Identification of novel imprinted transcripts in the Prader-Willi syndrome and Angelman syndrome deletion region: further evidence for regional imprinting control

Expanding deep phenotypic spectrum associated with atypical pathogenic structural variations overlapping 15q11-q13 imprinting region

BACKGROUND

The 15q11-q13 region is a genetic locus with genes subject to genomic imprinting, significantly influencing neurodevelopment. Genomic imprinting is an epigenetic phenomenon that causes differential gene expression based on the parent of origin. In most diploid organisms, gene expression typically involves an equal contribution from both maternal and paternal alleles, shaping the phenotype. Nevertheless, in mammals, including humans, mice, and marsupials, the functional equivalence of parental alleles is not universally maintained. Notably, during male and female gametogenesis, parental alleles may undergo differential marking or imprinting, thereby modifying gene expression without altering the underlying DNA sequence. Neurodevelopmental disorders, such as Prader-Willi syndrome (PWS) (resulting from the absence of paternally expressed genes in this region), Angelman syndrome (AS) (associated with the absence of the maternally expressed UBE3A gene), and 15q11-q13 duplication syndrome (resulting from the two common forms of duplications-either an extra isodicentric 15 chromosome or an interstitial 15 duplication), are the outcomes of genetic variations in this imprinting region.

METHODS

Conducted a genomic study to identify the frequency of pathogenic variants impacting the 15q11-q13 region in an ethnically homogenous population from Bangladesh. Screened all known disorders from the DECIPHER database and identified variant enrichment within this cohort. Using the Horizon analysis platform, performed enrichment analysis, requiring at least >60% overlap between a copy number variation and a disorder breakpoint. Deep clinical phenotyping was carried out through multiple examination sessions to evaluate a range of clinical symptoms.

RESULTS

This study included eight individuals with clinically suspected PWS/AS, all previously confirmed through chromosomal microarray analysis, which revealed chromosomal breakpoints within the 15q11-q13 region. Among this cohort, six cases (75%) exhibited variable lengths of deletions, whereas two cases (25%) showed duplications. These included one type 2 duplication, one larger atypical duplication, one shorter type 2 deletion, one larger type 1 deletion, and four cases with atypical deletions. Furthermore, thorough clinical assessments led to the diagnosis of four PWS patients, two AS patients, and two individuals with 15q11-q13 duplication syndrome.

CONCLUSION

Our deep phenotypic observations identified a spectrum of clinical features that overlap and are unique to PWS, AS, and Dup15q syndromes. Our findings establish genotype-phenotype correlation for patients impacted by variable structural variations within the 15q11-q13 region.

Embryo cryopreservation leads to sex-specific DNA methylation perturbations in both human and mouse placentas

In vitro fertilization (IVF) is associated with DNA methylation abnormalities and a higher incidence of adverse pregnancy outcomes. However, which exposure(s), among the many IVF interventions, contributes to these outcomes remains unknown. Frozen embryo transfer (ET) is increasingly utilized as an alternative to fresh ET, but reports suggest a higher incidence of pre-eclampsia and large for gestational age infants. This study examines DNA methylation in human placentas using the 850K Infinium MethylationEPIC BeadChip array obtained after 65 programmed frozen ET cycles, 82 fresh ET cycles and 45 unassisted conceptions. Nine patients provided placentas following frozen and fresh ET from consecutive pregnancies for a paired subgroup analysis. In parallel, eight mouse placentas from fresh and frozen ET were analyzed using the Infinium Mouse Methylation BeadChip array. Human and mouse placentas were significantly hypermethylated after frozen ET compared with fresh. Paired analysis showed similar trends. Sex-specific analysis revealed that these changes were driven by male placentas in humans and mice. Frozen and fresh ET placentas were significantly different from controls, with frozen samples hypermethylated compared with controls driven by males and fresh samples being hypomethylated compared with controls, driven by females. Sexually dimorphic epigenetic changes could indicate differential susceptibility to IVF-associated perturbations, which highlights the importance of sex-specific evaluation of adverse outcomes. Similarities between changes in mice and humans underscore the suitability of the mouse model in evaluating how IVF impacts the epigenetic landscape, which is valuable given limited access to human tissue and the ability to isolate specific interventions in mice.

