Two new cases of the Christchurch (Ch1) chromosome 21: evidence for clinical consequences of de novo deletion 21P-.

We performed an investigation of two unrelated cases with extremal variants of chromosome 21 without visible materials of the short arms (Christchurch or Ch1 chromosome). In the first case chromosome 21p- was initially detected during routine cytogenetic amniocentesis. Chromosomal variant was inherited from phenotypically normal father to phenotypically normal fetus (phenotypically normal boy after the birth). The second case of chromosome 21p- was detected in 7 years old boy, referred to cytogenetic analysis due to mental retardation and mild congenital malformation, including prenatal hypoplasia, microcephaly, low-set dysplastic ears, short nose, micrognatia, short neck. Molecular characterization of 21p-variant chromosomes was performed by the use of FISH with DNA probes specific to the short arm and centromeric region of chromosome 21 (telomeric, beta-satellite, ribosomal, classical satellite and alphoid DNA probes). Chromosomes 21p-hybridized positively only with telomeric DNA at both chromosomal ends and alphoid DNA probes at centromeric region of the first patient. In second case (de novo deletion of 21p), the Ch1 was associated with clinical phenotype and loss of telomeric and subtelomeric DNA in the p-arm of chromosome 21. Therefore, the complete absent of the short arm of chromosome 21 may be considered as abnormal. We propose that de novo deletion 21p- could have negative consequences due to absence of large portion of chromosomal DNA from the p-arm (telomeric, satellite or ribosomal DNAs) and following imbalance in organization and functioning of genome.

MethDB--a public database for DNA methylation data.

Methylation of cytosine in the 5 position of the pyrimidine ring is a major modification of the DNA in most organisms. In eukaryotes, the distribution and number of 5-methylcytosines (5mC) along the DNA is heritable but can also change with the developmental state of the cell and as a response to modifications of the environment. While DNA methylation probably has a number of functions, scientific interest has recently focused on the gene silencing effect methylation can have in eukaryotic cells. In particular, the discovery of changes in the methylation level during cancer development has increased the interest in this field. In the past, a vast amount of data has been generated with different levels of resolution ranging from 5mC content of total DNA to the methylation status of single nucleotides. We present here a database for DNA methylation data that attempts to unify these results in a common resource. The database is accessible via WWW (http://www.methdb.de). It stores information about the origin of the investigated sample and the experimental procedure, and contains the DNA methylation data. Query masks allow for searching for 5mC content, species, tissue, gene, sex, phenotype, sequence ID and DNA type. The output lists all available information including the relative gene expression level. DNA methylation patterns and methylation profiles are shown both as a graphical representation and as G/A/T/C/5mC-sequences or tables with sequence positions and methylation levels, respectively.

Genomic structure of a copy of the human TPTE gene which encompasses 87 kb on the short arm of chromosome 21.

The testis-expressed human TPTE is a putative transmembrane tyrosine phosphatase, probably involved in signal transduction pathways of the endocrine and/or the spermatogenetic function of the testis. TPTE was mapped to the pericentromeric region of human chromosomes 21 and 13, and to chromosomes 15, 22, and Y. It is unknown which of the TPTE copies are transcribed, contain intronic sequences, and/or have open reading frames. Here, in silico analysis of the genomic sequence of human chromosome 21 allowed the determination of the genomic structure of a copy of the TPTE gene. This copy consists of 24 exons and spans approximately 87 kb. The mapping position of this copy of TPTE on the short arm of chromosome 21 was confirmed by FISH using the BAC 15L0C0 clone as a probe that contains almost the entire TPTE gene. This is the first description of the genomic sequence of a non-RNR gene on the short arm of human acrocentric chromosomes.

Characterization of the human tubulin tyrosine ligase-like 1 gene (TTLL1) mapping to 22q13.1.

This paper reports the characterization of the human tubulin tyrosine ligase-like 1 gene (TTLL1), which maps to the chromosome region 22q13.1 and has been partially duplicated on three other acrocentric chromosomes: 13, 15 and 21. We describe the complete cDNA, TTLL1a, coding for the putative 423 amino acid long TTLL1 and alternative transcripts coding for truncated TTLL1. Likely TTLL1a corresponds to the 1.8 kb transcript that was detected in a wide range of tissues and has a stronger expression in heart, brain and testis. A 4.8 kb transcript was found only in brain tissues. We present an interspecies sequence comparison, revealing three conserved domains, named TTLD1, TTLD2 and TTLD3, that are specific to the TTLs and TTL-like proteins.

