CpG islands: features and distribution in the genomes of vertebrates

Transcriptional Regulation of the Chicken ASMT Gene- A Preliminary Analysis

1. Melatonin is an indole hormone that, among its myriad biological functions, regulates circadian and seasonal rhythms in animals. The ASMT gene plays an essential role in melatonin synthesis. However, in chickens, little is known about the regulatory elements governing its transcription.2. The following study identified the transcription start site of the chicken ASMT gene by 5'-RACE. Then, the proximal minimal promoter was identified using a series of 5' truncations of the ASMT promoter (e.g., -3502/+17, -2698/+17, -2003/+17, -1378/+17, and -254/+17). Site-directed mutagenesis, overexpression, and electrophoretic mobility shift assay (EMSA) were applied to show that the transcription factor Oct-1 binds to the promoter region of ASMT.3. The translation start site was located 19 bp upstream from the translational start site. The luciferase reporter assay confirmed that the core promoter of chicken ASMT gene was in the -254/+17 region. Using site-directed mutagenesis, overexpression, and EMSA, Oct-1 bound the promoter of ASMT.4. Overall, Oct1 plays an important role in the transcriptional regulation of chicken ASMT gene.

Hypermethylation in Calca Promoter Inhibited ASC Osteogenic Differentiation in Rats with Type 2 Diabetic Mellitus

The abnormal environment of type 2 diabetes mellitus (T2DM) leads to a substantial decrease in osteogenic function of stem cells. However, the gene sequence does not vary before and after disease for the patient. This phenomenon may be related to changes in osteogenesis-related gene expression caused by DNA methylation. In this study, we established T2DM models to extract adipose-derived stem cells (ASCs) for different gene identifications through DNA methylation sequencing. Specific fragments of methylation changes in the target gene (Calca) were identified by IGV analysis. CGRP was applied to compare the effects on ASCs-T2DM morphology via phalloidin staining, proliferation through CCK-8 assay, and osteogenic differentiation with osteogenic staining, qPCR, and repair of calvarial defect. Furthermore, 5-azacytidine (5-az) was used to intervene ASCs-T2DM to verify the relationship between the methylation level of the target fragment and expression of Calca. We found that the DNA methylation level of target fragment of Calca in ASCs-T2DM was higher than that in ASCs-C. CGRP intervention showed that it did not change the morphology of ASCs-T2DM but could improve proliferation within a certain range. Meanwhile, it could significantly enhance the formation of ALP and calcium nodules in ASCs-T2DM, increase the expression of osteogenesis-related genes in vitro, and promote the healing of calvarial defects of T2DM rat in a concentration-dependent manner. 5-az intervention indicated that the reduction of the methylation level in Calca target fragment of ASCs-T2DM indeed escalated the gene expression, which may be related to DNMT1. Taken together, the environment of T2DM could upregulate the methylation level in the promoter region of Calca and then decrease the Calca expression. The coding product of Calca revealed a promoting role for osteogenic differentiation of ASCs-T2DM. This result provides an implication for us to understand the mechanism of the decreased osteogenic ability of ASCs-T2DM and improve its osteogenic capacity.

Physical Chemistry of Epigenetics: Single-Molecule Investigations

The nucleosome is the fundamental building block of the eukaryotic genome, composed of an ∼147 base-pair DNA fragment wrapping around an octameric histone protein core. DNA and histone proteins are targets of enzymatic chemical modifications that serve as signals for gene regulation. These modifications are often referred to as epigenetic modifications that govern gene activities without altering the DNA sequence. Although the term epigenetics initially required inheritability, it now frequently includes noninherited histone modifications associated with gene regulation. Important epigenetic modifications for healthy cell growth and proliferation include DNA methylation, histone acetylation, methylation, phosphorylation, ubiquitination, and SUMOylation (SUMO = Small Ubiquitin-like Modifier). Our research focuses on the biophysical roles of these modifications in altering the structure and structural dynamics of the nucleosome and their implications in gene regulation mechanisms. As the changes are subtle and complex, we employ various single-molecule fluorescence approaches for their investigations. Our investigations revealed that these modifications induce changes in the structure and structural dynamics of the nucleosome and their thermodynamic and kinetic stabilities. We also suggested the implications of these changes in gene regulation mechanisms that are the foci of our current and future research.

Of Men and Mice: Modeling the Fragile X Syndrome

The Fragile X Syndrome (FXS) is one of the most common forms of inherited intellectual disability in all human societies. Caused by the transcriptional silencing of a single gene, the fragile x mental retardation gene FMR1, FXS is characterized by a variety of symptoms, which range from mental disabilities to autism and epilepsy. More than 20 years ago, a first animal model was described, the Fmr1 knock-out mouse. Several other models have been developed since then, including conditional knock-out mice, knock-out rats, a zebrafish and a drosophila model. Using these model systems, various targets for potential pharmaceutical treatments have been identified and many treatments have been shown to be efficient in preclinical studies. However, all attempts to turn these findings into a therapy for patients have failed thus far. In this review, I will discuss underlying difficulties and address potential alternatives for our future research.

MeDIP-seq and nCpG analyses illuminate sexually dimorphic methylation of gonadal development genes with high historic methylation in turtle hatchlings with temperature-dependent sex determination

Background

DNA methylation alters gene expression but not DNA sequence and mediates some cases of phenotypic plasticity. Temperature-dependent sex determination (TSD) epitomizes phenotypic plasticity where environmental temperature drives embryonic sexual fate, as occurs commonly in turtles. Importantly, the temperature-specific transcription of two genes underlying gonadal differentiation is known to be induced by differential methylation in TSD fish, turtle and alligator. Yet, how extensive is the link between DNA methylation and TSD remains unclear. Here we test for broad differences in genome-wide DNA methylation between male and female hatchling gonads of the TSD painted turtle Chrysemys picta using methyl DNA immunoprecipitation sequencing, to identify differentially methylated candidates for future study. We also examine the genome-wide nCpG distribution (which affects DNA methylation) in painted turtles and test for historic methylation in genes regulating vertebrate gonadogenesis.

Results

Turtle global methylation was consistent with other vertebrates (57% of the genome, 78% of all CpG dinucleotides). Numerous genes predicted to regulate turtle gonadogenesis exhibited sex-specific methylation and were proximal to methylated repeats. nCpG distribution predicted actual turtle DNA methylation and was bimodal in gene promoters (as other vertebrates) and introns (unlike other vertebrates). Differentially methylated genes, including regulators of sexual development, had lower nCpG content indicative of higher historic methylation.

