Skewed X-chromosome inactivation is a common feature of X-linked mental retardation disorders

Some deleterious X-linked mutations may result in a growth disadvantage for those cells in which the mutation, when on the active X chromosome, affects cell proliferation or viability. To explore the relationship between skewed X-chromosome inactivation and X-linked mental retardation (XLMR) disorders, we used the androgen receptor X-inactivation assay to determine X-inactivation patterns in 155 female subjects from 24 families segregating 20 distinct XLMR disorders. Among XLMR carriers, ~50% demonstrate markedly skewed X inactivation (i.e., patterns 80:20), compared with only ~10% of female control subjects (P<.001). Thus, skewed X inactivation is a relatively common feature of XLMR disorders. Of the 20 distinct XLMR disorders, 4 demonstrate a strong association with skewed X inactivation, since all carriers of these mutations demonstrate X-inactivation patterns 80:20. The XLMR mutations are present on the preferentially inactive X chromosome in all 20 informative female subjects from these families, indicating that skewing is due to selection against those cells in which the XLMR mutation is on the active X chromosome.     

A longitudinal study of X-inactivation ratio in human females

We investigated the effect of aging on X chromosome inactivation by performing a longitudinal study in a population of 178 normal females. We examined X-inactivation ratios (fraction of cells with the same X chromosome active) in two sets of peripheral blood DNA samples collected about two decades apart. We observed a strong correlation between the ratios of individual females at the two time points and found no significant difference between the two sets of measurements. These observations indicate that aging, per se (as opposed to being aged), has little effect on X-inactivation. However, we also found that several females who were older than 60 years of age at the time of the first measurement acquired significant changes in the X-inactivation ratio. We speculate that, if X-inactivation skewing is a frequently acquired trait in older females, it is acquired as the result of a discontinuous or catastrophic process and is not the result of constant selection for or against hematopoietic stem cells with a particular X chromosome active.     

Cytogenetics of ticks (Acari: Ixodoidea)

Chromosomes and sex determination of 9 species of Haemaphysalis assigned to 4 subgenera are described. H. (tAlloceraea) kitaokai possesses an XX∶XO sex chromosome system with 18 autosomes plus XX in females; 18 plus X in males. H. (Kaiseriana) hystricis has 18 +XX and 18 + XY in females and males, respectively, in most specimens, but a supernumerary chromosome is present in some individuals. A supernumerary chromosome was also observed in 1 male H. (Aborphysalis) formosensis. These two species are the second and third species of ticks reported to have supernumerary chromosomes. H. formosensis, H. (Kaiseriana) bispinosa, H. (Haemaphysalis) campanulata, H. (H.) flava, H. (H.) megaspinosa, H. (H.) japonica, and H. (H.) pentalagi possess 20 autosomes plus 2 sex chromosomes in females and 20+1 sex chromosomes in males. Phylogenetic relationships within the genus Haemaphysalis are briefly discussed.     

De novo interstitial triplication of MECP2 in a girl with neurodevelopmental disorder and random X chromosome inactivation

Loss-of-function mutations of the MECP2 gene are the cause of most cases of Rett syndrome in females, a progressive neurodevelopmental disorder characterized by severe mental retardation, global regression, hand stereotypies, and microcephaly. On the other hand, gain of dosage of this gene causes the MECP2 duplication syndrome in males characterized by severe mental retardation, absence of speech development, infantile hypotonia, progressive spasticity, recurrent infections, and facial dysmorphism. Female carriers of a heterozygous duplication show a skewed X-inactivation pattern which is the most probable cause of the lack of clinical symptoms. In this paper, we describe a girl with a complex de novo copy number gain at Xq28 and non-skewed X-inactivation pattern that causes mental retardation and motor and language delay. This rearrangement implies triplication of the MECP2 and IRAK1 genes, but it does not span other proximal genes located in the common minimal region of patients affected by the MECP2 duplication syndrome. We conclude that the triplication leads to a severe phenotype due to random X-inactivation, while the preferential X chromosome inactivation in healthy carriers may be caused by a negative selection effect of the duplication on some proximal genes like ARD1A or HCFC1.     

X-chromosomale Intelligenzminderung

X-linked intellectual disability (XLID) is a heterogeneous disorder; more than 100 XLID genes have been identified so far. Fragile X syndrome with CGG repeat expansions in the 5’-UTR of FMR1, is the most frequent monogenic form of ID. Other XLID genes with a comparatively high prevalence of mutations are ATRX, RPS6KA3, GPC3, SLC16A2, SLC6A8, and ARX. The causes of XLID are distributed as follows: molecular genetically proven mutations in 90% and copy-number variations (CNVs) in approximately 10%. Common CNVs are duplications of Xq28 that include MECP2 and the Xp11.22 duplication syndrome, with overexpression of HUWE1. Using current investigative methods, mutations in X?chromosomal genes can be proven to be the underlying cause in approximately 10% of male patients with ID. Over the next few years, new discoveries are to be expected, primarily in the noncoding regions of the X?chromosome, where further causes of the preponderance in male patients, which has not yet been fully explained, are presumably to be sought.     