Lack of association between polymorphisms of eight candidate genes and idiopathic dilated cardiomyopathy: the CARDIGENE study.

OBJECTIVES: The study investigated the potential role of eight candidate genes in the susceptibility to idiopathic dilated cardiomyopathy (IDC). BACKGROUND: Idiopathic dilated cardiomyopathy has a familial origin in 20% to 25% of cases, and several genetic loci have been identified in rare monogenic forms of the disease. These findings led to the hypothesis that genetic factors might also be involved in sporadic forms of the disease. In complex diseases that do not exhibit a clear pattern of familial aggregation, the candidate gene approach is a strategy widely used to identify susceptibility genes. All genes coding for proteins involved in biochemical or physiological abnormalities of cardiac function are potential candidates for IDC. METHODS: We studied 433 patients with IDC and 401 gender- and age-matched controls. Polymorphisms investigated were the I/D polymorphism of the angiotensin I-converting enzyme (ACE) gene, the T174M and M235T polymorphisms of the angiotensinogen (AGT) gene, the A-153G and A+39C polymorphisms of the angiotensin-II type 1 receptor (AGTR1) gene, the T-344C polymorphism of the aldosterone synthase (CYP11B2) gene, the G-308A polymorphism of the tumor necrosis factor-alpha (TNF) gene, the R25P polymorphism of the transforming growth factor beta1 (TGFB1) gene, the G+11/in23T polymorphism of the endothelial nitric oxide synthase (NOS3) gene and the C-1563T polymorphism of the brain natriuretic peptide (BNP) gene. RESULTS: None of the polymorphisms were significantly associated with the risk or the severity of the disease. CONCLUSIONS: We did not find evidence for an involvement of any of the 10 investigated polymorphisms in the susceptibility to IDC.

Juxta-centromeric region of human chromosome 21 is enriched for pseudogenes and gene fragments.

A physical map including four pseudogenes and 10 gene fragments and spanning 500 kb in the juxta-centromeric region of the long arm of human chromosome 21 is presented. cDNA fragments isolated from a selected cDNA library were characterized and mapped to the 831B6 YAC and to two BAC contigs that cover 250 kb of the region. An 85 kb genomic sequence located in the proximal region of the map was analyzed for putative exons. Four pseudogenes were found, including psiIGSF3, psiEIF3, psiGCT-rel whose functional copies map to chromosome 1p13, chromosome 2 and chromosome 22q11, respectively. The TTLL1 pseudogene corresponds to a new gene whose functional copy maps to chromosome 22q13. Ten gene fragments represent novel sequences that have related sequences on different human chromosomes and show 97-100% nucleotide identity to chromosome 21. These may correspond to pseudogenes on chromosome 21 and to functional genes in other chromosomes. The 85 kb genomic sequence was analyzed also for GC content, CpG islands, and repetitive sequence distribution. A GC-poor L isochore spanning 40 kb from satellite 1 was observed in the most centromeric region, next to a GC-rich H isochore that is a candidate region for the presence of functional genes. The pericentric duplication of a 7.8 kb region that is derived from the 22q13 chromosome band is described. We showed that the juxta-centromeric region of human chromosome 21 is enriched for retrotransposed pseudogenes and gene fragments transferred by interchromosome duplications, but we do not rule out the possibility that the region harbors functional genes also.

Identification of a genetic risk factor for idiopathic dilated cardiomyopathy. Involvement of a polymorphism in the endothelin receptor type A gene. CARDIGENE group.

