Microduplication of 15q13.3 and Xq21.31 in a family with tourette syndrome and comorbidities

Tourette syndrome (TS) is a childhood onset neurodevelopmental disorder. Although it is widely accepted that genetic factors play a significant role in TS pathogenesis the etiology of this disorder is largely unknown. Identification of rare copy number variations (CNVs) as susceptibility factors in several neuropsychiatric disorders such as attention deficit‐hyperactivity disorder (ADHD), autism and schizophrenia, suggests involvement of these rare structural changes also in TS etiology. In a male patient with TS, ADHD, and OCD (obsessive compulsive disorder) we identified two microduplications (at 15q13.3 and Xq21.31) inherited from a mother with subclinical ADHD. The 15q duplication included the CHRNA7 gene; while two genes, PABPC5 and PCDH11X, were within the Xq duplication. The Xq21.31 duplication was present in three brothers with TS including the proband, but not in an unaffected brother, whereas the 15q duplication was present only in the proband and his mother. The structural variations observed in this family may contribute to the observed symptoms, but further studies are necessary to investigate the possible involvement of the described variations in the TS etiology. © 2013 Wiley Periodicals, Inc.     

The causes and consequences of random and non-random X chromosome inactivation in humans

X chromosome (X) inactivation is a remarkable biological process including the choice and cis-limited inactivation of one X, as well as the stable maintenance of this silencing by epigenetic chromatin alterations. The process results in females generally being mosaic for two populations of cells--one with each parental X active. In this review, we discuss recent advances in our understanding of how inactivation works, as well as the causes and clinical implications of deviations from random inactivation.     

Keipert syndrome (Nasodigitoacoustic syndrome) is X-linked and maps to Xq22.2-Xq28

Keipert syndrome is a rare condition comprising sensorineural deafness associated with facial and digital abnormalities. To date, Keipert syndrome has been reported in six male patients including two sib pairs; however the genetic basis of Keipert syndrome is yet to be elucidated. We report on the diagnosis of Keipert syndrome in the nephew of the brothers in the first report of Keipert syndrome, with a pedigree consistent with X-linked recessive inheritance. Linkage analysis using microsatellite markers along the X-chromosome suggests that the gene for Keipert syndrome is located in the region Xq22.2-Xq28. We postulate the Keipert syndrome is caused by a novel gene at Xq22.2-Xq28.     

Clinical and molecular genetic characterization of two female patients harboring the Xq27.3q28 deletion with different ratios of X chromosome inactivation

A heterozygous deletion at Xq27.3q28 including FMR1, AFF2, and IDS causing intellectual disability and characteristic facial features is very rare in females, with only 10 patients having been reported. Here, we examined two female patients with different clinical features harboring the Xq27.3q28 deletion and determined the chromosomal breakpoints. Moreover, we assessed the X chromosome inactivation (XCI) in peripheral blood from both patients. Both patients had an almost overlapping deletion at Xq27.3q28, however, the more severe patient (Patient 1) showed skewed XCI of the normal X chromosome (79:21) whereas the milder patient (Patient 2) showed random XCI. Therefore, deletion at Xq27.3q28 critically affected brain development, and the ratio of XCI of the normal X chromosome greatly affected the clinical characteristics of patients with deletion at Xq27.3q28. As the chromosomal breakpoints were determined, we analyzed a change in chromatin domains termed topologically associated domains (TADs) using published Hi‐C data on the Xq27.3q28 region, and found that only patient 1 had a possibility of a drastic change in TADs. The altered chromatin topologies on the Xq27.3q28 region might affect the clinical features of patient 1 by changing the expression of genes just outside the deletion and/or the XCI establishment during embryogenesis resulting in skewed XCI.     

Molecular characterization of isochromosomes of Xq

We have undertaken a study of 35 patients with i(Xq) to determine whether those that are maternally derived originate by similar mechanisms to those that are paternally derived. Isochromosome formation is not associated with increased parental age and >90% of i(Xq) contain proximal Xp sequences suggesting that centromere misdivision is not a common mechanism of formation. Our results indicate that the majority of i(Xq) originate from a single X chromosome and the usual mechanisms of formation do not appear to differ according to the parent of origin.     