Conclusions

Ours is the first evidence suggesting that sexually dimorphic DNA methylation is pervasive in turtle gonads (perhaps mediated by repeat methylation) and that it targets numerous regulators of gonadal development, consistent with the hypothesis that it may regulate thermosensitive transcription in TSD vertebrates. However, further research during embryogenesis will help test this hypothesis and the alternative that instead, most differential methylation observed in hatchlings is the by-product of sexual differentiation and not its cause.

Electronic supplementary material

The online version of this article (doi:10.1186/s13072-017-0136-2) contains supplementary material, which is available to authorized users.

The caste- and sex-specific DNA methylome of the termite Zootermopsis nevadensis

Epigenetic inheritance plays an important role in mediating alternative phenotype in highly social species. In order to gain a greater understanding of epigenetic effects in societies, we investigated DNA methylation in the termite Zootermopsis nevadensis. Termites are the most ancient social insects, and developmentally distinct from highly-studied, hymenopteran social insects. We used replicated bisulfite-sequencing to investigate patterns of DNA methylation in both sexes and among castes of Z. nevadensis. We discovered that Z. nevadensis displayed some of the highest levels of DNA methylation found in insects. We also found strong differences in methylation between castes. Methylated genes tended to be uniformly and highly expressed demonstrating the antiquity of associations between intragenic methylation and gene expression. Differentially methylated genes were more likely to be alternatively spliced than not differentially methylated genes, and possessed considerable enrichment for development-associated functions. We further observed strong overrepresentation of multiple transcription factor binding sites and miRNA profiles associated with differential methylation, providing new insights into the possible function of DNA methylation. Overall, our results show that DNA methylation is widespread and associated with caste differences in termites. More generally, this study provides insights into the function of DNA methylation and the success of insect societies.

Evolution of Epigenetic Regulation in Vertebrate Genomes

Empirical models of sequence evolution have spurred progress in the field of evolutionary genetics for decades. We are now realizing the importance and complexity of the eukaryotic epigenome. While epigenome analysis has been applied to genomes from single-cell eukaryotes to human, comparative analyses are still relatively few and computational algorithms to quantify epigenome evolution remain scarce. Accordingly, a quantitative model of epigenome evolution remains to be established. We review here the comparative epigenomics literature and synthesize its overarching themes. We also suggest one mechanism, transcription factor binding site (TFBS) turnover, which relates sequence evolution to epigenetic conservation or divergence. Lastly, we propose a framework for how the field can move forward to build a coherent quantitative model of epigenome evolution.

Childhood abuse is associated with methylation of multiple loci in adult DNA

Background

Childhood abuse is associated with increased adult disease risk, suggesting that processes acting over the long-term, such as epigenetic regulation of gene activity, may be involved. DNA methylation is a critical mechanism in epigenetic regulation. We aimed to establish whether childhood abuse was associated with adult DNA methylation profiles.

Methods

In 40 males from the 1958 British Birth Cohort we compared genome-wide promoter DNA methylation in blood taken at 45y for those with, versus those without, childhood abuse (n = 12 vs 28). We analysed the promoter methylation of over 20,000 genes and 489 microRNAs, using MeDIP (methylated DNA immunoprecipitation) in triplicate.

Results

We found 997 differentially methylated gene promoters (311 hypermethylated and 686 hypomethylated) in association with childhood abuse and these promoters were enriched for genes involved in key cell signaling pathways related to transcriptional regulation and development. Using bisulfite-pyrosequencing, abuse-associated methylation (MeDIP) at the metalloproteinase gene, PM20D1, was validated and then replicated in an additional 27 males. Abuse-associated methylation was observed in 39 microRNAs; in 6 of these, the hypermethylated state was consistent with the hypomethylation of their downstream gene targets. Although distributed across the genome, the differentially methylated promoters associated with child abuse clustered in genome regions of at least one megabase. The observations for child abuse showed little overlap with methylation patterns associated with socioeconomic position.

Conclusions

Our observed genome-wide methylation profiles in adult DNA associated with childhood abuse justify the further exploration of epigenetic regulation as a mediating mechanism for long-term health outcomes.

Epigenetic conservation at gene regulatory elements revealed by non-methylated DNA profiling in seven vertebrates

Two-thirds of gene promoters in mammals are associated with regions of non-methylated DNA, called CpG islands (CGIs), which counteract the repressive effects of DNA methylation on chromatin. In cold-blooded vertebrates, computational CGI predictions often reside away from gene promoters, suggesting a major divergence in gene promoter architecture across vertebrates. By experimentally identifying non-methylated DNA in the genomes of seven diverse vertebrates, we instead reveal that non-methylated islands (NMIs) of DNA are a central feature of vertebrate gene promoters. Furthermore, NMIs are present at orthologous genes across vast evolutionary distances, revealing a surprising level of conservation in this epigenetic feature. By profiling NMIs in different tissues and developmental stages we uncover a unifying set of features that are central to the function of NMIs in vertebrates. Together these findings demonstrate an ancient logic for NMI usage at gene promoters and reveal an unprecedented level of epigenetic conservation across vertebrate evolution. DOI:http://dx.doi.org/10.7554/eLife.00348.001.

On the role of retinoblastoma family proteins in the establishment and maintenance of the epigenetic landscape

RB family members are negative regulators of the cell cycle, involved in numerous biological processes such as cellular senescence, development and differentiation. Disruption of RB family pathways are linked to loss of cell cycle control, cellular immortalization and cancer. RB family, and in particular the most studied member RB/p105, has been considered a tumor suppressor gene by more than three decades, and numerous efforts have been done to understand his molecular activity. However, the epigenetic mechanisms behind Rb-mediated tumor suppression have been uncovered only in recent years. In this review, the role of RB family members in cancer epigenetics will be discussed. We start with an introduction to epigenomes, chromatin modifications and cancer epigenetics. In order to provide a clear picture of the involvement of RB family in the epigenetic field, we describe the RB family role in the epigenetic landscape dynamics based on the heterochromatin variety involved, facultative or constitutive. We want to stress that, despite dissimilar modulations, RB family is involved in both mammalian varieties of heterochromatin establishment and maintenance and that disruption of RB family pathways drives to alterations of both heterochromatin structures, thus to the global epigenetic landscape.

