Human herpesvirus 6 (HHV-6) is transmitted from parent to child in an integrated form and characterization of cases with chromosomally integrated HHV-6 DNA

We obtained 7,566 peripheral blood mononuclear cell (PBMC) samples from 2,332 individuals and screened them for human herpesvirus infection. We identified five individuals who persistently harbored high copy numbers of human herpesvirus 6 (HHV-6) DNA in their PBMCs. HHV-6 DNA was also detected in other somatic tissues of these individuals. Five additional cases were identified among their family members. For two of these families, chromosomally integrated HHV-6 DNA (CIHHV-6) was detected in the PBMCs by fluorescence in situ hybridization. The prevalence of CIHHV-6 among all the subjects was 0.21%. The HHV-6 DNA was variant B in four families and variant A in one family. Antibodies to immediate early antigen and glycoprotein B were detected in 57 and 14% of individuals with CIHHV-6 and in 0 and 60% of healthy volunteers without CIHHV-6, respectively. HHV-6 could not be isolated from PBMCs with CIHHV-6. These cases shared no clinical features, and included three healthy individuals. Our data suggest that CIHHV-6 is rare but detectable in the general population and that hereditary transmission is one of the routes of HHV-6 transmission.

Cruciform DNA structure underlies the etiology for palindrome-mediated human chromosomal translocations

There is accumulating evidence to suggest that palindromic AT-rich repeats (PATRRs) represent hot spots of double-strand breakage that lead to recurrent chromosomal translocations in humans. As a mechanism for such rearrangements, we proposed that the PATRR forms a cruciform structure that is the source of genomic instability. To test this hypothesis, we have investigated the tertiary structure of a cloned PATRR. We have observed that a plasmid containing this PATRR undergoes a conformational change, causing temperature-dependent mobility changes upon agarose gel electrophoresis. The mobility shift is observed in physiologic salt concentrations and is most prominent when the plasmid DNA is incubated at room temperature prior to electrophoresis. Analysis using two-dimensional gel electrophoresis indicates that the mobility shift results from the formation of a cruciform structure. S1 nuclease and T7 endonuclease both cut the plasmid into a linear form, also suggesting cruciform formation. Furthermore, anti-cruciform DNA antibody reduces the electrophoretic mobility of the PATRR-containing fragment. Finally, we have directly visualized cruciform extrusions from the plasmid DNA with the size expected of hairpin arms using atomic force microscopy. Our data imply that for human chromosomes, translocation susceptibility is mediated by PATRRs and likely results from their unstable conformation.

Ras/MEK pathway is required for NGF-induced expression of tyrosine hydroxylase gene

Neurotrophins are essential for the development and survival of catecholaminergic neurons. However, the critical pathway for expression of the tyrosine hydroxylase (TH) gene induced by neurotrophin is still unclear. Here we found that Ras/MEK pathway is required for NGF-induced expression of the TH gene in PC12D cells. Induction of TH mRNA by NGF was abolished by pretreatment of the cells with U0126, an inhibitor for MEK1/2, but not with inhibitors for p38 MAPK, PI3K, and PKA. U0126 inhibited TH promoter activity at the same concentration as it acted on ERK1/2 phosphorylation. A dominant-negative form of Ras suppressed the NGF-induced activation of the TH reporter gene, and transient transfection of cells with wild-type Ras and an active form of MEK1 increased the TH promoter activity. The reporter assay also demonstrated that the Ras/MEK pathway acted on both the AP-1-binding motif and the cAMP-responsive element in the TH promoter.

Fukutin is required for maintenance of muscle integrity, cortical histiogenesis and normal eye development

Fukuyama-type congenital muscular dystrophy (FCMD), one of the most common autosomal-recessive disorders in Japan, is characterized by congenital muscular dystrophy associated with brain malformation due to a defect during neuronal migration. Through positional cloning, we previously identified the gene for FCMD, which encodes the fukutin protein. Here we report that chimeric mice generated using embryonic stem cells targeted for both fukutin alleles develop severe muscular dystrophy, with the selective deficiency of alpha-dystroglycan and its laminin-binding activity. In addition, these mice showed laminar disorganization of the cortical structures in the brain with impaired laminin assembly, focal interhemispheric fusion, and hippocampal and cerebellar dysgenesis. Further, chimeric mice showed anomaly of the lens, loss of laminar structure in the retina, and retinal detachment. These results indicate that fukutin is necessary for the maintenance of muscle integrity, cortical histiogenesis, and normal ocular development and suggest the functional linkage between fukutin and alpha-dystroglycan.

