Replication asynchrony between homologs 15q11.2: Cytogenetic evidence for genomic imprinting

Summary Replication kinetics of the Prader-Willi syndrome critical region (15q11.2) was investigated in seven normal healthy adult females using RBG replication bands. Replication asynchrony between homologs 15q11.2 was identified consistently in about 40% of cells in all individuals. It was limited to the stages in which Xp22, Xp11, Xq13 and Xq24/26 were visible in the late-replicating X chromosome. This asynchrony suggested that replication timing overlapped between 15q11.2 and the early replicating R-bands of the late X chromosome in some cells, and that the difference in replication timing between homologs was probably related to genomic imprinting; the latter has been suggested as a pathogenetic basis of Prader-Willi syndrome. As a result of an analysis of the proportions of asynchronous and synchronous cells in each replication stage, two types of cells were deduced providing 11 methylation mosaicism of genomic imprinting was assumed. The first type was composed of cells with normal replication in one homolog and delayed replication in the other. The second type was composed of cells with normal replication in both homologs. Our results provide cytogenetic evidence of methylation mosaicism for mammalian genomic imprinting.     

Human X chromosomes: synchrony of DNA replication in diploid and triploid fibroblasts with multiple active or inactive X chromosomes

We have analyzed patterns of DNA replication in X chromosomes from diploid cultured human fibroblasts and from three triploid 69,XXY fibroblast strains, using BrdU--33258 Hoechst--Giemsa techniques. Both X chromosomes in each of these Barr body-negative triploid strains were early-replicating. The results of gene dosage studies using (1) a histochemical stain to measure X-linked glucose-6-phosphate dehydrogenase (G6PD) activity in single cells and (2) cellulose acetate electrophoresis of G6PD activity in cell extracts also indicated that both Xs in these strains were genetically active. When we compared the synchrony of X chromosome DNA replication kinetics both between cells and within cells containing multiple inactive Xs, a marked variability and asynchrony was observed for late-replicating X chromosomes. In a culture of 47,XXX fibroblasts administered an 8-h terminal pulse of dT after growth in BrdU-containing medium, asynchrony was detected between the two late-replicating Xs in approximately 70% of cells examined. No such asynchrony was observed between the two early-replicating Xs in similarly cultured 69,XXY cells; in the triploid strains, the two Xs were distinguished by asynchronous replication in only approximately 15% of cells. The striking variability in late X chromosome replication kinetics appears, then, to be a property unique to inactive Xs and is not inherent to all X chromosomes.     

Tandem duplication dup(X)(q13q22) in a male proband inherited from the mother showing mosaicism of X-inactivation

Summary An aberrant X chromosome containing extra material in the long arm was observed in a psychomotoric retarded boy and his healthy, short-statured mother. The proband showed generalized muscular hypotony, growth retardation, and somatic anomalies including hypoplastic genitalia and cryptorchism.Chromosomal banding techniques suggested a tandem duplication of the segment Xq13Xq22.In the mother the vast majority of lymphocytes showed late replication of the aberrant X chromosome. Some of her cells, however, contained an apparently active aberrant X. Both the early- and late-replicating aberrant X exhibited late replication patterns very similar to those described for normal X chromosomes in lymphocytes. Asynchrony of DNA replication among the two segments Xq13Xq22 in the dup(X) was never observed.We consider that the clinical picture of the proband is caused by an excess of active X material.     

Isodicentric X chromosome in a patient with Turner syndrome — implications for localization of the X-inactivation center

Summary Cytogenetic analyses have previously shown that the region Xq11.2–q21 is retained in all structurally abnormal X chromosomes. From these observations the conclusion has been drawn that this critical region on the proximal long arm of the X chromosome contains the locus controlling X-inactivation. Structurally abnormal X chromosomes without the X-inactivation center would allow nullisomy, disomy, or trisomy for genes on the X chromosome, and this condition is presumed nonviable. We studied a 28-year-old woman with primary amenorrhea and features of Turner syndrome who had an unusual isodicentric chromosome of the short arm of X. This patient provided us with the opportunity to more closely define the location of the X-inactivation center. High resolution chromosome analysis showed a 46,X,idic(X)(pterq13.2::q13.2pter) chromosome pattern in 94% of her cells and a 45,X complement in 6%. Replication studies showed this derivative X chromosome to be late-replicating (inactive) in all cells analyzed. DNA analysis confirmed the breakpoint of the isodicentric chromosome to be proximal to PGK1. Based on these results, the locus for the X-inactivation center can be refined to be within Xq11.2–q13.2.     