The tumor suppressor role of CTCF

CTCF is an evolutionary conserved and ubiquitously expressed protein that binds thousands of sites in the human genome. Ectopic expression of CTCF in various normal and tumoral human cell lines inhibits cell division and clonogenicity, with the consequence to consider CTCF a potential tumor-suppressor factor. In this review article, we focused on the molecular mechanisms engaged by CTCF to modulate the expression of several key-regulators of differentiation, cellular senescence, cell cycle control and progression, whose expression is frequently altered in tumors. Moreover, we discussed common features of CTCF at each tumor-related DNA-binding sequence, such as protein-partners, post-translational modifications, and distinctive epigenetic marks establishment. The investigation of the molecular mechanisms engaged by CTCF to modulate tumor-related genes emphasizes the cell-type dependency of its tumor suppressor role. Indeed, the ability of CTCF to bind their promoters strictly depends by cell-type features as DNA methylation, BORIS-binding and post-translational modifications as PARYlation.

Long-range autocorrelations of CpG islands in the human genome

In this paper, we use a statistical estimator developed in astrophysics to study the distribution and organization of features of the human genome. Using the human reference sequence we quantify the global distribution of CpG islands (CGI) in each chromosome and demonstrate that the organization of the CGI across a chromosome is non-random, exhibits surprisingly long range correlations (10 Mb) and varies significantly among chromosomes. These correlations of CGI summarize functional properties of the genome that are not captured when considering variation in any particular separate (and local) feature. The demonstration of the proposed methods to quantify the organization of CGI in the human genome forms the basis of future studies. The most illuminating of these will assess the potential impact on phenotypic variation of inter-individual variation in the organization of the functional features of the genome within and among chromosomes, and among individuals for particular chromosomes.

Identification of sequence variants in genetic disease-causing genes using targeted next-generation sequencing

Background

Identification of gene variants plays an important role in research on and diagnosis of genetic diseases. A combination of enrichment of targeted genes and next-generation sequencing (targeted DNA-HiSeq) results in both high efficiency and low cost for targeted sequencing of genes of interest.

Methodology/Principal Findings

To identify mutations associated with genetic diseases, we designed an array-based gene chip to capture all of the exons of 193 genes involved in 103 genetic diseases. To evaluate this technology, we selected 7 samples from seven patients with six different genetic diseases resulting from six disease-causing genes and 100 samples from normal human adults as controls. The data obtained showed that on average, 99.14% of 3,382 exons with more than 30-fold coverage were successfully detected using Targeted DNA-HiSeq technology, and we found six known variants in four disease-causing genes and two novel mutations in two other disease-causing genes (the STS gene for XLI and the FBN1 gene for MFS) as well as one exon deletion mutation in the DMD gene. These results were confirmed in their entirety using either the Sanger sequencing method or real-time PCR.

Conclusions/Significance

Targeted DNA-HiSeq combines next-generation sequencing with the capture of sequences from a relevant subset of high-interest genes. This method was tested by capturing sequences from a DNA library through hybridization to oligonucleotide probes specific for genetic disorder-related genes and was found to show high selectivity, improve the detection of mutations, enabling the discovery of novel variants, and provide additional indel data. Thus, targeted DNA-HiSeq can be used to analyze the gene variant profiles of monogenic diseases with high sensitivity, fidelity, throughput and speed.

Identifying CpG islands by different computational techniques

CpG islands (CGIs) are generally regarded as important epigenetic regulatory elements due to their association with promoter regions. However, identification of functional CGIs is hampered by repetitive elements and species-specific particularities. Here, we compared the performance of different CGI detection programs on genomic sequences of human and mouse genes. Although mouse CGIs are shorter and G+C poorer than their human counterparts, the different tools tested in our study reliably identify CGIs in promoter regions in both species. Our study confirms that substantially fewer murine than human CGIs coincide with repetitive elements and indicates that such CGIs are subject to accelerated cytosine deamination. In addition, CpG depletion appears to anticorrelate with the epigenetic features of functional regulatory CGIs. Taking into account different deamination rates in unmethylated CGIs versus those in methylated CGIs might support the detection of functional CGIs in other species for which there is little epigenetic information available.

Distribution of DNA methylation, CpGs, and CpG islands in human isochores

DNA methylation is a major epigenetic modification of the genome that affects basic biological functions, such as gene expression and cell development. We used the human genome sequences and the DNA methylation data that are available in order to establish a map of the levels of GC and methylation in isochores. We also looked for the correlations that hold between GC levels and the distribution of the (1) dinucleotide CpG, (2) ratio 5mC/CpG, and (3) CpG islands. Our results show that methylation levels, CpG frequencies, and the density of CpG islands are positively correlated with the GC level of isochores. In contrast, the correlation between the 5mC/CpG ratio and GC is a negative one because the increase in methylation lags behind that of CpG, to reach a plateau in the GC-richest, gene-richest isochore families H2 and H3. In conclusion, there are more CpG targets that remain unmethylated in the GC-richest, gene-richest isochores in comparison with the other isochores. This conclusion supports the idea that the widespread methylation under consideration here has a general inhibitory effect on gene expression.

The evolution of isochore patterns in vertebrate genomes

Background

Previous work from our laboratory showed that (i) vertebrate genomes are mosaics of isochores, typically megabase-size DNA segments that are fairly homogeneous in base composition; (ii) isochores belong to a small number of families (five in the human genome) characterized by different GC levels; (iii) isochore family patterns are different in fishes/amphibians and mammals/birds, the latter showing GC-rich isochore families that are absent or very scarce in the former; (iv) there are two modes of genome evolution, a conservative one in which isochore patterns basically do not change (e.g., among mammalian orders), and a transitional one, in which they do change (e.g., between amphibians and mammals); and (v) isochores are tightly linked to a number of basic biological properties, such as gene density, gene expression, replication timing and recombination.

Results

The present availability of a number of fully sequenced genomes ranging from fishes to mammals allowed us to carry out investigations that (i) more precisely quantified our previous conclusions; (ii) showed that the different isochore families of vertebrate genomes are largely conserved in GC levels and dinucleotide frequencies, as well as in isochore size; and (iii) isochore family patterns can be either conserved or change within both warm- and cold-blooded vertebrates.

Conclusion

On the basis of the results presented, we propose that (i) the large conservation of GC levels and dinucleotide frequencies may reflect the conservation of chromatin structures; (ii) the conservation of isochore size may be linked to the role played by isochores in chromosome structure and replication; (iii) the formation, the maintainance and the changes of isochore patterns are due to natural selection.