Prader-Willi Syndrome: Molecular Mechanism and Epigenetic Therapy

Prader-Willi syndrome (PWS) is an imprinted neurodevelopmental disease characterized by cognitive impairments, developmental delay, hyperphagia, obesity, and sleep abnormalities. It is caused by a lack of expression of the paternally active genes in the PWS imprinting center on chromosome 15 (15q11.2-q13). Owing to the imprinted gene regulation, the same genes in the maternal chromosome, 15q11-q13, are intact in structure but repressed at the transcriptional level because of the epigenetic mechanism. The specific molecular defect underlying PWS provides an opportunity to explore epigenetic therapy to reactivate the expression of repressed PWS genes inherited from the maternal chromosome. The purpose of this review is to summarize the main advances in the molecular study of PWS and discuss current and future perspectives on the development of CRISPR/Cas9- mediated epigenome editing in the epigenetic therapy of PWS. Twelve studies on the molecular mechanism or epigenetic therapy of PWS were included in the review. Although our understanding of the molecular basis of PWS has changed fundamentally, there has been a little progress in the epigenetic therapy of PWS that targets its underlying genetic defects.

Hypogonadism in Patients with Prader Willi Syndrome: A Narrative Review

Prader-Willi syndrome (PWS) is a multisystemic complex genetic disorder related to the lack of a functional paternal copy of chromosome 15q11-q13. Several clinical manifestations are reported, such as short stature, cognitive and behavioral disability, temperature instability, hypotonia, hypersomnia, hyperphagia, and multiple endocrine abnormalities, including growth hormone deficiency and hypogonadism. The hypogonadism in PWS is due to central and peripheral mechanisms involving the hypothalamus-pituitary-gonadal axis. The early diagnosis and management of hypogonadism in PWS are both important for physicians in order to reach a better quality of life for these patients. The aim of this study is to summarize and investigate causes and possible therapies for hypogonadism in PWS. Additional studies are further needed to clarify the role of different genes related to hypogonadism and to establish a common and evidence-based therapy.

Neuronal differentiation defects in induced pluripotent stem cells derived from a Prader-Willi syndrome patient

Prader-Willi syndrome (PWS) is a neurodevelopmental disorder caused by a lack of expression of paternally inherited genes located in the15q11.2-q13 chromosome region. An obstacle in the study of human neurological diseases is the inaccessibility of brain material. Generation of induced pluripotent stem cells (iPSC cells) from patients can partially overcome this problem. We characterized the cellular differentiation potential of iPS cells derived from a PWS patient with a paternal 15q11-q13 deletion. A gene tip transcriptome array revealed very low expression of genes in the 15q11.2-q13 chromosome region, including SNRPN, SNORD64, SNORD108, SNORD109, and SNORD116, in iPS cells of this patient compared to that in control iPS cells. Methylation-specific PCR analysis of the SNRPN gene locus indicated that the PWS region of the paternal chromosome was deleted or methylated in iPS cells from the patient. Both the control and patient-derived iPS cells were positive for Oct3/4, a key marker of pluripotent cells. After 11 days of differentiation into neural stem cells (NSCs), Oct3/4 expression in both types of iPS cells was decreased. The NSC markers Pax6, Sox1, and Nestin were induced in NSCs derived from control iPS cells, whereas induction of these NSC markers was not apparent in NSCs derived from iPS cells from the patient. After 7 days of differentiation into neurons, neuronal cells derived from control iPS cells were positive for βIII-tubulin and MAP2. However, neuronal cells derived from patient iPS cells only included a few immunopositive neurons. The mRNA expression levels of the neuronal marker βIII-tubulin were increased in neuronal cells derived from control iPS cells, while the expression levels of βIII-tubulin in neuronal cells derived from patient iPS cells were similar to those of NSCs. These results indicate that iPS cells derived from a PWS patient exhibited neuronal differentiation defects.