The phenotypic effects of small,distal Xq deletions

Summary The effects of small, distal Xq deletions (Xq26 qter) have been reviewed in light of three cases of our own and five from the literature. The symptoms caused by such deletions range from apparently none through irregular menstruation to secondary amenorrhea (or premature menopause) to primary amenorrhea. That the abnormal chromosome has any effects when it is inactivated may best be explained by one or by a combination of the following hypotheses. (1) the Xq — chromosome might exert an effect during development when cells in which it is active compete with cells in which it is inactivated, assuming that the inactivation of the two X chromosomes is originally random. (2) a more probable hypothesis is that there is a position effect when a break has occurred in the critical region Xq13q27 which apparently must be intact in both X chromosomes to allow normal development of the ovaries. (3) this position effect might, in turn, affect the oocytes (and thus the ovary) after the inactive X chromosome is reactivated before meiosis or the deletion as such might have a direct effect on the ovaries.     

Regional assignment of the gene locus for steroid sulfatase

Summary The gene locus for steroid sulfatase, deficiency of which causes X-linked ichthyosis, is assigned to Xp11Xpter by analysis of 24 man-Chinese hamster somatic cell hybrids. High steroid sulfatase,activity in a hybrid clone having retained only part of Xq is explained by demonstration of an additional late-replicating human X chromosome. This observation confirms previous evidence for noninactivation of the STS locus.     

Allocyclic early replicating X chromosome in mice: Genetic inactivity and shift into a late replicator in early embryogenesis

The allocyclic X chromosome in early female mouse embryos undergoes DNA replication either late or early in the S phase. Earlier studies indicated that the early-replicating X chromosome is restricted to the trophectoderm and primitive endoderm cell lineages in which the allocyclic X is almost exclusively paternal in origin. There has been, however, no compelling evidence for the genetic inactivity of the early-replicating X chromosome and a shift from early to late replication or vice versa. The present study employing a combination of 3H-thymidine autoradiography and BrdU labeling-acridine orange fluorescence staining in day-6 female mouse embryos found that the early-replicating X chromosome can change directly into a late-replicating one. The activity state of the early-replicating X chromosome was examined by electrophoretic determination of the X linked enzyme, phosphoglycerate kinase (PGK-1), in tissues isolated from 6.0-day and day-8.5 Pgk-1a/Pgk-1b embryos. Only the maternally derived Pgk-1 allele was expressed in the proximal endoderm and extraembryonic ectoderm of 6.0-day and the chorion of 8.5-day embryos. Thus, the early-replicating, paternally derived X chromosome found in about 70%-80% of the cells in these tissues seems to be repressed like the late-replicating one.     

Tissue-specific heterogeneity in DNA replication patterns of human X chromosomes

Regional DNA replication kinetics in human X chromosomes have been analysed using BrdU-33258 Hoechst-Giemsa techniques in five cell types from human females: amniotic fluid cells, fetal and adult skin fibroblasts, and fetal and adult peripheral lymphocytes. In all cell types, the late-replicating X chromosome can be distinguished from its active, earlyreplicating homologue, and both the early and late X exhibit temporally and regionally characteristic internal sequences of DNA replication. The replication pattern of the early X in amniotic fluid cells and skin fibroblasts is similar to that of the early X in lymphocytes, although certain discrete regions are later-replicating in these monolayer tissue culture cells than are the corresponding regions in lymphocytes. However, DNA replication kinetics in late X chromosomes from amniotic fluid cells and skin fibroblasts are strikingly different from those observed in lymphocytes with respect both to the initiation and termination of DNA synthesis. The predominant late X pattern observed in 80–95% of lymphocytes, in which replication terminates in the long arm in bands Xq21 and Xq23, was never seen in amniotic fluid cells or skin fibroblasts. Instead, in these cell types, bands Xq25 and Xq27 are the last to complete DNA synthesis, while bands Xq21 and Xq23 are earlier-replicating; this pattern is similar to the alternative replication sequence observed in 5–20% of lymphocyte late X chromosomes. This replication sequence heterogeneity is consistent with the existence of tissue-specific influences on the control of DNA replication in human X chromosomes.     