Epigenetic gene regulation in cancer

The observation that cancer cells suffer profound alterations in the DNA methylation profile, with functional consequences in the activity of key genes, together with the recognition that epigenetic alterations might be as important as genetic defects in the origin of cancers has started a new era in cancer research. In a few years, key discoveries have abruptly changed our vision of the determinants of cancer. Breakthroughs in the cancer epigenetics field include the finding of a tumor-type specificity of genes that suffer epigenetic deregulation at both DNA methylation and histone modifications, the interconnection between different epigenetic marks, the identification of mechanisms of targeting of epigenetic alterations, including the participation of Polycomb group (PcG) proteins, or the involvement of small RNAs, which regulate hundreds of target genes. All these findings have multiple implications: first, they shed light on the mechanistic insights by which epigenetic defects complement genetic alterations in the development and progression of cancer; second, epigenetic alterations appear to play a prominent role in the initiation of cancer. In addition, because epigenetic changes are reversible, enzymes involved in their maintenance stand as targets for a variety of compounds for therapy.

Germline methylation patterns inferred from local nucleotide frequency of repetitive sequences in the human genome

Given the genomic abundance and susceptibility to DNA methylation, interspersed repetitive sequences in the human genome can be exploited as valuable resources in genome-wide methylation studies. To learn about the relationships between DNA methylation and repeat sequences, we performed a global measurement of CpG dinucleotide frequencies for interspersed repetitive sequences and inferred germline methylation patterns in the human genome. Although extensive CpG depletion was observed for most repeat sequences, those in the proximity to CpG islands have been relatively removed from germline methylation being the potential source of germline activation. We also investigated the CpG depletion patterns of Alu pairs to see whether they might play an active role in germline methylation. Two kinds of Alu pairs, direct or inverted pairs classified according to the orientation, showed contrast CpG depletion patterns with respect to separating distance of Alus, i.e., as two Alu elements are more closely spaced in a pair, a higher extent of CpG depletion was observed in inverted orientation and vice versa for directly repetitive Alu pairs. This suggests that specific organization of repetitive sequences, such as inverted Alu pairs, might play a role in triggering DNA methylation consistent with a homology-dependent methylation hypothesis.

The neoselectionist theory of genome evolution

The vertebrate genome is a mosaic of GC-poor and GC-rich isochores, megabase-sized DNA regions of fairly homogeneous base composition that differ in relative amount, gene density, gene expression, replication timing, and recombination frequency. At the emergence of warm-blooded vertebrates, the gene-rich, moderately GC-rich isochores of the cold-blooded ancestors underwent a GC increase. This increase was similar in mammals and birds and was maintained during the evolution of mammalian and avian orders. Neither the GC increase nor its conservation can be accounted for by the random fixation of neutral or nearly neutral single-nucleotide changes (i.e., the vast majority of nucleotide substitutions) or by a biased gene conversion process occurring at random genome locations. Both phenomena can be explained, however, by the neoselectionist theory of genome evolution that is presented here. This theory fully accepts Ohta's nearly neutral view of point mutations but proposes in addition (i) that the AT-biased mutational input present in vertebrates pushes some DNA regions below a certain GC threshold; (ii) that these lower GC levels cause regional changes in chromatin structure that lead to deleterious effects on replication and transcription; and (iii) that the carriers of these changes undergo negative (purifying) selection, the final result being a compositional conservation of the original isochore pattern in the surviving population. Negative selection may also largely explain the GC increase accompanying the emergence of warm-blooded vertebrates. In conclusion, the neoselectionist theory not only provides a solution to the neutralist/selectionist debate but also introduces an epigenomic component in genome evolution.

TLR9 and the recognition of self and non-self nucleic acids

Toll-like receptors (TLRs) are involved in the innate recognition of foreign material and their activation leads to both innate and adaptive immune responses directed against invading pathogens. TLR9 is intracellularly expressed in the endo-lysosomal compartments of specialized immune cells. TLR9 is activated in response to DNA, in particular DNA containing unmethylated CpG motifs that are more prevalent in microbial than mammalian DNA. By detecting foreign DNA signatures TLR9 can sense the presence of certain viruses or bacteria inside the cell and mount an immune response. However, under certain conditions, TLR9 can also recognize self-DNA and this may promote immune pathologies with uncontrolled chronic inflammation. The autoimmune disease systemic lupus erythematosis (SLE) is characterized by the presence of immune stimulatory complexes containing autoantibodies against endogenous DNA and DNA- and RNA-associated proteins. Recent evidence indicates that the autoimmune response to these complexes involves TLR9 and the related single-stranded RNA-responsive TLRs 7 and 8, and therefore some breakdown in the normal ability of these TLRs to distinguish self and foreign DNA. Evidence suggests that immune cells use several mechanisms to discriminate between stimulatory and nonstimulatory DNA; however, it appears that TLR9 itself binds rather indiscriminately to a broad range of DNAs. We therefore propose that there is an additional recognition step by which TLR9 senses differences in the structures of bound DNA.

DNA methylation in reptiles

Very recent investigations have provided evidence for a higher DNA methylation level in polar and sub-antarctic fishes compared to temperate/tropical fishes, the latter being in turn higher than the DNA methylation level of warm-blooded vertebrates. These results confirm and extend the finding [Jabbari, K., Cacciò, S., Pais de Barros, J.P., Desgres, J., Bernardi G., 1997. Evolutionary changes in CpG and methylation levels in the genome of vertebrates. Gene 205, 109-118] that DNA methylation level of vertebrates is inversely related to body temperature. Here we studied the methylation level of reptilian genomes. The species previously analyzed exhibited methylation levels closer to those of mammals and birds rather than to those of fishes and amphibians. The sample was, however, too small to reach a final conclusion. Here we used Reversed-Phase-High-Performance Liquid Chromatography (RP-HPLC) to analyze the DNA methylation levels of 43 reptiles representing three out of four orders and 20 families. Such analysis has shown that snakes and lizards exhibit methylation levels covering the whole range comprised between those of temperate/tropical fish and mammals, while turtles, and, more so, crocodiles are close to mammals. We discuss some ecological and physiological data that explain these results.