Isodicentric X chromosome and mosaicism: Report on two cases of 45,X/46,X,idic(Xq)/47,X,idic(Xq),idic(Xq) and review of the literature

We present 2 instances of Ullrich-Turner syndrome with mosaicism 45,X/46,X,idic(Xq)/47,X,idic(Xq),idic(Xq) and X-isochromosomes with 2 C-bands. The mosaicism with the 3 cell lines point to the presence of the isodicentric chromosome in the zygote and a subsequent nondisjunction event. © 1993 Wiley-Liss, Inc.     

Autism spectrum disorder in females with ARHGEF9 alterations and a random pattern of X chromosome inactivation

Proper function of GABAergic synapses depends upon the postsynaptic compartment anchoring of neurotransmitter receptors to the membrane by gephyrin and collybistin (Cb). In humans, Cb is encoded by ARHGEF9 on Xq11.1. ARHGEF9 alterations, some inherited from unaffected mothers, have been reported in males with autism, seizures and severe neurodevelopmental abnormalities. In females, a spectrum of mild to moderate phenotype has been detected. We report two unrelated females with autism and mild intellectual disability. High resolution X-chromosome microarray analysis revealed de novo intragenic deletions in ARHGEF9 of 24?kb and 56?kb involving exons 5–8 and exons 3–8 and leading to truncated forms of collybistin. Peripheral blood samples revealed random X-chromosome inactivation in both patients. To explain phenotypic variability in female patients, we propose a model for disruption of collybistin and various irregular interactions in post-synaptic neurons based on X inactivation patterns. Our findings highlight the importance of ARHGEF9 integrity and suggest further research on its correlation with autism and neurobehavioral problems.     

Skewing of X chromosome inactivation in autoimmunity

Approximately 5% of the population in Western countries is affected by autoimmune diseases (AID), with a significantly higher prevalence in women. Genetic factors are known to be crucial determinants of susceptibility as shown by family and twin studies, although no specific genes predisposing women to autoimmunity have been identified thus far. Several studies indicate that X chromosome abnormalities, such as inactivation patterns, characterize some female-predominant AID. We herein review the most recent evidence on the role of the X chromosome in the breakdown of immune tolerance and discuss its potential implications. Future efforts will help to identify specific X chromosome regions containing candidate genes for disease susceptibility.     

Skewing of X chromosome inactivation in autoimmunity

Approximately 5% of the population in Western countries is affected by autoimmune diseases (AID), with a significantly higher prevalence in women. Genetic factors are known to be crucial determinants of susceptibility as shown by family and twin studies, although no specific genes predisposing women to autoimmunity have been identified thus far. Several studies indicate that X chromosome abnormalities, such as inactivation patterns, characterize some female-predominant AID. We herein review the most recent evidence on the role of the X chromosome in the breakdown of immune tolerance and discuss its potential implications. Future efforts will help to identify specific X chromosome regions containing candidate genes for disease susceptibility.     

A gene for nonsyndromic X-linked mental retardation (MRX77) maps to Xq12-Xq21.33

Nonsyndromic X-linked mental retardation (MRX) is a highly heterogeneous condition in which mental retardation appears to be the only consistent manifestation. According to the most recent data, 77 MRX families with a lod score of >2 have been mapped and eight genes have been cloned. We hereby report on a linkage analysis performed on a Greek family with apparently nonsyndromic MRX. The affected males have moderate to severe mental retardation, severe speech problems, and aggressive behavior. Two-point linkage analysis with 26 polymorphic markers spanning the entire X chromosome was carried out. We could assign the causative gene to a 27 Mb interval in Xq12-Xq21.33. The maximum LOD score was found for markers DXS1225, DXS8114, and DXS990 at 2.36, 2.06, 2.06, respectively at theta = 0.00. Recombination was observed for DXS983 at the proximal side and DXS6799 at the distal side. Nineteen other MRX families have been described with a partial overlapping disease gene interval in proximal Xq. No mutations were found in the MRX77 family for three known or candidate MRX genes, from this region OPHN1, RSK4, and ATR-X. These data indicate that the Xq12-Xq21.33 interval contains at least one additional MRX gene.     