BACKGROUND: Idiopathic dilated cardiomyopathy is a frequent cause of heart failure, a major concern of public health. Although idiopathic dilated cardiomyopathy may be familial, most cases are sporadic and the disease is considered to be multifactorial, for which genetic factors may account for a significant part. METHODS AND RESULTS: We hypothesized that genetic abnormalities of the endothelin pathway may be involved in idiopathic dilated cardiomyopathy pathophysiology and therefore examined the possible association between idiopathic dilated cardiomyopathy and polymorphisms in genes encoding endothelin 1, endothelin type A and type B receptors, in a case-control study (433 patients and 400 age- and sex-matched control subjects). Analysis of the Exon 8 C/T polymorphism in the endothelin receptor type A gene indicated that individuals who are homozygote for the T allele were at significantly increased risk for the disease (odds ratio: 1.9; 95% confidence interval: 1.2 to 3. 01;P<0.006). Analysis of the other polymorphisms indicated that no significant difference was observed in genotype or allele frequencies between cases and controls. CONCLUSIONS: The variant in the Exon 8 of the endothelin receptor type A gene appears as a genetic risk factor for idiopathic forms of heart failure. These results provide a new approach to the pathophysiology of idiopathic dilated cardiomyopathy.

Hypothesis: for the worst and for the best, L1Hs retrotransposons actively participate in the evolution of the human centromeric alphoid sequences.

A number of questions concerning the evolution and the function of the alpha satellite DNA sequences present at the centromere of all human chromosomes are still open. In this paper, we present data which could contribute to understanding these points. It is shown here that the alphoid sequences within which L1 elements are found are quite divergent from those of the homogeneous alphoid subsets present at each centromere where none has so far been detected. In addition, a number of L1s are detected close to the ends of the alpha satellite blocks. A fairly high proportion exhibit a polymorphism of presence/absence. Strikingly, several L1s localized at a distance from each other are always either present or absent simultaneously. This is interpreted as resulting from intrachromosomal recombination, through distant L1s, leading to deletion of several of them at once together with their surrounding alphoid sequences. The parameters determining which portion of the several megabases of alphoid sequences is actually involved in the centromeric function are not known. From the above data we suggest that the alpha satellite domain within which DNA sequences are recruited to form a centromere is both homogeneous in sequence and uninterrupted by L1s or any other retrotransposons. Conversely, non-centromere competent alphoid sequences would be both divergent and punctuated by scattered L1 elements, particularly at the borders of the alphoid blocks. On the grounds of these data and hypotheses, a model is presented in which it is postulated that accumulation of L1 insertions within a centromere competent alphoid domain is ruining this competence, the consequence being damage to or even loss of the centromere-forming capability of the chromosome. Restoration of fully centromere-forming competence is supposed to occur by two alternative means, either de-novo amplification of a homogeneous and uninterrupted alphoid domain or by unequal crossing over with a homologue harbouring a large competent one. If L1 retrotransposons are acting detrimentally to centromere integrity (for the worst), one must also consider them as having positive consequences on chromosomes by preventing their centromeres from swelling indefinitely by the addition of alphoid sequences (for the best). The data and ideas presented here fit well with those already put forward by Csink and Henikoff (1998) using the example of Drosophila.

Characterization of a unique genetic variant in the beta1-adrenoceptor gene and evaluation of its role in idiopathic dilated cardiomyopathy. CARDIGENE Group.

The genetic factors that underlie idiopathic dilated cardiomyopathy (IDCM) have not yet been elucidated. Since beta1-adrenoceptors are downregulated in patients with IDCM, and since beta-blocker therapy is consistently beneficial in this setting, we hypothesized that genetic variation in the beta1-adrenoceptor might affect susceptibility to and/or severity of IDCM. As no intragenic polymorphism was available, a systematic screening of the gene was first performed. The organization and sequence of the human beta1-adrenoceptor gene were established using polymerase chain reaction, single-strand conformation polymorphism analysis and sequencing. The gene comprises 1434 bp and no intron was observed. We found a unique and frequent polymorphism (C1165G) which predicts an Arg389Gly substitution. The association of this polymorphism with IDCM was then analysed using the PCR-restriction fragment length polymorphism method in the CARDIGENE population, a clinically well-characterized population of IDCM. Genotypic distribution was in agreement with Hardy-Weinberg equilibrium. There were no differences in the beta1-adrenoceptor allele frequencies between IDCM (n=426; C/G=0.76/0.24) and age- and sex-matched control subjects (n=395; C/G=0.78/0.22). Within the patient group, no association was observed with the severity of the disease. In conclusion, the genomic organization of beta1-adrenoceptor is described here for the first time. We found a unique and frequent polymorphism in the coding sequence of the gene. No association was observed between IDCM and the genetic variant. Its possible involvement in other cardiac diseases related to the beta1-adrenoceptor remains to be analysed.