Quantitative aspects of ribosomal RNA synthesis during ovarian development in two mutants of Drosophia melanogaster

A quantitative polyacrylamide gel electrophoresis procedure for the analysis of microgram quantities of RNA has been developed. The method was used to determine the rates of rRNA synthesis and the molar ratios of various RNA species in Drosophila females homozygous for either of two X chromosome inversions that result in sterility of the females and produce lethality in X/0 males. Evidence is presented that in these genotypes the rate of rRNA synthesis during oogenesis is unimpaired but the mature oocyte has a 10–12% reduction in rRNA content.     

Susceptibility to db gene and streptozotocin-induced diabetes in C57BL mice: control by gender-associated,MHC-unlinked traits

H-2 haplotype differences distinguish the related C57BL/KsJ (BKs) and C57BL/6J (B6) inbred strains. BKs mice are more susceptible to diabetes induction by a recessive obesity gene, diabetes (db), or by multi-dose streptozotocin (MSZ) administration. The purpose of this study was to evaluate whether the H-2 differences were the important genetic background modifiers determining inbred strain susceptibility or resistance to these diabetogenic stresses. Diabetes susceptibility of BKs.B6-H-2 ^b congenic mice was compared with that of the parental BKs and B6 stocks. In addition, diabetes severity was studied in (B6 × BKs)F₁ and F₂ db/db mice and an H-2 segregation analysis was performed. BKs susceptibility genes expressed in a dominant fashion in the F₁ generation, and were transmitted to F₂ db/db males without apparent segregation. No association between H-2 ^b haplotype and B6-type diabetes resistance was found in response to either the db mutation or to MSZ. Insulitis, associated with development of hyperglycemia in BKs males, also occurred in the H-2 ^b congenic stock. However, an apparent interaction between H-2 ^b haplotype, the db mutation (on chromosome 4), and male gender (Y chromosome?) was indicated by a segregation ratio distortion in recovery of this genotype. A more moderate diabetes in some F₂ db/db females suggested that non-MHC-linked genes controlling sex steroid metabolism were the important determinants of diabetogenic sensitivities in the C57BL stocks. In support of the latter, strain differences were demonstrated in activity levels of steroid sulfatase, which is regulated by a sex-linked gene likely expressed on both the X and Y chromosome, and which may control tissue levels of active androgens and estrogens. We show that the diabetes-susceptible F₁ hybrids exhibit the higher activity associated with the BKs strain.     

Mutations in DDX3X Are a Common Cause of Unexplained Intellectual Disability with Gender-Specific Effects on Wnt Signaling

Intellectual disability (ID) affects approximately 1%–3% of humans with a gender bias toward males. Previous studies have identified mutations in more than 100 genes on the X chromosome in males with ID, but there is less evidence for de novo mutations on the X chromosome causing ID in females. In this study we present 35 unique deleterious de novo mutations in DDX3X identified by whole exome sequencing in 38 females with ID and various other features including hypotonia, movement disorders, behavior problems, corpus callosum hypoplasia, and epilepsy. Based on our findings, mutations in DDX3X are one of the more common causes of ID, accounting for 1%–3% of unexplained ID in females. Although no de novo DDX3X mutations were identified in males, we present three families with segregating missense mutations in DDX3X, suggestive of an X-linked recessive inheritance pattern. In these families, all males with the DDX3X variant had ID, whereas carrier females were unaffected. To explore the pathogenic mechanisms accounting for the differences in disease transmission and phenotype between affected females and affected males with DDX3X missense variants, we used canonical Wnt defects in zebrafish as a surrogate measure of DDX3X function in vivo. We demonstrate a consistent loss-of-function effect of all tested de novo mutations on the Wnt pathway, and we further show a differential effect by gender. The differential activity possibly reflects a dose-dependent effect of DDX3X expression in the context of functional mosaic females versus one-copy males, which reflects the complex biological nature of DDX3X mutations.     

Methods and results from the genome-wide association group at GAW20

Background

X chromosome inactivation (XCI) is an important gene regulation mechanism in females to equalize the expression levels of X chromosome between two sexes. Generally, one of two X chromosomes in females is randomly chosen to be inactivated. Nonrandom XCI (XCI skewing) is also observed in females, which has been reported to play an important role in many X-linked diseases. However, there is no statistical measure available for the degree of the XCI skewing based on family data in population genetics.