Fukuyama-type congenital muscular dystrophy (FCMD) and alpha-dystroglycanopathy

Fukuyama-type congenital muscular dystrophy (FCMD), Walker-Warburg syndrome (WWS), and muscle-eye-brain (MEB) disease are clinically similar autosomal recessive disorders characterized by congenital muscular dystrophy, lissencephaly, and eye anomalies. Through positional cloning, we identified the gene for FCMD and MEB, which encodes the fukutin protein and the protein O-linked mannose beta1, 2-N-acetylglucosaminy ltransferase (POMGnT1), respectively. Recent studies have revealed that posttranslational modification of alpha-dystroglycan is associated with these congenital muscular dystrophies with brain malformations. In this review Fukuyama-type congenital muscular dystrophy (FCMD), other CMDs with brain malformations, and their relation with alpha-dystroglycan are discussed.

The constitutional t(17;22): another translocation mediated by palindromic AT-rich repeats

We have demonstrated that the breakpoints of the constitutional t(11;22) are located at palindromic AT-rich repeats (PATRRs) on 11q23 and 22q11. As a mechanism for this recurrent translocation, we proposed that the PATRR forms a cruciform structure that induces the genomic instability leading to the rearrangement. A patient with neurofibromatosis type 1 (NF1) had previously been found to have a constitutional t(17;22) disrupting the NF1 gene on 17q11. We have localized the breakpoint on 22q11 within the 22q11-specific low-copy repeat where the breakpoints of the constitutional t(11;22)s reside, implying a similar palindrome-mediated mechanism for generation of the t(17;22). The NF1 gene contains a 195-bp PATRR within intron 31. We have isolated the junction fragments from both the der(17) and the der(22). The breakpoint on 17q11 is close to the center of the PATRR. A published breakpoint of an additional NF1-afflicted patient with a constitutional t(17;22) is also located close to the center of the same PATRR. Our data lend additional support to the hypothesis that PATRR-mediated genomic instability can lead to a variety of translocations.

Long AT-rich palindromes and the constitutional t(11;22) breakpoint

The constitutional t(11;22) is the most frequently occurring non-Robertsonian translocation in humans. The breakpoint (BP) of the t(11;22) has been identified within palindromic AT-rich repeats (PATRRs) on chromosomes 11 and 22, suggesting that hairpin/cruciform structures mediate double-strand breaks leading to the translocation. To further characterize the mechanism of the translocation, identification of the precise location of the translocation BP is essential. Thus, the PATRRs from normal chromosomes 11 have been analyzed in detail. The majority of individuals have a PATRR that is 445 bp in length with a nearly symmetrical structure. The shorter, previously reported 204 bp PATRR has been shown to be a rare polymorphism. There are several nucleotide differences between the proximal and distal arms of the 445 bp palindrome (cis-morphisms) that correspond to five polymorphic sites within the PATRR. Using these data, the junction fragments of 40 unrelated t(11;22) families have been examined to determine the position of their 11q23 BPs. Sequence analysis demonstrates that BPs are located at the center of the longer PATRR in 39 of 40 cases. The data suggest that the center of the palindrome is susceptible to double-strand breaks leading to translocations that sustain small symmetrical deletions at the BP junction. The sequence of the larger, chromosome 22 PATRR deduced from junction fragments has three cis-morphisms, and the derivative chromosomes sustain symmetric deletions at the center of 22q11 PATRR. In one unusual case, the BPs on both chromosomes appear to correspond to these cis-morphic sites, suggesting that double-strand breaks at mismatched regions caused this variant translocation. De novo t(11;22) BPs have been analyzed using translocations detected in sperm samples from normal males. cis-Morphisms reveal no exclusive utilization of a particular allele in meiosis to produce the translocation. Our data lend support to the hypothesis that palindrome-mediated double-strand breaks in meiosis cause illegitimate recombination between 11q23 and 22q11 resulting in this recurrent translocation.