Genotype-Phenotype Relationships and Endocrine Findings in Prader-Willi Syndrome

Prader-Willi syndrome (PWS) is a complex imprinting disorder related to genomic errors that inactivate paternally-inherited genes on chromosome 15q11-q13 with severe implications on endocrine, cognitive and neurologic systems, metabolism, and behavior. The absence of expression of one or more genes at the PWS critical region contributes to different phenotypes. There are three molecular mechanisms of occurrence: paternal deletion of the 15q11-q13 region; maternal uniparental disomy 15; or imprinting defects. Although there is a clinical diagnostic consensus criteria, DNA methylation status must be confirmed through genetic testing. The endocrine system can be the most affected in PWS, and growth hormone replacement therapy provides improvement in growth, body composition, and behavioral and physical attributes. A key feature of the syndrome is the hypothalamic dysfunction that may be the basis of several endocrine symptoms. Clinical and molecular complexity in PWS enhances the importance of genetic diagnosis in therapeutic definition and genetic counseling. So far, no single gene mutation has been described to contribute to this genetic disorder or related to any exclusive symptoms. Here we proposed to review individually disrupted genes within the PWS critical region and their reported clinical phenotypes related to the syndrome. While genes such as MKRN3, MAGEL2, NDN, or SNORD115 do not address the full spectrum of PWS symptoms and are less likely to have causal implications in PWS major clinical signs, SNORD116 has emerged as a critical, and possibly, a determinant candidate in PWS, in the recent years. Besides that, the understanding of the biology of the PWS SNORD genes is fairly low at the present. These non-coding RNAs exhibit all the hallmarks of RNA methylation guides and can be incorporated into ribonucleoprotein complexes with possible hypothalamic and endocrine functions. Also, DNA conservation between SNORD sequences across placental mammals strongly suggests that they have a functional role as RNA entities on an evolutionary basis. The broad clinical spectrum observed in PWS and the absence of a clear genotype-phenotype specific correlation imply that the numerous genes involved in the syndrome have an additive deleterious effect on different phenotypes when deficiently expressed.

Genetics of Prader-Willi syndrome and Prader-Will-Like syndrome

The Prader-Willi syndrome (PWS) is a human imprinting disorder resulting from genomic alterations that inactivate imprinted, paternally expressed genes in human chromosome region 15q11-q13. This genetic condition appears to be a contiguous gene syndrome caused by the loss of at least 2 of a number of genes expressed exclusively from the paternal allele, including SNRPN, MKRN3, MAGEL2, NDN and several snoRNAs, but it is not yet well known which specific genes in this region are associated with this syndrome. Prader-Will-Like syndrome (PWLS) share features of the PWS phenotype and the gene functions disrupted in PWLS are likely to lie in genetic pathways that are important for the development of PWS phenotype. However, the genetic basis of these rare disorders differs and the absence of a correct diagnosis may worsen the prognosis of these individuals due to the endocrine-metabolic malfunctioning associated with the PWS. Therefore, clinicians face a challenge in determining when to request the specific molecular test used to identify patients with classical PWS because the signs and symptoms of PWS are common to other syndromes such as PWLS. This review aims to provide an overview of current knowledge relating to the genetics of PWS and PWLS, with an emphasis on identification of patients that may benefit from further investigation and genetic screening.

Differential regulation of non-protein coding RNAs from Prader-Willi Syndrome locus

Prader-Willi Syndrome (PWS) is a neurogenetic disorder caused by the deletion of imprinted genes on the paternally inherited human chromosome 15q11-q13. This locus harbours a long non-protein-coding RNA (U-UBE3A-ATS) that contains six intron-encoded snoRNAs, including the SNORD116 and SNORD115 repetitive clusters. The 3′-region of U-UBE3A-ATS is transcribed in the cis-antisense direction to the ubiquitin-protein ligase E3A (UBE3A) gene. Deletion of the SNORD116 region causes key characteristics of PWS. There are few indications that SNORD115 might regulate serotonin receptor (5HT2C) pre-mRNA processing. Here we performed quantitative real-time expression analyses of RNAs from the PWS locus across 20 human tissues and combined it with deep-sequencing data derived from Cap Analysis of Gene Expression (CAGE-seq) libraries. We found that the expression profiles of SNORD64, SNORD107, SNORD108 and SNORD116 are similar across analyzed tissues and correlate well with SNORD116 embedded U-UBE3A-ATS exons (IPW116). Notable differences in expressions between the aforementioned RNAs and SNORD115 together with the host IPW115 and UBE3A cis-antisense exons were observed. CAGE-seq analysis revealed the presence of potential transcriptional start sites originated from the U-UBE3A-ATS spanning region. Our findings indicate novel aspects for the expression regulation in the PWS locus.