Molecular cytogenetic analysis of a duplication Xp in a female with an abnormal phenotype and random X inactivation

We describe a female infant with severe abnormal phenotype with a de novo partial duplication of the short arm of the X chromosome. Chromosome painting confirmed the origin of this X duplication. Molecular cytogenetic analysis with fluorescence in situ hybridization (FISH) was performed with YAC probes, further delineating the breakpoints. The karyotype was 46, X dup(X)(p11-p21.2).Cytogenetic replication studies showed that the normal and duplicated X chromosomes were randomly inactivated in lymphocytes. In most females with structurally abnormal X chromosomes, the abnormal chromosome is inactivated and they are phenotypically apparently normal relatives of phenotypically abnormal males having dupX. Therefore, in this case, there is functional disomy of Xp11-p21.2 in the cells with an active dup(X), most likely resulting in abnormal clinical findings in the patient.     

X chromosome inactivation in fibroblasts of mentally retarded female carriers of the fragile site Xq27.3: application of the probe M27 beta to evaluate X inactivation status.

Over 30% of female carriers of the fragile X [fra(X)] syndrome are clinically affected. A nonrandom X chromosome inactivation in these cases could be a plausible explanation. A review of previous studies addressing this question showed inconclusive results; thus, we analysed the X inactivation pattern in fibroblasts of 4 unrelated, mentally retarded fra(X) carriers with a high expression of the fragile site Xq27.3. Using Southern analysis with a highly polymorphic probe M27 beta that recognizes methylation differences between the active and inactive X chromosome we found a 50/50 inactivation pattern in 2 cases and skewed patterns in the other 2. As biased patterns were also observed in control females we conclude that at present no evidence exists for a nonrandom X chromosome inactivation in the fra(X) syndrome in females.     

Phenotype in X chromosome rearrangements: pitfalls of X inactivation study

OBJECTIVE: X inactivation pattern in X chromosome rearrangements usually favor the less unbalanced cells. It is correlated to a normal phenotype, small size or infertility. We studied the correlation between phenotype and X inactivation ratio in patients with X structural anomalies. PATIENTS AND METHODS: During the 1999-2005 period, 12 X chromosome rearrangements, including three prenatal cases, were diagnosed in the Laboratoire de Cytogénétique of Strasbourg. In seven cases, X inactivation ratio could be assessed by late replication or methylation assay. RESULTS: In three of seven cases (del Xp, dup Xp, t(X;A)), X inactivation ratio and phenotype were consistent. The four other cases showed discrepancies between phenotype and X inactivation pattern: mental retardation and dysmorphism in a case of balanced X-autosome translocation, schizophrenia and autism in two cases of XX maleness and MLS syndrome (microphthalmia with linear skin defects) in a case of Xp(21.3-pter) deletion. CONCLUSION: Discrepancies between X inactivation ratio and phenotype are not rare and can be due to gene disruption, position effect, complex microrearrangements, variable pattern of X inactivation in different tissues or fortuitous association. In this context, the prognostic value of X inactivation study in prenatal diagnosis will be discussed.     

Spreading of X chromosome inactivation via a hierarchy of defined Polycomb stations