Unexpectedly high rate of de novo constitutional t(11;22) translocations in sperm from normal males

Junction fragments from the constitutional t(11;22)(q23;q11) translocation have previously been cloned and sequenced. Here we report a high incidence of translocation-specific PCR products in sperm DNA from normal individuals. Somatic DNA from these and other normal individuals or from people with chromosomal breakage syndromes do not yield PCR junction fragments, indicating that this translocation originates during meiosis.

Fluorescence in situ hybridization analysis of peripheral blood cells in Pearson marrow-pancreas syndrome

We used a dual-color fluorescence in situ hybridization technique to estimate deleted mitochondrial DNA at a single-cell level and determine any correlation with the disease progression in lymphocytes from patients with Pearson marrow-pancreas syndrome. The method demonstrated a shift in heteroplasmy, paralleling the hematologic improvement.

Structure and chromosomal localization of the RAE28/HPH1 gene, a human homologue of the polyhomeotic gene

The Polycomb group of (Pc-G) genes and trithorax group of genes are known to play a crucial role in the maintenance of the transcriptional repression state of Hox genes, probably through modification of the chromatin configuration. The rae28/mph1 gene is a mammalian homologue of the Drosophila polyhomeotic gene, which belongs to the Pc-G genes. As reported previously, we established mice deficient in the rae28/mph1 gene and showed that these homozygous animals displayed the developmental defects compatible with a human congenital disorder, CATCH22 syndrome. In this study we analyzed the structural organization of the human counterpart of the rae28/mph1 gene (RAE28/HPH1) and its processed pseudogene (psiPH), which are located on, respectively, human chromosome 12p13 and 12q13. The HPH1 gene consists of 15 exons spanning approximately 26 kb and its structural organization is well conserved between mouse and human. These genetic information of the RAE28/HPH1 gene may provide an important clue for further examination of its involvement in human congenital disorders related to CATCH22 syndrome.

Evolutionarily conserved low copy repeats (LCRs) in 22q11 mediate deletions, duplications, translocations, and genomic instability: an update and literature review

Several constitutional rearrangements, including deletions, duplications, and translocations, are associated with 22q11.2. These rearrangements give rise to a variety of genomic disorders, including DiGeorge, velocardiofacial, and conotruncal anomaly face syndromes (DGS/VCFS/CAFS), cat eye syndrome (CES), and the supernumerary der(22)t(11;22) syndrome associated with the recurrent t(11;22). Chromosome 22-specific duplications or low copy repeats (LCRs) have been directly implicated in the chromosomal rearrangements associated with 22q11.2. Extensive sequence analysis of the different copies of 22q11 LCRs suggests a complex organization. Examination of their evolutionary origin suggests that the duplications in 22q11.2 may predate the divergence of New World monkeys 40 million years ago. Based on the current data, a number of models are proposed to explain the LCR-mediated constitutional rearrangements of 22q11.2.

Defining a common region of DNA amplification at 22q11.2-12 in head and neck squamous cell carcinomas by quantitative FISH analysis

By comparative genomic hybridization (CGH) with 17 head and neck squamous cell carcinoma (HNSCC) cell lines, we previously detected an amplified region as a distinct peak at 22q11.2-12 in 3 cell lines. Because the possible presence of an oncogene was strongly suggested, the region was mapped in more detail by defining the minimum region that was commonly amplified by using fluorescence in situ hybridization (FISH) with a series of cosmids. Eighteen cosmid clones on 22q11.2-12 were assigned to their locations as a fractional length map and hybridized to cells from three HNSCC cell lines. The three cosmid clones, cHKA-118, cHKAD-26, and D22S938, showed the highest levels of amplification, and the size of the amplicon was calculated to be approximately 1.7 Mb in the OM1 and HSC6 cell lines. Several genes related to oncogenesis, including PRKM1, map to this locus. Thus, the definition of the common region with the highest level of copy number increases by FISH provides a starting point for identifying the gene that may play an important role in the development of HNSCC.