Genome-wide and parental allele-specific analysis of CTCF and cohesin DNA binding in mouse brain reveals a tissue-specific binding pattern and an association with imprinted differentially methylated regions

DNA binding factors are essential for regulating gene expression. CTCF and cohesin are DNA binding factors with central roles in chromatin organization and gene expression. We determined the sites of CTCF and cohesin binding to DNA in mouse brain, genome wide and in an allele-specific manner with high read-depth ChIP-seq. By comparing our results with existing data for mouse liver and embryonic stem (ES) cells, we investigated the tissue specificity of CTCF binding sites. ES cells have fewer unique CTCF binding sites occupied than liver and brain, consistent with a ground-state pattern of CTCF binding that is elaborated during differentiation. CTCF binding sites without the canonical consensus motif were highly tissue specific. In brain, a third of CTCF and cohesin binding sites coincide, consistent with the potential for many interactions between cohesin and CTCF but also many instances of independent action. In the context of genomic imprinting, CTCF and/or cohesin bind to a majority but not all differentially methylated regions, with preferential binding to the unmethylated parental allele. Whether the parental allele-specific methylation was established in the parental germlines or post-fertilization in the embryo is not a determinant in CTCF or cohesin binding. These findings link CTCF and cohesin with the control regions of a subset of imprinted genes, supporting the notion that imprinting control is mechanistically diverse.

Small RNA-induced transcriptional gene regulation in mammals mechanisms, therapeutic applications, and scope within the genome

Argonaute-bound small RNAs, derived from RNA interference and related pathways, are well-known effectors of posttranscriptional gene silencing (PTGS). Yet, these complexes also play an important role in affecting gene expression at the transcriptional level, either by transcriptional gene silencing (TGS) or activation (TGA). Our current understanding of how small RNAs are able to both activate and suppress transcription is unclear. In this review, we briefly outline the biogenesis of small RNAs and explore the mechanisms behind the various phenomena attributed to AGO-bound small RNA-mediated transcriptional regulation. The therapeutic potential of TGS and TGA is examined, emphasizing the distinct advantages over PTGS approaches with examples of application to cancer and diseases associated with viruses, aberrant splicing, and dysregulated heterochromatin. Finally, the influence of promoter architecture on gene susceptibility to transcriptional regulation is discussed in the light of how this impacts the scope of small RNA-induced transcriptional regulation within the genome.

Insights into synaptic function from mouse models of human cognitive disorders

Modern approaches to the investigation of the molecular mechanisms underlying human cognitive disease often include multidisciplinary examination of animal models engineered with specific mutations that spatially and temporally restrict expression of a gene of interest. This approach not only makes possible the development of animal models that demonstrate phenotypic similarities to their respective human disorders, but has also allowed for significant progress towards understanding the processes that mediate synaptic function and memory formation in the nondiseased state. Examples of successful mouse models where genetic manipulation of the mouse resulted in recapitulation of the symptomatology of the human disorder and was used to significantly expand our understanding of the molecular mechanisms underlying normal synaptic plasticity and memory formation are discussed in this article. These studies have broadened our knowledge of several signal transduction cascades that function throughout life to mediate synaptic physiology. Defining these events is key for developing therapies to address disorders of cognitive ability.