Results

In this article, we propose a statistical approach to measure the degree of the XCI skewing based on family trios, which is represented by a ratio of two genotypic relative risks in females. The point estimate of the ratio is obtained from the maximum likelihood estimates of two genotypic relative risks. When parental genotypes are missing in some family trios, the expectation-conditional-maximization algorithm is adopted to obtain the corresponding maximum likelihood estimates. Further, the confidence interval of the ratio is derived based on the likelihood ratio test. Simulation results show that the likelihood-based confidence interval has an accurate coverage probability under the situations considered. Also, we apply our proposed method to the rheumatoid arthritis data from USA for its practical use, and find out that a locus, rs2238907, may undergo the XCI skewing against the at-risk allele. But this needs to be further confirmed by molecular genetics.

Conclusions

The proposed statistical measure for the skewness of XCI is applicable to complete family trio data or family trio data with some paternal genotypes missing. The likelihood-based confidence interval has an accurate coverage probability under the situations considered. Therefore, our proposed statistical measure is generally recommended in practice for discovering the potential loci which undergo the XCI skewing.

     

Novel Mutation in the <Emphasis Type="Italic">MECP2</Emphasis> Gene Identified in a Group of Rett Syndrome Patients from Ukraine

Mutations in the MECP2 gene are known to cause Rett syndrome (RTT)—a neurodevelopmental disorder, one of the most common causes of intellectual disability in females, with an incidence of 1 in 10000–15000. We have investigated exons 3 and 4 of the MECP2 gene, that coding MBD and TRD domains of the MeCP2 protein, in 21 RTT patients from Ukraine by PCR-DGGE analysis followed by Sanger sequencing of PCR fragments with abnormal migration profiles. In 13 of 21 (61.9%) patients 7 different mutations were identified one nonsense mutation—c. NC_000023.11:g.154031326G>A (MECP2:c.502C>T) and 4 missense mutation NC_000023.11:g.154031409G>T (MECP2:c.419C>T), NC_000023.11:g.154031355G>A (MECP2:c.473C>T), NC_000023.11:g.154031354A>C (MECP2:c.472A>C), NC_000023.11:g.154031431G>A (MECP2:c.397C>T) located in exon 4, a rare RTT-causing splice site mutation NC_000023.10:g.153296903T>G (MECP2:c.378-2A>C) in intron 3 and deletion NC_000023.10:g.1532 96079_153296122del44 in exon 4. The novel mutation MECP2:c.472A>C identified in our study in patients withclassic RTT phenotype leds to T158P substitution. It is one more confirmation of crucial role that 158 codon in MECP2 protein function.     

De Novo Loss-of-Function Mutations in USP9X Cause a Female-Specific Recognizable Syndrome with Developmental Delay and Congenital Malformations

Mutations in more than a hundred genes have been reported to cause X-linked recessive intellectual disability (ID) mainly in males. In contrast, the number of identified X-linked genes in which de novo mutations specifically cause ID in females is limited. Here, we report 17 females with de novo loss-of-function mutations in USP9X, encoding a highly conserved deubiquitinating enzyme. The females in our study have a specific phenotype that includes ID/developmental delay (DD), characteristic facial features, short stature, and distinct congenital malformations comprising choanal atresia, anal abnormalities, post-axial polydactyly, heart defects, hypomastia, cleft palate/bifid uvula, progressive scoliosis, and structural brain abnormalities. Four females from our cohort were identified by targeted genetic testing because their phenotype was suggestive for USP9X mutations. In several females, pigment changes along Blaschko lines and body asymmetry were observed, which is probably related to differential (escape from) X-inactivation between tissues. Expression studies on both mRNA and protein level in affected-female-derived fibroblasts showed significant reduction of USP9X level, confirming the loss-of-function effect of the identified mutations. Given that some features of affected females are also reported in known ciliopathy syndromes, we examined the role of USP9X in the primary cilium and found that endogenous USP9X localizes along the length of the ciliary axoneme, indicating that its loss of function could indeed disrupt cilium-regulated processes. Absence of dysregulated ciliary parameters in affected female-derived fibroblasts, however, points toward spatiotemporal specificity of ciliary USP9X (dys-)function.     