Alu-mediated PCR artifacts and the constitutional t(11;22) breakpoint

The breakpoints of the recurrent t(11;22)(q23;q11) have recently been cloned. We identified palindromic AT-rich repeats (PATRRs) on 11q23 and 22q11 as the mechanism responsible for the rearrangement. Contradictory to our results, A.S. Hill et al. (Hum. Mol. Genet., 9, 1525-1532) suggested that Alu-mediated recombination is responsible. To clarify this discrepancy, the cloned 4.5 kb der(11) junction fragment has been completely sequenced. This sequence has been compared with that of an inverse PCR-generated der(11) junction fragment obtained by Hill et al. This reveals that the inverse PCR product has sustained a deletion between two Alu elements, such that the true breakpoint region is deleted from the PCR product. Utilizing PCR primers designed by Hill et al. to amplify across the der(11) breakpoint, we obtained a deleted PCR product even when our cloned der(11) junction fragment was used as template. Further, we find that the PCR primers that they utilized for amplification of the der(22) junction fragment are not located on the der(22). They are oriented in opposite directions within the region deleted from the der(11) PCR product, generating an artifact derived from the der(11) chromosome. Analysis of the truncated PCR products indicates a mixture of sequences from two distinct Alu elements, suggesting that the putative junction fragment described by Hill et al. is an Alu-mediated PCR artifact. These data suggest that caution should be exercised when analyzing PCR-based data, particularly when amplification is carried out in a region containing repeat structures with specific, difficult-to-amplify sequences.

Segregation of a pure form of spastic paraplegia and NOR insertion into Xq11.2

A 3-year-old boy, his 7-year-old brother, and a maternal uncle had a pure form of spastic paraplegia and a variant X chromosome with a faintly stained gap at Xq11.2. The mother of the propositus also had the variant X chromosome but was clinically unaffected. Three other unaffected females in the family did not have the variant X chromosome. The gaps in the variant X chromosome from the affected members and the mother were Ag-NOR staining positive, C-banding negative, rDNA FISH analysis positive, and alpha-satellite FISH analysis negative. The gap, therefore, represented an insertion of the nucleolus organizer region (NOR) derived from the short arm of an acrocentric chromosome. The variant X chromosome of the mother was randomly inactivated, as evidenced by BrdU replication analysis of her Epstein-Barr virus-transformed lymphoblastoid cells. Because mutations of the proteolipid protein gene at Xq21 have been responsible for a pure form of spastic paraplegia, this was also investigated but found to be negative in all affected relatives. Summing up these findings, it is proposed that the NOR insertion in the affected members of the family disrupted a hitherto unknown gene for a pure form of spastic paraplegia, situated at Xq11.2, and caused the disorder.

Tightly clustered 11q23 and 22q11 breakpoints permit PCR-based detection of the recurrent constitutional t(11;22)

Palindromic AT-rich repeats (PATRRs) on chromosomes 11q23 and 22q11 at the constitutional t(11;22) breakpoint are predicted to induce genomic instability, which mediates the translocation. A PCR-based translocation-detection system for the t(11;22) has been developed with PCR primers flanking the PATRRs of both chromosomes, to examine the involvement of the PATRRs in the recurrent rearrangement. Forty unrelated carriers of the t(11;22) balanced translocation, plus two additional, independent cases with the supernumerary-der(22) syndrome, were analyzed to compare their translocation breakpoints. Similar translocation-specific junction fragments were obtained from both derivative chromosomes in all 40 carriers of the t(11;22) balanced translocation and from the der(22) in both of the offspring with unbalanced supernumerary-der(22) syndrome, suggesting that the breakpoints in all cases localize within these PATRRs and that the translocation is generated by a similar mechanism. This PCR strategy provides a convenient technique for rapid diagnosis of the translocation, indicating its utility for prenatal and preimplantation diagnosis in families including carriers of the balanced translocation.