DNA methylation and body temperature in fishes

Previous investigations from our laboratory [Jabbari, K., Cacciò, S., Pais de Barros, J.P., Desgres, J., Bernardi G., 1997. Evolutionary changes in CpG and methylation levels in the genome of vertebrates. Gene 205, 109-118.] led to the discovery of two different methylation levels in the genomes of vertebrates, a higher one exhibited by fishes and amphibians and a lower one shown by mammals and birds. It was also noted that data from the literature indicated a higher CpG level in fishes and amphibians compared to mammals and birds. Such observations led to suggesting the existence of two equilibria and to speculate that the transitions between the two equilibria in DNA methylation and CpG levels were due to a higher deamination rate in warm-blooded vertebrates related to their higher body temperature. Here we used Reverse-Phase High-Performance Liquid Chromatography (RP-HPLC) analysis to study methylation levels in a number of fish genomes living at different temperatures. We found that polar fishes exhibit DNA methylation levels that are higher than those of tropical and temperate fishes, the latter being in turn higher than the methylation levels of warm-blooded vertebrates, as expected from previous work. A closer analysis of the data revealed that, among Antarctic fishes, the Channichthyidae (the icefishes, deprived of haemoglobin) had the highest methylation level, and that, among temperate and tropical fishes the latter showed the lowest methylation level. These results confirm the existence of an inverse relationship between DNA methylation and body temperature, when the latter is maintained over evolutionary times.

The evolution of introns in human duplicated genes

In previous work [Jabbari, K., Rayko, E., Bernardi, G., 2003. The major shifts of human duplicated genes. Gene 317, 203-208], we investigated the fate of ancient duplicated genes after the compositional transitions that occurred between the genomes of cold- and warm-blooded vertebrates. We found that the majority of duplicated copies were transposed to the "ancestral genome core", the gene-dense genome compartment that underwent a GC enrichment at the compositional transitions. Here, we studied the consequences of the events just outlined on the introns of duplicated genes. We found that, while intron number was highly conserved, total intron size (the sum of intron sizes within any given gene) was smaller in the GC-rich copies compared to the GC-poor copies, especially in dispersed copies (i.e., copies located on different chromosomes or chromosome arms). GC-rich copies also showed higher densities of CpG islands and Alus, whereas GC-poor copies were characterized by higher densities of LINEs. The features of the copies that underwent the compositional transition and became GC-richer are suggestive of, or related to, functional changes.

Methyl-CpG-binding proteins in cancer: blaming the DNA methylation messenger

In recent years, epigenetic alterations have come to prominence in cancer research. In particular, hypermethylation of CpG islands located in the promoter regions of tumor-suppressor genes is now firmly established as an important mechanism for gene inactivation in cancer. One of the most remarkable achievements in the field has been the identification of the methyl-CpG-binding domain family of proteins, which provide mechanistic links between specific patterns of DNA methylation and histone modifications. Although many of the current data indicate that methyl-CpG-binding proteins play a key role in maintaining a transcriptionally inactive state of methylated genes, MBD4 is also known to be involved in excision repair of T:G mismatches. The latter is a member of this family of proteins and appears to play a role in reducing mutations at 5-methylcytosine. This review examines the contribution of methyl-CpG-binding proteins in the epigenetic pathway of cancer.Key words: methyl-CpG-binding, MeCP2, DNA methylation, Rett syndrome, cancer epigenetics.

A genomic basis for the evolution of vertebrate transcription factors containing amino Acid runs

We have previously shown that polyAla (A) tract-containing proteins frequently present runs of glycine (G), proline (P), and histidine (H) and that, in their ORFs, GC content at all codon positions is higher than that in the rest of the genome. In this study, we present new analyses of these human proteins/ORFs. We detected striking differences in codon usage for A, G, and P in and out of runs. After dividing the ORFs, we found that 5' halves were richer in runs than 3' halves. Afterward, when removing the runs, we observed that the run-rich halves (grouped irrespectively of their 5' or 3' position) had a marked statistical tendency to have more homo- and hetero-dicodons for A, G, P, and H than the run-poor halves. This suggests that, in addition to the necessary GC-rich genomic background, a specific codon organization is probably required to generate these coding repeats. Homo-dicodons may indeed provide primers for run formation through polymerase slippage. The compositional analysis of human HOX genes, the most polyAla-rich family, and their comparison with their zebrafish homologs, support these hypotheses and suggest possible effects of genomic environment on ORF evolution and organismal diversification.

Cytosine methylation and CpG, TpG (CpA) and TpA frequencies

An analysis of dinucleotide frequencies was carried out on DNAs from insects and mammals, as well as on large DNA sequences from the genomes of Drosophila melanogaster, Anopheles gambiae, puffer fish (Takifugu rubripes), zebra fish (Danio rerio) and human. These organisms were chosen because Drosophila and Anopheles DNAs have an extremely low level of methylation, human DNA a high level and fish DNA a two-fold higher level compared to human. The results indicate that: (i) CpG deficiency and the corresponding TpG (CpA) excess show no correlation with the level of DNA methylation; indeed, genomes endowed with strikingly different levels of DNA methylation (such as those of Drosophila and human) exhibited similar TpG (CpA) levels; (ii) the correlation between GC levels of large (50 kb) DNA sequences and TpA or CpG shortage levels do not appear to be due to CpG methylation followed by deamination; (iii) CpG dinucleotides are more frequent in fishes than in mammals; interestingly, the monotreme Ornitorhinchus anatinus shows an intermediate CpG frequency. The implications of these results are discussed.

Compositional patterns in reptilian genomes

Sauropsids form a complex group of vertebrates including squamates (lizards and snakes), turtles, crocodiles, sphenodon and birds (which are often considered as a separate class). Although avian genomes have been relatively well studied, the genomes of the other groups have remained only sparsely characterized. Moreover, the nuclear sequences available in databanks are still very limited. In the present study, we have analysed the compositional patterns, i.e. the GC (molar fraction of guanine and cytosine in DNA) distributions, of 31 reptilian (particularly snake) genomes by analytical ultracentrifugation of DNAs in CsCl gradients. The profiles were characterized by their modal buoyant density rho(o), mean buoyant density < rho>, asymmetry < rho>- rho(o), and heterogeneity H. The modal buoyant density distribution of reptilian DNAs clearly distinguishes two groups. The snakes fall in the same range of modal densities as most mammals, whereas crocodiles, turtles and lizards show higher values (>1.700 g/cm(3)). As far as the more important compositional properties of asymmetry and heterogeneity are concerned, previous studies showed that amphibians and fishes share relatively low values, whereas birds and mammals are characterized by highly heterogeneous and asymmetric patterns (with the exception of Muridae, which have a lower heterogeneity). The present results show that the snake genomes cover a broad range of asymmetry and heterogeneity values, whereas the genomes of crocodiles and turtles cover a narrow range that is intermediate between those of fishes/amphibians and those of mammals/birds.

