleotide groups, WW (AA, AU, UA, UU) and SS (CC, CG, GC, GG) have significantly different frequencies in exons and introns of the two plant groups. These results suggest that the mechanisms of splice-site recognition and binding may differ between dicot and monocot plants.

The highest gene concentrations in the human genome are in telomeric bands of metaphase chromosomes

Chromosome in situ suppression hybridization has been carried out on human metaphase chromosomes to localize the G+C-richest human DNA fraction (which only represents 3.5% of the genome), as isolated by preparative equilibrium centrifugation in Cs2SO4/3,6-bis(acetatomercurimethyl)-1,4-dioxane density gradient. This fraction essentially corresponds to isochore family H3. The rationale for carrying out this experiment is that this isochore family has, by far, the highest gene concentration, the highest concentration in CpG islands, the highest transcriptional and recombinational activity, and a distinct chromatin structure. The in situ hybridization results obtained show that the H3 isochore family is localized in two coincident sets of bands of human metaphase chromosomes: telomeric bands and chromomycin A3-positive 4',6-diamidino-2-phenylindole-negative bands. This result is the first step toward a complete compositional map of the human karyotype. Because the G+C gradient across isochore families is paralleled by a gene concentration gradient, such a map has structural, functional, and evolutionary relevance.

Compositional properties of telomeric regions from human chromosomes

We have investigated the GC levels of third codon position of genes localized in G- (Giemsa), R-(reverse) and T-(telomeric) bands of human metaphase chromosomes, as well as the hybridization of telomeric probes on fractionated human DNA. The first set of results shows much higher GC levels for genes localized in T-bands than in G- or R-bands (the latter being higher than the former). The second set of data shows that telomeric probes corresponding to T-bands hybridize on the GC-richest family (H3) of isochores, whereas telomeric probes corresponding to R-bands hybridize on GC-rich families H1 and H2; in agreement with these findings, the telomeric repeat common to all chromosomes hybridized on isochore families H1, H2 and H3.

CpG islands, genes and isochores in the genomes of vertebrates

We have shown that human genes associated with CpG islands increase in number as they increase in % of guanine + cytosine (GC) levels, and that most genes associated with CpG islands are located in the GC-richest compartment of the human genome. This is an independent confirmation of the concentration gradient of CpG islands (detected as HpaII tiny fragments, or HTF) which was demonstrated in the genome of warm-blooded vertebrates [Aïssani and Bernardi, Gene 106 (1991) 173-183]. We then reassessed the location of CpG islands using the data currently available and confirmed that CpG islands are most frequently located in the 5'-flanking sequences of genes and that they overlap genes to variable extents. We have shown that such extents increase with the increasing GC levels of genes, the GC-richest genes being completely included in CpG islands. Under such circumstances, we have investigated the properties of the 'extragenic' CpG islands located in the 5'-flanking segments of homologous genes from both warm- and cold-blooded vertebrates. We have confirmed that, in cold-blooded vertebrates, CpG islands are often absent; when present, they have lower GC and CpG levels; the latter attain, however, statistically expected values. Finally, we have shown that CpG doublets increase with the increasing GC of exons, introns and intergenic sequences (including 'extragenic' CpG islands) in the genomes from both warm- and cold-blooded vertebrates. The correlations found are the same for both classes of vertebrates, and are similar for exons, introns and intergenic sequences (including 'extragenic' CpG islands). The findings just outlined indicate that the origin and evolution of CpG islands in the vertebrate genome are associated with compositional transitions (GC increases) in genes and isochores.

The isopycnic, compartmentalized integration of Rous sarcoma virus sequences

Rous sarcoma virus (RSV) can cause tumors in hamsters, which harbor complete or partially deleted RSV sequences, in their genomes. Here we have studied the localization of RSV sequences integrated into the genome of cell lines derived from six independent hamster tumors. We have found that integration occurred in the isochores richest in guanine + cytosine, of the host genome, as it had been previously observed for bovine leukemia and hepatitis B viral sequences. The integration of RSV proviral sequences is, therefore, 'isopycnic' (i.e., it takes place in host genome sequences which compositionally match the viral sequences) and compartmentalized (i.e., it occurs in a small compositional compartment of the host genome). The hamster genome compartment hosting RSV sequences precisely corresponds to a compartment of the human genome which is the most active in both transcription and recombination. The notion of a compartmentalized, isopycnic integration of RSV proviral sequences fits, therefore, with the viral integration into transcriptionally active and recombinogenic regions of the host genome observed by other authors, but is broader, in that it includes, in addition, the requirement for a compositional match between host genome sequences and expressed viral sequences.