Heterochromatin dysregulation in human diseases

Heterochromatin is a repressive chromatin state that is characterized by densely packed DNA and low transcriptional activity. Heterochromatin-induced gene silencing is important for mediating developmental transitions, and in addition, it has more global functions in ensuring chromosome segregation and genomic integrity. Here we discuss how altered heterochromatic states can impair normal gene expression patterns, leading to the development of different diseases. Over the last years, therapeutic strategies that aim toward resetting the epigenetic state of dysregulated genes have been tested. However, due to the complexity of epigenetic gene regulation, the "first-generation drugs" that function globally by inhibiting epigenetic machineries might also introduce severe side effects. Thus detailed understanding of how repressive chromatin states are established and maintained at specific loci will be fundamental for the development of more selective epigenetic treatment strategies in the future.

Obsessive-compulsive disorder and related disorders: a comprehensive survey

Our aim was to present a comprehensive, updated survey on obsessive-compulsive disorder (OCD) and obsessive-compulsive related disorders (OCRDs) and their clinical management via literature review, critical analysis and synthesis. Information on OCD and OCRD current nosography, clinical phenomenology and etiology, may lead to a better comprehension of their management. Clinicians should become familiar with the broad spectrum of OCD disorders, since it is a pivotal issue in current clinical psychiatry.

Genomic analysis of the chromosome 15q11-q13 Prader-Willi syndrome region and characterization of transcripts for GOLGA8E and WHCD1L1 from the proximal breakpoint region

BACKGROUND

Prader-Willi syndrome (PWS) is a neurobehavioral disorder characterized by neonatal hypotonia, childhood obesity, dysmorphic features, hypogonadism, mental retardation, and behavioral problems. Although PWS is most often caused by a paternal interstitial deletion of a 6-Mb region of chromosome 15q11-q13, the identity of the exact protein coding or noncoding RNAs whose deficiency produces the PWS phenotype is uncertain. There are also reports describing a PWS-like phenotype in a subset of patients with full mutations in the FMR1 (fragile X mental retardation 1) gene. Taking advantage of the human genome sequence, we have performed extensive sequence analysis and molecular studies for the PWS candidate region.

RESULTS

We have characterized transcripts for the first time for two UCSC Genome Browser predicted protein-coding genes, GOLGA8E (golgin subfamily a, 8E) and WHDC1L1 (WAS protein homology region containing 1-like 1) and have further characterized two previously reported genes, CYF1P1 and NIPA2; all four genes are in the region close to the proximal/centromeric deletion breakpoint (BP1). GOLGA8E belongs to the golgin subfamily of coiled-coil proteins associated with the Golgi apparatus. Six out of 16 golgin subfamily proteins in the human genome have been mapped in the chromosome 15q11-q13 and 15q24-q26 regions. We have also identified more than 38 copies of GOLGA8E-like sequence in the 15q11-q14 and 15q23-q26 regions which supports the presence of a GOLGA8E-associated low copy repeat (LCR). Analysis of the 15q11-q13 region by PFGE also revealed a polymorphic region between BP1 and BP2. WHDC1L1 is a novel gene with similarity to mouse Whdc1 (WAS protein homology region 2 domain containing 1) and human JMY protein (junction-mediating and regulatory protein). Expression analysis of cultured human cells and brain tissues from PWS patients indicates that CYFIP1 and NIPA2 are biallelically expressed. However, we were not able to determine the allele-specific expression pattern for GOLGA8E and WHDC1L1 because these two genes have highly related sequences that might also be expressed.

CONCLUSION

We have presented an updated version of a sequence-based physical map for a complex chromosomal region, and we raise the possibility of polymorphism in the genomic orientation of the BP1 to BP2 region. The identification of two new proteins GOLGA8E and WHDC1L1 encoded by genes in the 15q11-q13 region may extend our understanding of the molecular basis of PWS. In terms of copy number variation and gene organization, this is one of the most polymorphic regions of the human genome, and perhaps the single most polymorphic region of this type.

From microscopes to microarrays: dissecting recurrent chromosomal rearrangements

Submicroscopic chromosomal rearrangements that lead to copy-number changes have been shown to underlie distinctive and recognizable clinical phenotypes. The sensitivity to detect copy-number variation has escalated with the advent of array comparative genomic hybridization (CGH), including BAC and oligonucleotide-based platforms. Coupled with improved assemblies and annotation of genome sequence data, these technologies are facilitating the identification of new syndromes that are associated with submicroscopic genomic changes. Their characterization reveals the role of genome architecture in the aetiology of many clinical disorders. We review a group of genomic disorders that are mediated by segmental duplications, emphasizing the impact that high-throughput detection methods and the availability of the human genome sequence have had on their dissection and diagnosis.