Characterisation of two topoisomerase 1 genes in the pufferfish (Fugu rubripes)

Eukaryotic DNA topoisomerase I manipulates the higher order structures of DNA. Only one functional topoisomerase 1 (top1) gene has previously been identified in any individual eukaryotic species. Here we report the identification and characterisation of two top1 genes in the pufferfish, Fugu rubripes. This shows that the copy number of top1, like that of other topoisomerases, may vary between eukaryotes. Both Fugu genes have 21 exons; a gene structure similar to that of human TOP1. Despite this conservation of structure, and some non-coding elements, both genes are less than a tenth of the size of the human gene. Sequence and phylogenetic analyses have shown that this duplication is ancient and also affects other species in the fish lineage.

The compositional transition between the genomes of cold- and warm-blooded vertebrates: codon frequencies in orthologous genes

The genomes of the ancestors of mammals and birds underwent a compositional change in which the gene-richest regions increased their GC levels. Here we investigated this compositional transition by analyzing the levels of G and C in third codon positions, as well as the codon frequencies of orthologous genes from human, chicken and Xenopus. The results may be summed up as follows: (i) GC-poor genes, that did not undergo the compositional transition, showed only minor differences in orthologous sets from Xenopus, human and chicken; this is remarkable in view of the very many nucleotide substitutions that occurred over the long evolutionary times separating these species; (ii) GC-rich genes, that underwent the compositional transition, showed large differences between Xenopus and warm-blooded vertebrates, but not between chicken and human. In other words, the independent changes that occurred in avian and mammalian genes, on the average, were the same.

The compositional evolution of vertebrate genomes

The compositional evolution of vertebrate genomes is characterized: (i) by one predominant conservative mode, in which nucleotide changes occur, but the base composition of DNA sequences in general, and of coding sequences in particular, does not change; and (ii) by three different shifting or transitional modes, in which nucleotide changes are accompanied by changes in the base composition of sequences. Investigations on these evolutionary modes have shed new light on a central problem in molecular evolution, namely the role played by natural selection in modulating the mutational input. This review will present first the intragenomic shifts, the 'major shifts' and the 'minor shift', and then the 'whole-genome', or 'horizontal', shift. In each case, the shifts were preceded and followed by a conservative mode of evolution. This review expands on a previous one [Bernardi, Gene 241 (2000) 3-17], and summarizes the evidence that the changes of the compositional patterns of the genome and their maintenance are controlled by Darwinian natural selection.

The covariation between TpA deficiency, CpG deficiency, and G+C content of human isochores is due to a mathematical artifact

CpG and TpA dinucleotides are underrepresented in the human genome. The CpG deficiency is due to the high mutation rate from C to T in methylated CpG's. The TpA suppression was thought to reflect a counterselection against TpA's destabilizing effect in RNA. Unexpectedly, the TpA and CpG deficiencies vary according to the G+C contents of sequences. It has been proposed that the variation in CpG suppression was correlated with a particular chromatin organization in G+C-rich isochores. Here, we present an improved model of dinucleotide evolution accounting for the overlap between successive dinucleotides. We show that an increased mutation rate from CpG to TpG or CpA induces both an apparent TpA deficiency and a correlation between CpG and TpA deficiencies and G+C content. Moreover, this model shows that the ratio of observed over expected CpG frequency underestimates the real CpG deficiency in G+C-rich sequences. The predictions of our model fit well with observed frequencies in human genomic data. This study suggests that previously published selectionist interpretations of patterns of dinucleotide frequencies should be taken with caution. Moreover, we propose new criteria to identify unmethylated CpG islands taking into account this bias in the measure of CpG depletion.

Diversity and phylogenetic implications of CsCl profiles from rodent DNAs

Buoyant density profiles of high-molecular-weight DNAs sedimented in CsCl gradients, i.e., compositional distributions of 50- to 100-kb genomic fragments, have revealed a clear difference between the murids so far studied and most other mammals, including other rodents. Sequence analyses have revealed other, related, compositional differences between murids and nonmurids. In the present study, we obtained CsCl profiles of 17 rodent species representing 13 families. The modal buoyant densities obtained for rodents span the full range of values observed in other eutherians. More remarkably, the skewness (asymmetry, mean - modal buoyant density) of the rodent profiles extends to values well below those of other eutherians. Scatterplots of these and related CsCl profile parameters show groups of rodent families that agree largely with established rodent taxonomy, in particular with the monophyly of the Geomyoidea superfamily and the position of the Dipodidae family within the Myomorpha. In contrast, while confirming and extending previously reported differences between the profiles of Myomorpha and those of other rodents, the CsCl data question a traditional hypothesis positing Gliridae within Myomorpha, as does the recently sequenced mitochondrial genome of dormouse. Analysis of CsCl profiles is presented here as a rapid, robust method for exploring rodent and other vertebrate systematics.

Evolution of CpG islands within the myc gene family

CpG islands are discrete regions of DNA with significantly greater frequencies of CpG doublets than bulk genomic DNA. They are most frequently associated with the 5'-ends of housekeeping genes and are involved in the regulation of their expression. In this study, the structure and evolution of CpG islands within genes of the myc family were evaluated with the protein-coding sequences of animals and their transducing viruses. These evaluations relied on a gene tree for the entire myc family to test the origins of CpG islands within their two protein-coding exons. Overall, CG-very rich and CG-rich islands are associated with exon 2 of the different myc genes of warm-blooded vertebrates and with exon 3 of the N-myc and s-myc sequences of mammals, but not birds. These overall distributions of well-developed islands can be related to the major transitions of the CG-rich genomes of warm-blooded vertebrates from the CG-poor ones of other animals. In turn, the greater variability of well-developed islands within exon 3 of the N-myc gene and among the different retrogenes of the myc family can be attributed to their reduced functional constraints, as evidenced by their limited and very restricted patterns of expression, respectively.

Cytosine deamination plays a primary role in the evolution of mammalian isochores

DNA melting is rate-limiting for cytosine deamination, from which we infer that the rate of cytosine deamination should decline twofold for each 10% increase in GC content. Analysis of human DNA sequence data confirms that this is the case for 5-methylcytosine. Several lines of evidence further confirm that it is also the case for unmethylated cytosine and that cytosine deamination causes the majority of all C-->T and G-->A transitions in mammals. Thus, cytosine deamination and DNA base composition each affect the other, forming a positive feedback loop that facilitates divergent genetic drift to high or low GC content. Because a 10 degrees C increase in temperature in vitro increases the rate of cytosine deamination 5. 7-fold, cytosine deamination must be highly dependent on body temperature, which is consistent with the dramatic differences between the isochores of warm-blooded versus cold-blooded vertebrates. Because this process involves both DNA melting and positive feedback, it would be expected to spread progressively (in evolutionary time) down the length of the chromosome, which is consistent with the large size of isochores in modern mammals.