Analysis of alphoid DNA variation and kinetochore size in human chromosome 21: evidence against pathological significance of alphoid satellite DNA diminutions.

Centromeric alpha satellite DNA sequences are linked to the kinetochore CENP-B proteins and therefore may be involved in the centromeric function. The high heterogeneity of size of the alphoid blocks raises the question of whether small amount of alphoid DNA or "deletion" of this block may have a pathological significance in the human centromere. In the present study, we analysed the correlation between size variations of alphoid DNA and kinetochore sizes in human chromosome 21 by molecular cytogenetic and immunochemical techniques. FISH analyses of alpha satellite DNA sizes in chromosome 21 homologues correlated well with the variation of their physical size as determined by pulsed field gel electrophoresis (PFGE). By contrast, the immunostaining study of the same homologous chromosomes with antikinetochore antibodies suggested that there is no positive correlation between the alpha satellite DNA block and kinetochore sizes. FISH analysis of chromosome 21-specific alphoid DNA and immunostaining of kinetochore extended interphase chromatin fibers indicate that centromeric kinetochore-specific proteins bind to restricted areas of centromeric DNA arrays. Thus, probably, restricted regions of centromeric DNA play an important role in kinetochore formation, centromeric function and abnormal chromosome segregation leading to non-disjunction.

Genetic and physical analyses of the centromeric and pericentromeric regions of human chromosome 5: recombination across 5cen.

Human centromeres are poorly understood at both the genetic and the physical level. In this paper, we have been able to distinguish the alphoid centromeric sequences of chromosome 5 from those of chromosome 19. This result was obtained by pulsed-field gel electrophoresis after cutting genomic DNA with restriction endonucleases NcoI (chromosome 5) and BamHI (chromosome 19). We could thus define a highly polymorphic marker, representing length variations of the D5Z1 domain located at the q arm boundary of the chromosome 5 centromere. The centromeric region of chromosome 5 was then analyzed in full detail. We established an approximately 4.6-Mb physical map of the whole region with five rare-cutting enzymes by using nonchimeric YACs, two of which were shown to contain the very ends of 5cen on both sides. The p-arm side of 5cen was shown to contain an alphoid subset (D5Z12) different from those described thus far. Two genes and several putative cDNAs could be precisely located close to the centromere. Several L1 elements were shown to be present within alpha satellites at the boundary between alphoid and nonalphoid sequences on both sides of 5cen. They were used to define STSs that could serve as physical anchor points at the junction of 5cen with the p and q arms. Some STSs were placed on a radiation hybrid map. One was polymorphic and could therefore be used as a second centromeric genetic marker at the p arm boundary of 5cen. We could thus estimate recombination rates within and around the centromeric region of chromosome 5. Recombination is highly reduced within 5cen, with zero recombinants in 58 meioses being detected between the two markers located at the two extremities of the centromere. In its immediate vicinity, 5cen indeed exerts a direct negative effect on meiotic recombination within the proximal chromosomal DNA. This effect is, however, less important than expected and is polarized, as different rates are observed on both arms if one compares the 0 cM/Mb of the p proximal first 5.5 Mb and the 0.64 cM/Mb of the q proximal first 5 Mb to the sex-average 1.02 cM/Mb found throughout the entire chromosome 5. Rates then become close to the average when one goes further within the arms. Finally, most recombinants (21/22), irrespective of the arm, are of female origin, thus showing that recombination around 5cen is essentially occurring in the female lineage.

Structure and function of alleles in the 3' end region of human apoB gene.

OBJECTIVE: To study the structure of alleles in the 3' end of the apoB gene in Han, Mongolian and Tibetan populations in China as well as the roles in the regulation of gene expression. METHODS: DNA were obtained from human leukocytes by phenol-chloroform extraction and ethanol precipitation. PCR were carried out in a 50 microliters volume containing 50 ng genomic DNA as template. The Ssp1-digested products were loaded on a gradient acrylamide gel and run for 3 hours. The constructs containing alleles were tested in cultured HepG2 and HeLa cells using transient assays. RESULTS: Sixteen alleles with different repeat number were characterized. All of the alleles varying from HVE22 to HVE52, allele HVE34 was the most common (58.4%), followed by allele HVE36 (13.8%) and HVE32 (10.5%). 258 PCR products were digested with Ssp1 and run in 4-12% PAGE. We detected the fragments of 266bp, 91 bp, 61 bp and 39 bp in almost all samples. The small alleles (including HVE22, HVE24, HVE26 and HVE36) decreased the expressive activity of the luciferase reporter, in contrary, the large alleles (including HVE44, HVE46 and HVE48) elevated obviously the expressive activity of the luciferase reporter. CONCLUSIONS: More alleles with different number of tandem repeats in 3' end of apoB gene exist in the Chinese populations. The alleles in 3' end minisatellite of human apoB gene could control the expression of the gene itself.