Analysis of candidate imprinted genes in PWS subjects with atypical genetics: a possible inactivating mutation in the SNURF/SNRPN minimal promoter

Prader-Willi syndrome (PWS) is a neurodevelopmental disorder associated with abnormalities of chromosome 15q11q13. The majority of cases result either from a deletion approximately 4 Mb in size, affecting chromosome 15 of paternal origin or from UPD(15)mat; these account for approximately 70 and approximately 20-25% of PWS cases, respectively. In the remaining 3-5% of PWS cases where neither the deletion nor UPD is detectable, PWS is thought to be caused either by a defect in the imprinting centre resulting in a failure to reset the paternally inherited chromosome 15 derived from the paternal grandmother or, very occasionally, from a balanced translocation involving a breakpoint in 15q11q13. Nine probands with a firm clinical diagnosis of PWS but who had neither a typical deletion in the PWS region nor UPD(15)mat were investigated for inactivating mutations in 11 genes located in the PWS region, including SNURF and SNRPN, which are associated with the imprinting centre. Other genes studied for mutations included MKRN3, NDN, IPW, HBII-85, HBII-13, HBII-436, HBII-438a, PAR1 and PAR5. A possibly inactivating mutation in the SNRPN minimal promoter region was identified. No other inactivating mutations were found in the remainder of our panel of PWS subjects with atypical genetics. Expression levels of several of the candidate genes for PWS were also investigated in this series of probands. The results indicate that PWS may result from a stochastic partial inactivation of important genes.

Microarray analysis of gene/transcript expression in Angelman syndrome: deletion versus UPD

Angelman syndrome (AS) is a neurodevelopmental disorder due to a functional deficit, usually a deletion, of the UBE3A gene located in the 15q11-q13 chromosome region. We report the first microarray analysis of gene expression in AS using a custom cDNA microarray to compare expression patterns from lymphoblastoid cell lines from control males and AS subjects with a 15q deletion or uniparental paternal disomy 15. Expression patterns of genes known to be biallelically expressed or paternally or maternally expressed were consistent with expectations. We detected paternal or maternal allelic bias in the expression of several genes and transcripts (e.g., GABRA5, GABRB3, WI-14946). Additionally, mechanisms controlling paternal allele expression appear to be faithfully replicated in each paternal chromosome in individuals with paternal disomy. Our results indicate that interconnected mechanisms can produce subtle and unexpected changes in gene expression that may help explain the phenotypic differences observed among the genetic subtypes of AS.

Imprinting analysis of 10 genes and/or transcripts in a 1.5-Mb MEST-flanking region at human chromosome 7q32

MEST is one of the imprinted genes in human. With the assistance of our integration map and the complete sequence in the registry, we mapped a total of 16 genes/transcripts at the 1.5-Mb MEST-flanking region at 7q32. This region has been suggested to form an imprinted gene cluster, because MEST and its three flanking genes/transcripts (MESTIT1, CPA4, and COPG2IT1) were reported to be imprinted, although two (TSGA14 and COPG2) were shown to escape imprinting. In this study, 10 other genes/transcripts were examined for their imprinting status in human fetal tissues. The results indicated that 8 genes/transcripts (NRF1, UBE2H, HSPC216, KIAA0265, FLJ14803, CPA2, CPA1, and DKFZp667F0312) were expressed biallelically. The imprinting status of two (TSGA13 and CPA5) was not conclusive, because of their weak and/or tissue-specific expression and inconstant results. These findings provided evidence that only 4 of the 16 genes/transcripts located to the region show monoallelic expression, while others are not involved in imprinting. Therefore, it is less likely that the MEST-flanking 7q32 region forms a large imprinted domain.

Microarray analysis of gene/transcript expression in Prader-Willi syndrome: deletion versus UPD

BACKGROUND

Prader-Willi syndrome (PWS), the most common genetic cause of marked obesity, is caused by genomic imprinting and loss of expression of paternal genes in the 15q11-q13 region. There is a paucity of data examining simultaneous gene expression in this syndrome.