Isochores and the evolutionary genomics of vertebrates

The nuclear genomes of vertebrates are mosaics of isochores, very long stretches (>>300kb) of DNA that are homogeneous in base composition and are compositionally correlated with the coding sequences that they embed. Isochores can be partitioned in a small number of families that cover a range of GC levels (GC is the molar ratio of guanine+cytosine in DNA), which is narrow in cold-blooded vertebrates, but broad in warm-blooded vertebrates. This difference is essentially due to the fact that the GC-richest 10-15% of the genomes of the ancestors of mammals and birds underwent two independent compositional transitions characterized by strong increases in GC levels. The similarity of isochore patterns across mammalian orders, on the one hand, and across avian orders, on the other, indicates that these higher GC levels were then maintained, at least since the appearance of ancestors of warm-blooded vertebrates. After a brief review of our current knowledge on the organization of the vertebrate genome, evidence will be presented here in favor of the idea that the generation and maintenance of the GC-richest isochores in the genomes of warm-blooded vertebrates were due to natural selection.

Identification of the gene-richest bands in human prometaphase chromosomes

The human genome is a mosaic of long, compositionally homogeneous DNA segments, the isochores, that can be partitioned into five families, two GC-poor families (L1 and L2), representing 63% of the genome, and three GC-rich families (H1, H2 and H3), representing 24%, 7.5% and 4-5% of the genome, respectively. Gene concentration increases with increasing GC levels, reaching a level 20-fold higher in H3 compared with L isochores. In-situ hybridization of DNA from different isochore families provides, therefore, information on the chromosomal distribution of genes. Using this approach, three subsets of reverse or Giemsa-negative bands, H3+, H3* and H3-, containing large, moderate, and no detectable amounts, respectively, of the gene-richest H3 isochores were identified at a resolution of 400 bands. H3+ bands largely coincide with the most heat-denaturation-resistant bands, the chromomycin-A3-positive, DAPI-negative bands, the bands with the highest CpG island concentrations, and the earliest replicating bands. Here, we have defined the H3+ bands at a 850-band resolution, and have thus identified the human genome regions, having an average size of 4 Mb, that are endowed with the highest gene density.

The establishment and maintenance of DNA methylation patterns in mouse somatic cells

Somatic cell DNA methylation patterns in mammals are established during embryonic development and are then maintained somewhat faithfully for the remainder of the individual's lifetime. Pattern formation can be divided into a series of linked steps that include demethylation, de novo methylation, methylation spreading, methylation blocking, and maintenance methylation. In this review, these steps will be combined to present a model for the formation and maintenance of a methylation pattern in the 5' region of the mouse Aprt gene. This model suggests that an apparently 'stable' methylation pattern results from a dynamic equilibrium between forces that promote and inhibit methylation spreading.

Different hydrophobicities of orthologous proteins from Xenopus and human

A compositional transition was previously detected by comparing orthologous coding sequences from cold- and warm-blooded vertebrates (see Bernardi, G., Hughes, S., Mouchiroud, D., 1997. The major compositional transitions in the vertebrate genome. J. Mol. Evol. 44, S44-S51 for a review). The transition is characterized by higher GC levels (GC is the molar ratio of guanine+cytosine in DNA) and, especially, by higher GC3 levels (GC3 is the GC level of third codon positions) in coding sequences from warm-blooded vertebrates. This transition essentially affects GC-rich genes, although the nucleotide substitution rate is of the same order of magnitude in both GC-poor and GC-rich genes. In order to understand the evolutionary basis of the changes, we have compared the hydrophobicity of orthologous proteins from Xenopus and human. Although the differences are small in proteins encoded by coding sequences ranging from 0 to 65% in GC3, they are large in the proteins encoded by sequences characterized by GC3 values higher than 65%. The latter proteins are more hydrophobic in human than in Xenopus.

The biology of eukaryotic promoter prediction--a review

Computational prediction of eukaryotic promoters from the nucleotide sequence is one of the most attractive problems in sequence analysis today, but it is also a very difficult one. Thus, current methods predict in the order of one promoter per kilobase in human DNA, while the average distance between functional promoters has been estimated to be in the range of 30-40 kilobases. Although it is conceivable that some of these predicted promoters correspond to cryptic initiation sites that are used in vivo, it is likely that most are false positives. This suggests that it is important to carefully reconsider the biological data that forms the basis of current algorithms, and we here present a review of data that may be useful in this regard. The review covers the following topics: (1) basal transcription and core promoters, (2) activated transcription and transcription factor binding sites, (3) CpG islands and DNA methylation, (4) chromosomal structure and nucleosome modification, and (5) chromosomal domains and domain boundaries. We discuss the possible lessons that may be learned, especially with respect to the wealth of information about epigenetic regulation of transcription that has been appearing in recent years.

Evolutionary genomics of vertebrates and its implications

The discovery that the vertebrate genomes of warm-blooded vertebrates are mosaics of isochores, long DNA segments homogeneous in base composition, yet belonging to families covering a broad spectrum of GC levels, has led to two major observations. The first is that gene density is strikingly non-uniform in the genome of all vertebrates, gene concentration increasing with increasing GC levels. (Although the genomes of cold-blooded vertebrates are characterized by smaller compositional heterogeneities than those of warm-blooded vertebrates and high GC levels are not attained, their gene distribution is basically similar to that of warm-blooded vertebrates.) The second observation is that the GC-richest and gene-richest isochores underwent a compositional transition (characterized by a strong increase in GC level) between cold- and warm-blooded vertebrates. Evidence to be discussed favors the idea that this compositional transition and the ensuing highly heterogeneous compositional pattern was due to, and was maintained by, natural selection.

CpG doublets, CpG islands and Alu repeats in long human DNA sequences from different isochore families

A computer analysis of 946 human DNA sequences larger than 50kb and representing about 118Mb of DNA has led to the following observations. (i) Positive correlations hold between CpG levels and the GC levels of isochores and coding sequences, as expected from previous results. (ii) The correlation between CpG levels and the GC levels of pseudogenes is characterized by lower CpG values (at comparable GC levels) and by a lower slope compared with the correlation with coding sequences; this finding suggests that an extensive methylation followed by deamination has taken place on CpG doublets from inactive genes leading to a further CpG shortage. (iii) The frequency of CpG islands in long human sequences increases with increasing GC and almost parallels gene frequency. (iv) The frequency of Alu sequences also increases with increasing GC, but attains a maximum in H2 isochores, in agreement with previous experimental data. (v) The ratio 5mC/CpG (namely, the methylation level over available sites) decreases with increasing GC levels of isochores. This decrease is due only to a small extent to the increase of (unmethylated) CpG islands in GC-rich isochores, and takes place in spite of the increase of strongly methylated Alu sequences in GC-rich isochores; this stresses the much lower relative methylation (5mC/CpG) of single-copy sequences located in GC-rich isochores relative to those located in GC-poor isochores. (vi) CpG levels of Alus and CpG islands are positively correlated with the GC levels of the long sequences in which they are located. (vii) The CpG levels of both Alus and CpG islands increase with their GC levels.