46,X,i(Xq)/47,XX,+13 mosaicism

A 10-year-old girl with short stature and other features of Turner's syndrome was found to be a mosaic consisting of 46,X,i(Xq) and 47,XX,+13 cell lines, a hitherto undescribed situation. She had none of the clinical features of trisomy 13 syndrome, with a possible exception of postaxial polydactyly of the left foot. Her PHA-stimulated blood lymphocytes and EB virus-transformed B lymphocytes both revealed the Xi(Xq)/XX,+13 mosaicism, while her skin fibroblasts showed an exclusively 46,X,i(Xq) karyotype. Studies using Q-and R-banding heteromorphisms as markers indicated that the patient started as a 13 trisomic zygote resulting from a maternal meiotic error, followed by the loss of chromosome 13 at an early mitotic division. C-banding analysis revealed two C banding blocks in the iso X chromosome, an indication that the chromosome was dicentric. BrdU-Hoechst-Giemsa analysis revealed that the iso X chromosome was late-replicating with both its arms either synchronously or asynchronously replicating. The iso X chromosome was thus designated as idic (Xq)(p11:p11). In view of the presence of the XX cell line, it was concluded that the patient started as an XX,+13 zygote, followed by two mitotic events, the loss of a chromosome 13 and the formation of the iso X chromosome, occurring either simultaneously or in succession.     

Bends in human mitotic metaphase chromosomes, including a bend marking the X-inactivation center.

Bends in mitotic metaphase chromosomes are not distributed randomly throughout the karyotype. The frequency of bends at centromeres is positively correlated with the relative length of the chromosomes and negatively correlated with the centromere index (more bends in metacentrics, fewer in acrocentrics). The frequency of bends in the noncentromeric regions (except at Xq13-Xq21) is positively correlated with the relative length of chromosome arms. A bend at Xq13.3 to Xq21.1 was more frequent than a bend in any other region of the karyotype, centromeric or noncentromeric. It was observed in one member of the X-chromosome pair in 63% of 46,XX cells. In contrast, it was observed in only 2% of 46,XY cells. RBG-staining showed that this specific bend is confined to the lyonized X chromosome. These observations in cells from normal subjects were confirmed using G-banding and RBG-staining on cells from nine subjects with different X-chromosome abnormalities and on metaphases from amniotic fluid cell and lymphocyte cultures. The "center for Barr body condensation" has been localized to the region between Xq11.2 and Xq21.1. The functional and structural relationship is unclear, but we believe this highly specific bend may represent a visible manifestation of the condensation process; it could represent the first folded (and last unfolded) position, upon or around which the rest of the chromosome condenses. The late replication of this region may also be a factor. The smallest region of overlap (SRO) for the X-chromosome inactivation center and the specific chromosome bend is Xq13.3 to Xq21.1.     

On the frequency of telomeric chromosomal changes induced by culture conditions suitable for fragile X expression

Summary Under culture conditions suitable for the expression of the fragile site Xq27, nonspecific telomeric structural changes similar to the specific fra(X) formation occurred apparently on every chromosome arm. Significant differences between individuals seem to exist. The total frequency of nonspecific terminal lesions not located on the long arm of the X chromosome was 0.22±0.17 per cell in 37 cultures examined. If telomeric lesions on Xq occur in more than 0.7% of the cells from a single culture in males and more than 1.5% of the cells from single culture in females, then this probably indicates a specific fra(X) expression. Lower percentages may be the result of nonspecific telomeric structural changes in Xq. These are expected to occur in the normal X as well and may, therefore, give rise to false positive diagnoses in the detection of hemi-, hetero-, and perhaps also homozygous fra(X) carriers.     