Informative genetic polymorphic markers within the centromeric regions of human chromosomes 17 (D17S2205) and 11 (D11S4975).

We have taken advantage of the presence of retrotransposed L1 elements within the centromeric alphoid sequences of the human genome to characterize polymorphic markers at the centromeres of human chromosomes 17 and 11 (D17S2205 and D11S4975, respectively). They correspond to microsatellites found at the 3' ends of L1 elements inserted within the alpha satellite sequences of the two chromosomes. They were detected after PCR by direct analysis in sequencing gels. Eight and five alleles, respectively, were found with heterozygosities of 0.67 and 0.68. They were converted into STSs by designing primers specific for each. D17S2205 and D11S4975 can be used as genuine anchor-informative genetic points for chromosomes 17 and 11. Both markers have been placed on the available genetic maps of their centromeric regions. The alphoid domain within which D17S2205 is embedded is ancestral to the canonical ones on chromosome 17 that exhibit several haplotypes in present-day human populations.

Molecular cloning of a human cDNA IGSF3 encoding an immunoglobulin-like membrane protein: expression and mapping to chromosome band 1p13.

We report the isolation and characterization of a novel cDNA IGSF3 that contains a 3648-bp open reading frame encoding an apparent immunoglobulin (Ig)-like membrane protein characterized by eight Ig domains. IGSF3 has an overall structural similarity and strong sequence similarity to V7, a human leukocyte surface protein. The IGSF3 mRNA is highly expressed in placenta, kidney, and lung, but is also present in a wide range of other human tissues. Although a small internal sequence of the IGSF3 cDNA hybridizes to a YAC derived from the centromeric region of chromosome 21, in situ hybridization experiments on human metaphase chromosomes show that the gene corresponding to the long cDNA that we cloned is located in chromosome band 1p13 and that related sequences are located on chromosomes 2 and 13. These data serve to emphasize the potential difficulties in transcriptional mapping in centromeric regions.

Construction of a human BcgI DNA fragment library.

A library made up of 36bp DNA fragments generated by digestion of human DNA with the restriction endonuclease Bcg I has been constructed. It contains 2.5x106 independent clones, representing several times the total human genome which should contain about 400000 such fragments. It is proposed to make use of these BcgI fragments to clone part of the coding sequences contained in the minor H3 isochore which represents 3% of the human genomic DNA and a quarter of all genes.

[Study of alpha-satellite DNA in cosmid libraries, specific for chromosomes 13, 21, and 22, using fluorescence in situ hybridization]. / Issledovanie al'fa-satellitnykh DNK v sostave kosmidnykh bibliotek, spetsifichnykh dlia khromosome 13, 21, i 22, s pomoshch'iu fliuorestsentnoi gibridizatsii in situ.

Fluorescent in situ hybridization (FISH) was employed in mapping the alpha-satellite DNA that was revealed in the cosmid libraries specific for human chromosomes 13, 21, and 22. In total, 131 clones were revealed. They contained various elements of centromeric alphoid DNA sequences of acrocentric chromosomes, including those located close to SINEs, LINEs, and classical satellite sequences. The heterochromatin of acrocentric chromosomes was shown to contain two different groups of alphoid sequences: (1) those immediately adjacent to the centromeric regions (alpha 13-1, alpha 21-1, and alpha 22-1 loci) and (2) those located in the short arm of acrocentric chromosomes (alpha 13-2, alpha 21-2, and alpha 22-2 loci). Alphoid DNA sequences from the alpha 13-2, alpha 21-2, and alpha 22-2 loci are apparently not involved in the formation of centromeres and are absent from mitotically stable marker chromosomes with a deleted short arm. Robertsonian translocations t(13q; 21q) and t(14q; 22q), and chromosome 21p-. The heterochromatic regions of chromosomes 13, 21, and 22 were also shown to contain relatively chromosome-specific repetitive sequences of various alphoid DNA families, whose numerous copies occur in other chromosomes. Pools of centromeric alphoid cosmids can be of use in further studies of the structural and functional properties of heterochromatic DNA and the identification of centromeric sequences. Moreover, these clones can be employed in high-resolution mapping and in sequencing the heterochromatic regions of the human genome. The detailed FISH analysis of numerous alphoid cosmid clones allowed the identification of several new, highly specific DNA probes of molecular cytogenetic studies--in particular, the interphase and metaphase analyses of chromosomes 2, 9, 11, 14, 15, 16, 18, 20, 21-13, 22-14, and X.