The regional integration of retroviral sequences into the mosaic genomes of mammals

We have reviewed here three sets of data concerning the integration of retroviral sequences in the mammalian genome: (i) our experimental localization of a number of proviruses integrated in isochores characterized by different GC levels; (ii) results from other laboratories on the localization of retroviral sequences in open chromatin regions and/or next to CpG islands; and (iii) our compositional analysis of genes located in the neighborhood of integrated retroviral sequences. The three sets of data have provided a very consistent picture in that a compartmentalized, isopycnic integration of expressed proviruses appears to be the rule ('isopycnic' refers to the compositional match between viral and host sequences around the integration site). The results reviewed here suggest that: (i) integration of proviral sequences is targeted initially towards 'open chromatin regions'; while these exist in both GC-rich and GC-poor isochores, the 'open chromatin regions' of GC-rich isochores are the main targets for integration of retroviral sequences because of their much greater abundance; (ii) isopycnicity is associated with stability of integration; indeed, even non-expressed integrated retroviral sequences tend to show an isopycnic localization in the genome; (iii) transcription of integrated viral sequences (like transcription of host genes) appears to be associated, as a rule, with an isopycnic localization, as indicated by transcribed sequences that show an isopycnic integration and act in trans; (iv) selection plays a role in the choice of specific sites within an isopycnic region; in exceptional cases [such as mouse mammary tumor virus (MMTV) activating GC-rich oncogenes], selection may override isopycnicity.

Evolutionary changes in CpG and methylation levels in the genome of vertebrates

We have analysed the levels of 5-methylcytosine (5mC) in DNAs from 42 vertebrates, and compiled, including data from literature, a table of genomic 5mC and GC levels (as well as the available c-values, i.e., the haploid genome sizes) of 87 species from all vertebrate classes. An analysis of the data indicates that (i) two positive correlations hold between the 5mC and GC levels of the genomes of fishes/amphibians and mammals/birds, respectively; (ii) the genomes of fishes and amphibians are, on average, about twice as methylated as those of mammals, birds and reptiles, this difference being unrelated to the amounts of repetitive DNA sequences; (iii) the 5mC and CpG observed/expected values show no overlap between the two groups of vertebrates and suggest the existence of two equilibria. The transition separating the two equilibria appears to have taken place at the time of appearance of reptiles. Its possible cause(s) and its implications are discussed.

Methylation patterns in the isochores of vertebrate genomes

5-Methylcytosine (5mC) levels were determined in compositional DNA fractions corresponding to different isochore families from the genomes of Xenopus, chicken, mouse and human, four vertebrates which show different isochore patterns. The results obtained indicate that: (i) positive correlations exist between the 5mC levels and the GC levels of isochores within any given genome; and (ii) DNA from Xenopus isochore families is twice as methylated as DNA from the isochores having the same GC levels from mouse, human and chicken. Moreover, the positive correlations holding between CpG levels and the GC3 levels of coding sequences of warm-blooded vertebrates were shown to comprise two regions with a border at approx. 75% GC3. The correlation corresponding to the higher region (which comprises only very rare high GC3 values in the case of Xenopus) has a higher slope than that corresponding to the lower GC3 values, a phenomenon due in all likelihood, to the increasing contribution of CpG islands. Finally, the observed/expected CpG ratio is higher in Xenopus than in warm-blooded vertebrates.

Structural and compositional features of untranslated regions of eukaryotic mRNAs

The important role of 5' and 3' untranslated regions of eukaryotic mRNAs in gene regulation and expression is now widely accepted. In order to study the general structural and compositional features of these sequences we developed UTRdb, a specialized database of 5' and 3'-UTR sequences from seven different taxonomic groups of eukaryotic mRNAs cleaned of redundancy. The analysis of the UTR sequences contained in this database showed that 5'-UTR sequences, on average 200 nucleotides long, are 1.5-3 times shorter than the corresponding 3'-UTR sequences in the various taxonomic groups considered here. As to their compositional properties on average 5'-UTR sequences resulted in all cases GC richer than 3'-UTR sequences, and significant correlations were found between the GC content of 5' and 3'-UTR sequences and the GC content of the third silent codon positions of the corresponding protein coding genes. The dinucleotide analysis showed a differential depletion of CpG in vertebrate 5' and 3'-UTR, with 5'-UTR sequences being more CpG-rich, and a generalized depletion of TpA in both 5' and 3'-UTR was observed in all eukaryotic sequence collections.

Genomic organization of the human KAI1 metastasis-suppressor gene

Decreased expression of the human KAI1 metastasis-suppressor gene is involved in the progression of human prostatic cancer and possibly lung and breast cancer. To evaluate the frequency of mutation and allelic loss during the progression of human cancer, as well as to determine the regulatory mechanism for the expression of the KAI1 gene in normal and cancerous tissues, we characterized the 5'-promoter region, exon/intron organization, and transcription initiation site of the human KAI1 gene. About 80 kb of DNA was identified as the human KAI1 gene, which contains 8 kb of 5'-region, 10 exons, 9 introns, and 8 kb of DNA following exon 10. The coding region starts in exon 3 and ends in exon 10. The size of intron 1 is 29 kb, which almost equals the sizes of all other introns combined. A CpG island is present in the 5'-promoter region and extends to exon 1 and intron 1. The promoter region has no TATA or CCAAT box but has many putative binding motifs for various transcription factors, including nine Sp1 sites and five AP2 sites. These results suggest a diverse regulatory mechanism for the expression of the KAI1 gene in human tissues. The transcription initiation site of the KAI1 gene is located 181 bp upstream of the first nucleotide of the translation initiation codon. Comparisons of gene structures between KAI1 and seven other members of the transmembrane 4 superfamily revealed that the splicing sites relative to the different structural domains of the predicted proteins are well conserved, suggesting that these genes are evolutionarily related and that they arose through gene duplication and divergent evolution.