Genetic alteration of the DCX gene in Japanese patients with subcortical laminar heterotopia or isolated lissencephaly sequence

We examined mutations of the doublecortin (DCX) gene, which is responsible for X-linked subcortical laminar heterotopia (SCLH) and lissencephaly, in eight unrelated Japanese patients, four with SCLH and four with isolated lissencephaly sequence (ILS). Polymerase chain reaction (PCR) disclosed a deletion of part of the DCX gene in one male ILS patient. Single-strand conformational polymorphism analysis and subsequent sequence analysis were carried out in the remaining seven patients. One male ILS patient had a nonsense mutation in exon V, which would result in premature termination of the gene product. One female SCLH patient had a missense mutation in exon IV. Our results indicate that in the Japanese, as has been seen elsewhere, abnormality of the DCX gene is the common cause of SCLH and ILS.

Regions of genomic instability on 22q11 and 11q23 as the etiology for the recurrent constitutional t(11;22)

The constitutional t(11;22)(q23;q11) is the only known recurrent, non-Robertsonian translocation. To analyze the genomic structure of the breakpoint, we have cloned the junction fragments from the der(11) and der(22) of a t(11;22) balanced carrier. On chromosome 11 the translocation occurs within a short, palindromic AT-rich region (ATRR). Likewise, the breakpoint on chromosome 22 has been localized within an ATRR that is part of a larger palindrome. Interestingly, the 22q11 breakpoint falls within one of the 'unclonable' gaps in the genomic sequence. Further, a sequenced chromosome 11 BAC clone, spanning the t(11;22) breakpoint in 11q23, is deleted within the palindromic ATRR, suggesting instability of this region in bacterial clones. Several unrelated t(11;22) families demonstrate similar breakpoints on both chromosomes, indicating that their translocations are within the same palindrome. It is likely that the palindromic ATRRs produce unstable DNA structures in 22q11 and 11q23 that are responsible for the recurrent t(11;22) translocation.

Chromosome 22q11 deletion complicated by dissecting pulmonary arterial aneurysm and jejunal atresia in an infant

We present an autopsy case of a 46-day-old male infant with chromosome 22q11 deletion, which is considered the primary cause of several diseases, including DiGeorge syndrome and velocardiofacial syndrome. The patient had 2 notable congenital abnormalities: multiple dissecting pulmonary arterial aneurysms distributed in both lungs and multiple jejunal atresia with apple-peel deformity. The former, a very rare pathologic condition especially in infancy, was found incidentally at autopsy and was the primary cause of death. To our knowledge, neither of these lesions has been reported previously in a patient with chromosome 22q11 deletion.

Genomic organization of the human chondromodulin-1 gene containing a promoter region that confers the expression of reporter gene in chondrogenic ATDC5 cells

Chondromodulin-1 (ChM-1) is a cartilage-specific glycoprotein that stimulates the growth of chondrocytes and inhibits the tube formation of endothelial cells. To clarify the tissue-specific expression and the role of ChM-1 in pathophysiological conditions, we analyzed the structure of the human ChM-1 gene and its promoter. On the screening of a human genomic cosmid library using the human ChM-1 complimentary DNA (cDNA) as a probe, two clones were obtained that contained ChM-1 cDNA. The restriction enzyme map and nucleotide sequence revealed the human ChM-1 gene consisting of seven exons and exon-intron boundaries. The human ChM-1 gene was assigned to chromosome 13q14-21 by fluorescence in situ hybridization (FISH) using the clone as a probe. A primer extension analysis using total RNA extracted from human cartilage revealed a major transcription start site with the sequence CGCT+1GG. The region approximately 3-kilobase (kb) nucleotides upstream of the translation start site was then sequenced and analyzed in terms of promoter activity. We found that a region 446 base pairs (bp) upstream of the start site had promoter activity in COS7, HeLa, and ATDC5 cells. In structure the promoter is a TATA-less type without a GC-rich region. The transcription factors Sox9, Og12, and Cart-1 did not affect the promoter activity. The transcription factor Ying-Yang1 suppressed the promoter activity but GABP protein did not change the promoter activity. The construct containing -446/+87 fused to the SV40 enhancer and green fluorescent protein (GFP) exhibited expression of GFP corresponding to the differentiation of ATDC5 cells to mature chondrocytes. These results suggest that the element -446/+87 confers the cartilage-specific expression of this gene by some factor(s) other than Sox9, Og12, and Cart-1.