Chromosome nondisjunction in <Emphasis Type="Italic">Drosophila</Emphasis> strains mutant for tumor suppressor Merlin

The effect of mutation for gene Merlin on chromosome disjunction in Drosophila during meiosis was genetically studied. Chromosome nondisjunction was not registered in females heterozygous for this mutation and containing structurally normal X chromosomes. In cases when these females additionally contained inversion in one of chromosomes X, a tendency toward the appearance of nondisjunction events was observed in individuals containing mutation in the heterozygote. The genetic construct was obtained allowing the overexpression of protein corresponding to a sterile allele Mer ³ in the germ cell line. This construct relieves the lethal effect of Mer ⁴ mutation. The ectopic expression of this mutant protein leads to chromosome nondisjunction in male meiosis.     

Cytogenetic analysis of recombination in males of Drosophila ananassae

Cytogenetic studies of recombination in males of Drosophila ananassae were carried out by examining F₁ males derived from the mating of marker females, b se; bri ru of the BS stock, with males of two wild strains, TNG and L8. The male recombination values in both sections b-se (chromosome 2) and bri-ru (chromosome 3) are high in TNG F₁ but extremely low in L8 F₁ We demonstrate the presence of chiasmata in TNG F₁ males at a frequency capable of accounting for the observed recombination values. A unique series of “iso-site aberrations” was also observed in TNG F₁ males. Because of a parallelism in the distribution pattern between the chiasmata and the isosite aberrations, we propose that recombination in males of D. ananassae is meiotic in origin and that the iso-site aberrations are related to chiasma formation.     

Sex chromosomal dimorphisms narrated by X-chromosome translocation in a spiny frog (<Emphasis Type="Italic">Quasipaa boulengeri</Emphasis>)

Background

In the general model of sex chromosome evolution for diploid dioecious organisms, the Y (or W) chromosome is derived, while the homogametic sex presumably represents the ancestral condition. However, in the frog species Quasipaa boulengeri, heteromorphisms caused by a translocation between chromosomes 1 and 6 are not related to sex, because the same heteromorphic chromosomes are found both in males and females at the cytological level. To confirm whether those heteromorphisms are unrelated to sex, a sex-linked locus was mapped at the chromosomal level and sequenced to identify any haplotype difference between sexes.

Results

Chromosome 1 was assigned to the sex chromosome pair by mapping the sex-linked locus. X-chromosome translocation was demonstrated and confirmed by the karyotypes of the progeny. Translocation heteromorphisms were involved in normal and translocated X chromosomes in the rearranged populations. Based on phylogenetic inference using both male and female sex-linked haplotypes, recombination was suppressed not only between the Y and normal X chromosomes, respectively the Y and translocated X chromosomes, but also between the normal and translocated X chromosomes. Both males and females shared not only the same translocation heteromorphisms but also the X chromosomal dimorphisms in this frog.

Conclusions

The reverse of the typical situation, in which the X is derived and the Y has remained unchanged, is known to be very rare. In the present study, X-chromosome translocation has been known to cause sex chromosomal dimorphisms. The X chromosome has gone processes of genetic differentiation and/or structural changes by chance, which may facilitate sex chromosome differentiation. These sex chromosomal dimorphisms presenting in both sexes may represent the early stages of sex chromosome differentiation and aid in understanding sex chromosome evolution.

     

Estimating the stability of the proposed imprinted state of the fragile-X mutation when transmitted by females

Summary Fragile-X syndrome is a major cause of mental retardation in humans. The X-inactivation imprinting model accounts for the unusual pattern of inheritance and expression of this syndrome. According to this model, the fragile-X mutation creates a local block to the attempted reactivation of the mutant X chromosome prior to oogenesis. This local block results in an imprinted fragile-X chromosome that is deleterious in males and in females for whom this chromosome is predominantly the active X chromosome. The imprinted state of the fragile-X mutation is inferred to be stable when transmitted by an imprinted female because the penetrance of the syndrome in sons of affected females is estimated to be 1.0. To provide a more precise estimate of the stability of the proposed fragile-X imprint, we have analyzed published pedigrees that include restriction fragment length polymorphism and cytogenetic data from sibships with mothers who are interpreted as having an imprinted fragile-X allele. We conclude that the fragile-X imprint was stable in 46 out of 48 female meioses. This analysis leads to a preliminary estimate of about 96% for the stability of the imprint through female meiosis. Two imprinted females had progeny who appeared to be carriers of a nonimprinted fragile-X allele. If this interpretation is correct, then reversion from the imprinted to the nonimprinted state, or erasure, can occasionally occur when the mutant fragile-X allele is transmitted by an imprinted female. We discuss the genetic and epigenetic significance of possible female erasure. We request DNA and cytogenetic information from unpublished pedigrees to quantify further the stability, during female meiosis, of the proposed imprinted state of the mutant fragile-X allele.