Regional assignment of arylsulfatase A,mitochondrial aconitase and NADH-cytochrome b5 reductase by somatic cell hybridization

Summary By using somatic cell hybrids between HPRT deficient hamster cells and fibroblasts derived from a patient with a X/22 translocation t(X;22)(q13;q112), we have assigned the genes for human ARSA, DIA 1, and ACO 2 to region q112qter of human chromosome 22 and the gene for human PGK close to the breakpoint in band Xq13.     

The origin of telocentric chromosomes in man: A girl with tel(Xq)

Summary A mentally retarded girl with several Turner symptoms had the chromosome constitution 46,X,tel(Xq). The abnormal X chromosome appeared to be completely telocentric and stable. It was late-replicating and formed a smaller than normal Barr body. The origin of telocentric chromosomes is discussed.     

Inactivation centers in the human X chromosome.

Reported cases with a structurally abnormal X chromosome were compiled. These included 17 balanced and 26 unbalanced X-autosome translocations, each with inactivation of either a derivative X or a derivative of any of the autosomes. A further 52 cases with various structural rearrangements were studied. The shortest late-replicating segment in each arm pter leads to p21 and q13 leads to qter. In both cases, they were detected in all or most metaphases, thus making the results convincing. In one case, the distal part of Xq, q25 or 26 leads to qter was probably inactivated in a small proportion of the cells. It appears reasonable to assume that the former two segments and probably also the third include an "inactivation center(s)." In a male with a 46,Y,dup(X)(q13q22), no part of dup X replicated late although it contained extra chromosome material.     

Cytogenetic and molecular analysis of an unbalanced translocation (X;7) (q28;p15) in a dysmorphic girl

Summary A severely retarded and dysmorphic girl, carrying an unbalanced X/7 translocation with breakpoints at Xq28 and 7p14, was analyzed by cytogenetic, biochemical and molecular techniques. The X/7 translocated chromosome was found to replicate consistently late in the 105 metaphases analyzed. In 83 of these cells, late replication was limited to the X portion of the abnormal chromosome, whereas in 22 cells incomplete spreading into the autosomal fragment was observed. Southern blot and in situ hybridization experiments with probe G80 (locus D7S373) (previously localized to 7p13–15) and G98 (localized to 7p14–15) assigns the former to 7p15 and the latter to 7p14, thus suggesting the order 7ter-G80-G98-cen. The activity of the enzyme phosphoserine phosphatase localized to 7pter p14 was increased. Southern blotting experiments with 19 probes spanning the entire X chromosome demonstrated that the translocated chromosome had lost a portion of Xq28 (locus DXS51) but still retained part of Xq27 (F9 locus). The results confirm that the proband is trisomic for the region 7p15-pter and monosomic for the region Xq28-qter. Comparing her phenotype with those of other cases of partial trisomy or monosomy 7p, we confirm that band 7p21 is probably involved in skull development.     

Exclusion mapping of the gene for X-linked neural tube defects in an Icelandic family

Various polymorphic markers with a random distribution along the X chromosome were used in a linkage analysis performed on a family with apparently Xlinked recessive inheritance of neural tube defects (NTD). The lod score values were used to generate an exclusion map of the X chromosome; this showed that the responsible gene was probably not located in the middle part of Xp or in the distal region of Xq. A further refining of these results was achieved by haplotype analysis, which indicated that the gene for X-linked NTD was located either within Xp21.1-pter, distal from the DMD locus, or in the region Xq12–q24 between DXS106 and DXS424. Multipoint linkage analysis revealed that the likelihood for gene location is highest for the region on Xp. The region Xq26–q28, which has syntenic homology with the segment of the murine X chromosome carrying the locus for bent tail (Bn), a mouse model for X-linked NTD, is excluded as the location for the gene underlying X-linked NTD in the present family. Thus, the human homologue of the Bn gene and the present defective gene are not identical, suggesting that more than one gene on the X chromosome plays a role in the development of the neural tube.     