X chromosome inactivation (XCI) achieves dosage balance in mammals by repressing one of two X chromosomes in females. During XCI, the long noncoding Xist RNA and Polycomb proteins spread along the inactive X (Xi) to initiate chromosome-wide silencing. Although inactivation is known to commence at the X-inactivation center (Xic), how it propagates remains unknown. Here, we examine allele-specific binding of Polycomb repressive complex 2 (PRC2) and chromatin composition during XCI and generate a chromosome-wide profile of Xi and Xa (active X) at nucleosome-resolution. Initially, Polycomb proteins are localized to ∼150 strong sites along the X and concentrated predominantly within bivalent domains coinciding with CpG islands (“canonical sites”). As XCI proceeds, ∼4000 noncanonical sites are recruited, most of which are intergenic, nonbivalent, and lack CpG islands. Polycomb sites are depleted of LINE repeats but enriched for SINEs and simple repeats. Noncanonical sites cluster around the ∼150 strong sites, and their H3K27me3 levels reflect a graded concentration originating from strong sites. This suggests that PRC2 and H3K27 methylation spread along a gradient unique to XCI. We propose that XCI is governed by a hierarchy of defined Polycomb stations that spread H3K27 methylation in cis.X chromosome inactivation (XCI) provides an excellent model by which to study Polycomb regulation and the role of long noncoding RNAs (lncRNAs) in inducing facultative heterochromatin (Lyon 1999; Wutz and Gribnau 2007; Payer and Lee 2008; Lee 2011). XCI is controlled by the X-inactivation center (Xic), an X-linked region that controls the counting of X chromosomes, the mutually exclusive choice of Xa and Xi, and the recruitment and propagation of silencing complexes. The 17-kb Xist RNA initiates the silencing step as it accumulates on the X (Brockdorff et al. 1992; Brown et al. 1992; Clemson et al. 1996). Although recent studies have shown that Xist RNA directly recruits Polycomb repressive complex 2 (PRC2) to the Xi (Zhao et al. 2008) and that loading of the Xist-PRC2 complex occurs first at a YY1-bound nucleation center located within the Xic (Jeon and Lee 2011), how the silencing complexes spread throughout the X after this obligatory nucleation step remains a major unsolved problem.Because autosomes with ectopic Xic sequences are subject to long-range silencing (Wutz and Gribnau 2007; Payer and Lee 2008), it is thought that spreading elements cannot be unique to the X. One hypothesis suggests that repetitive elements of the LINE1 class facilitate spreading (Lyon 2000). However, this hypothesis has been difficult to test, as linking repeats to locus-specific function has been complicated by their repetitive nature. Some studies have provided correlative evidence (Bailey et al. 2000; Wang et al. 2006; Chow et al. 2010), whereas others find that species lacking active LINE1s nonetheless possess XCI (Cantrell et al. 2009). Other classes of repeats may be more enriched on the X (Chow et al. 2005). Matrix-associated proteins, such as HNRNPU (also known as SAF-A), have also been proposed to facilitate spreading (Helbig and Fackelmayer 2003; Hasegawa et al. 2010; Pullirsch et al. 2010), but a direct link has also not been demonstrated.In general, the identification of spreading elements has been thwarted by the lack of high-throughput approaches that distinguish Xi and Xa at sufficient resolution. Epigenomic studies have primarily focused on male cells (Bernstein et al. 2006; Boyer et al. 2006; Barski et al. 2007; Mikkelsen et al. 2007; Ku et al. 2008), though one recent ChIP-seq analysis with partial allele-specific coverage used female mouse embryonic stem (ES) cells but without addressing PRC2 binding. The reported 1.2-fold enrichment of H3K27me3 on Xi (Marks et al. 2009) is unexpectedly low and at odds with intense cytological H3K27me3 immunostaining (Plath et al. 2003; Silva et al. 2003)—likely caused by low-density polymorphisms between Xi and Xa. As a result, the quest for an Xi chromatin state map and spreading elements has remained unrealized.In principle, silencing complexes could initially load at the Xic and spread serially from nucleosome to nucleosome. Alternatively, they could spread outwardly via “way stations” located at defined sites along the X that would anchor and relay silencing complexes (Gartler and Riggs 1983). To test these models, we herein devise an allele-specific ChIP-seq strategy that enables the generation of chromosome-wide developmental profiles at unprecedented allelic resolution. We report a high-density Xi chromatin state map and identification of discrete Polycomb stations.     

Specific patterns of histone marks accompany X chromosome inactivation in a marsupial

The inactivation of one of the two X chromosomes in female placental mammals represents a remarkable example of epigenetic silencing. X inactivation occurs also in marsupial mammals, but is phenotypically different, being incomplete, tissue-specific and paternal. Paternal X inactivation occurs also in the extraembryonic cells of rodents, suggesting that imprinted X inactivation represents a simpler ancestral mechanism. This evolved into a complex and random process in placental mammals under the control of the XIST gene, involving notably variant and modified histones. Molecular mechanisms of X inactivation in marsupials are poorly known, but occur in the absence of an XIST homologue. We analysed the specific pattern of histone modifications using immunofluorescence on metaphasic chromosomes of a model kangaroo, the tammar wallaby. We found that all active marks are excluded from the inactive X in marsupials, as in placental mammals, so this represents a common feature of X inactivation throughout mammals. However, we were unable to demonstrate the accumulation of inactive histone marks, suggesting some fundamental differences in the molecular mechanism of X inactivation between marsupial and placental mammals. A better understanding of the epigenetic mechanisms underlying X inactivation in marsupials will provide important insights into the evolution of this complex process. Edda Koina and Julie Chaumeil contributed equally to this work.