Chromosome 22-specific low copy repeats and the 22q11.2 deletion syndrome: genomic organization and deletion endpoint analysis

The 22q11.2 deletion syndrome, which includes DiGeorge and velocardiofacial syndromes (DGS/VCFS), is the most common microdeletion syndrome. The majority of deleted patients share a common 3 Mb hemizygous deletion of 22q11.2. The remaining patients include those who have smaller deletions that are nested within the 3 Mb typically deleted region (TDR) and a few with rare deletions that have no overlap with the TDR. The identification of chromosome 22-specific duplicated sequences or low copy repeats (LCRs) near the end-points of the 3 Mb TDR has led to the hypothesis that they mediate deletions of 22q11.2. The entire 3 Mb TDR has been sequenced, permitting detailed investigation of the LCRs and their involvement in the 22q11.2 deletions. Sequence analysis has identified four LCRs within the 3 Mb TDR. Although the LCRs differ in content and organization of shared modules, those modules that are common between them share 97-98% sequence identity with one another. By fluorescence in situ hybridization (FISH) analysis, the end-points of four variant 22q11.2 deletions appear to localize to the LCRs. Pulsed-field gel electrophoresis and Southern hybridization have been used to identify rearranged junction fragments from three variant deletions. Analysis of junction fragments by PCR and sequencing of the PCR products implicate the LCRs directly in the formation of 22q11.2 deletions. The evolutionary origin of the duplications on chromosome 22 has been assessed by FISH analysis of non-human primates. Multiple signals in Old World monkeys suggest that the duplication events may have occurred at least 20-25 million years ago.

Interstitial deletion of 14q, 46, XY, del (14) (q24.3q32.1) associated with status nonepileptic myoclonia and delayed myelination

A Japanese boy with interstitial deletion of the long arm of chromosome 14, including band 14q31, is described. The characteristic dysmorphic facial features, such as dolichocephaly, bushy eyebrows, horizontal narrow palpebral fissures, long philtrum, etc, and mental and motor developmental delay were observed. Other characteristic clinical manifestations were anuresis and status nonepileptic myoclonia The finding of delayed myelination of the cerebral white matter was observed on magnetic resonance examination, suggesting that an unknown factor related to myelination in the central nervous system might be localized in band 14q31.

Mutation analysis of a Japanese patient with fucosidosis

Fucosidosis is a rare autosomal recessive disorder resulting from a deficiency of alpha-L-fucosidase. Recently, various mutations have been reported in this disease, but it is difficult to elucidate the phenotype from the genetic mutations. We report a patient with chronic infantile type fucosidosis, with a compound heterozygote of a nonsense mutation (W148X, Trp at codon 148 to stop codon) and a large deletion, including all exons. This is the first report of a large deletion demonstrated in fucosidosis. It is interesting that this patient has a relatively mild clinical course despite the absence of the mRNA. This case also indicates the difficulty in determining the phenotype from the genotype in fucosidosis.

The human homolog of Sex comb on midleg (SCMH1) maps to chromosome 1p34

Polycomb group genes were originally identified in Drosophila as repressors required to maintain the silenced state of homeotic loci. About ten Polycomb group genes have been cloned in Drosophila, and mammalian homologs have been identified for most of these. Here, we isolate cDNAs encoding two isoforms of a human homolog of Drosophila Sex comb on midleg (Scm), named Sex comb on midleg homolog-1 (SCMH1). Overall, SCMH1 has 94% identity to its mouse counterpart Scmh1, and 41% identity to Scm, and contains two 1(3)mbt domains, and the SPM domain that are characteristic of Scm. SCMH1 is widely expressed in adult tissues, and maps to chromosome 1p34.