Analysis of DNA replication during S-phase by means of dynamic chromosome banding at high resolution

The characteristic patterns of dynamic banding (replication banding) were analysed. Extremely high resolution (850 to 1,250 bands per genome) G- and R-band patterns were obtained after 5-bromo-2-deoxyuridine (BrdUrd) incorporation either during the early or the late S-phase. We synchronized human lymphocytes with high concentrations of thymidine or BrdUrd as blocking agents, followed by low concentrations of BrdUrd or thymidine respectively as releasing agents, and obtained R- or G-band patterns respectively. The dynamic R-and G-band patterns were complementary for all chromosomes, even for the late-replicating X chromosome. There was no overlapping and every part of each chromosome was positively stained by one of the two banding procedures. The complementarity of the two patterns shows that both high thymidine and high BrdUrd concentrations blocked S-phase progression near the R-band to G-band replication transition in the middle of S-phase. Some bands of the inactive X chromosome replicate before this transition concurrently with R-band replication. The 48 different telomeric regions could be classified into 5 distinct morphotypes based upon the distribution of early and late-replicating DNA in each telomeric region. The dynamic band patterns are particularly useful for the study of the structural and physiological organization of chromosomes at high resolution and should prove invaluable for assessing the replication behavior of rearranged chromosomes.     

Identification of trophoblast in chorionic villi biopsy samples

Summary Genetic linkage studies were carried out in families with X-linked hypohidrotic ectodermal dysplasia (C-S-T syndrome). A DNA probe DXYS1 (pDP34), which maps both to the proximal part of the long arm of the X chromosome, Xq13-Xq21, and proximally on Yp, was used to detect a TaqI restriction fragment length polymorphism of the X-chromosomal locus in the DNA samples from 11 families. This locus was found to be closely linked to the X-linked hypohidrotic ectodermal dysplasia locus, with a lod score of 2.66 at recombination fraction () of 0.06 (90% confidence limits 0.01–0.26). Only one crossover was observed in nineteen meioses. This indicates that the probe DXYS1 is closely linked to the X-linked hypohidrotic ectodermal dysplasia locus and is likely to facilitate carrier detection and prenatal diagnosis tests.     

What causes the abnormal phenotype in a 49,XXXXY male?

Summary The chromosome replication pattern of a man with 49,XXXXY was analyzed using ³H-thymidine and autoradiography as well as BrdU and acridine orange. The former technique showed a highly irregular replication pattern; the latter revealed one early replicating X chromosome, and the other three more or less asynchronously replicating. Two hypotheses seem to explain best the abnormal phenotype of males with an XXXXY sex chromosome constitution: (1) The number of the always active regions (tip of Xp) and of the possibly always active regions (the Q-dark regions on both sides of the centromere) is increased from one to four. (2) The replication pattern of the late-replicating X chromosomes is highly asynchronous, which might affect the phenotype. The possibility that more than one X chromosome might remain active in some cells, an even more abnormal and obviously deleterious situation, is still open.     

Two sisters with a distal deletion at the Xq26/Xq27 interface: DNA studies indicate that the gene locus for factor IX is present

Summary Two sisters with premature menopause and a small deletion of the long arm of one of their X chromosomes [del (X)(pterq26.3:)] were investigated with polymorphic DNA probes near the breakpoint. The deleted chromosome retained the factor IX (F9) locus and the loci DXS51 (52A) and DXS100 (pX45h), which are proximal to F9. However, the factor VIII (F8) locus was not present, nor were two loci tightly linked to this locus, DXS52 (St14) and DXS15 (DX13) This deletion refines the location of the F9 locus to Xq26 or to the interface Xq26/Xq27, thus placing it more proximally than has been previously reported. The DNA obtained from these patients should be valuable in the mapping of future probes derived from this region of the X chromosome.