Site-specific retrotransposition of L1 elements within human alphoid satellite sequences.

In the course of a search for microsatellites as centromeric polymorphic markers at the 3' ends of Alu or L1 elements, we observed a much higher frequency of L1 than Alu elements embedded within alpha satellite DNA. By sequence analysis of the L1 elements at their alphoid locus of insertion, we found that the insertion site was specific, with the consensus being (Py)2-10/ (Pu)3-7. All potential sites within the consensus alphoid 171-bp repeat are occupied by such elements. This confirms the finding by Feng et al. (1996; Human retrotransposon encodes a conserved endonuclease required for retrotransposition, Cell 87:905-916) that the progenitor L1 elements encode a site-specific endonuclease and that they generate copies that are inserted at these specific sites. The analysis of retrotransposed L1 elements within the alphoid domains of the acrocentric chromosomes showed that a number of loci are shared among all five acrocentrics. This sheds light on the manner in which centromeric regions of these chromosomes are exchanging information during evolution.

A compositional map of the cen-q21 region of human chromosome 21.

A compositional map of the centromere and of the subcentromeric region of the long arm of human chromosome 21 was established by determining the GC levels (GC is the molar fraction of guanine+cytosine in DNA) of 11 YACs (yeast artificial chromosomes) covering this 13-14 Mb region which extends from the alpha-satellite sequences of the C(entromeric) band q11.1, through R(everse) band q11.2, to the proximal part of G(iemsa) band q21. The entire region is made up of GC-poor, or L, isochores with only one GC-rich H1 isochore, at least 2 Mb in size, located in band q21. The almost identical GC levels of the centromeric alpha-satellite repeats (38.5%), of R band q11.2 (39%), and of G bands (38-40%) provide a direct demonstration that base composition cannot be the only cause of the cytogenetic differences between C, G, and the majority of R bands, namely the H3- R bands (which do not contain the GC-richest H3 isochores). The results obtained also show that isochores may be as long as 6 Mb, at least in the GC-poor regions of the genome, and support previous observations suggesting that YACs from isochore borders are unstable and/or difficult to clone. Genes and CpG islands are very rare in the GC-poor region investigated, as expected from the fact that their concentration is proportional to the GC levels of the isochores in which they are contained.

DNA polymorphisms in linkage disequilibrium at the 3' end of the human APO AII gene: relationships with lipids, apolipoproteins and coronary heart disease.

Two investigations were undertaken to analyze the 3' region of the apolipoprotein AII (Apo AII) gene in patients with myocardial infarction (MI) and controls. Previous studies have suggested that a MspI polymorphism in this gene may be associated with hypertriglyceridaemia, high levels of HDL cholesterol and Apo AII. To verify this hypothesis, the distribution of MspI genotypes and their possible associations with several plasma lipid variables were studied in 882 subjects (411 cases with MI and 471 controls) from the ECTIM study. There were no differences in genotype and allele frequencies between cases and controls, and no differences in lipid variable levels in controls carrying the less frequent MspI allele vs other controls. Using single-strand conformation polymorphism (SSCP) analysis, we detected a new polymorphism which caused by a C-to-T transition located in the third intron near the splice junction site (acceptor). This polymorphism modifies a Bst N1 restriction site. The ECTIM population was screened for this new marker, and no significant associations with MI and plasma lipid levels were found. Our results suggest that these two variants located in the coding region of the Apo AII gene are unlikely to contribute significantly to the level of plasma lipid variables and the risk of coronary heart disease (CHD) in the European population.