METHODS

We generated cDNA microarrays representing 73 non-redundant genes/transcripts from the 15q11-q13 region, the majority within the PWS critical region and others distally on chromosome 15. We used our custom microarrays to compare gene expression from actively growing lymphoblastoid cell lines established from nine young adult males (six with PWS (three with deletion and three with UPD) and three controls).

RESULTS

There was no evidence of expression of genes previously identified as paternally expressed in the PWS cell lines with either deletion or UPD. We detected no difference in expression of genes with known biallelic expression located outside the 15q11-q13 region in all cell lines studied. There was no difference in expression levels of biallelically expressed genes (for example, OCA2) from within 15q11-q13 when comparing UPD cell lines with controls. However, two genes previously identified as maternally expressed (UBE3A and ATP10C) showed a significant increase in expression in UPD cell lines compared with control and PWS deletion subjects. Several genes/transcripts (for example, GABRA5, GABRB3) had increased expression in UPD cell lines compared with deletion, but less than controls indicating paternal bias.

CONCLUSIONS

Our results suggest that differences in expression of candidate genes may contribute to phenotypic differences between PWS subjects with deletion or UPD and warrant further investigations.

Association analysis of chromosome 15 gabaa receptor subunit genes in autistic disorder

Gamma-aminobutyric acid (GABA) is the major inhibitory neurotransmitter in the brain, acting via the GABAA receptors. The GABAA receptors are comprised of several different homologous subunits, forming a group of receptors that are both structurally and functionally diverse. Three of the GABAA receptor subunit genes (GABRB3, GABRA5 and GABRG3) form a cluster on chromosome 15q11-q13, in a region that has been genetically associated with autistic disorder (AutD). Based on these data, we examined 16 single nucleotide polymorphisms (SNPs) located within GABRB3, GABRA5 and GABRG3 for linkage disequilibrium (LD) in 226 AutD families (AutD patients and parents). Genotyping was performed using either OLA (oligonucleotide ligation assay), or SSCP (single strand conformation polymorphism) followed by DNA sequencing. We tested for LD using the Pedigree Disequilibrium Test (PDT). PDT results gave significant evidence that AutD is associated with two SNPs located within the GABRG3 gene (exon5_539T/C, p=0.02 and intron5_687T/C, p=0.03), suggesting that the GABRG3 gene or a gene nearby contributes to genetic risk in AutD.

The gene TSGA14, adjacent to the imprinted gene MEST, escapes genomic imprinting

We identified the gene TSGA14, encoding the testis-specific protein A14 and located 50 kb proximal to the imprinted gene MEST in a head-to-head orientation. TSGA14 has at least two transcripts: a long-type (l-type) transcript, and a short-type (s-type) transcript. Since the COPG2IT1 gene in the vicinity of MEST has been reported to be imprinted, we presumed that TSGA14 might also be imprinted. We thus analyzed the imprinting status of TSGA14 l-type and s-type transcripts in various fetal tissues. TSGA14 l-type transcript, which consists of 11 exons and encodes a l-type isoform with 373 amino acids, is biallelically expressed in the fetal tissues including the testis. TSGA14 s-type transcript, which consists of three exons and encodes a s-type isoform with 54 amino acids, also showed biallelic expression in the fetal brain and liver. No allele-specific methylation in the TSGA14 CpG island was detected. The fact that COPG2 and TSGA14, both neighbors of MEST, escape genomic imprinting suggests that the 7q32 imprinted region may be small and not similar to other imprinted domains, such as those at 15q11-13 and 11p15.5.

The MAGE proteins: emerging roles in cell cycle progression, apoptosis, and neurogenetic disease

Since the identification of the first MAGE gene in 1991, the MAGE family has expanded dramatically, and over 25 MAGE genes have now been identified in humans. The focus of studies on the MAGE proteins has been their potential for cancer immunotherapy, as a result of the finding that peptides derived from MAGE gene products are bound by major histocompatibility complexes and presented on the cell surface of cancer cells. However, the normal physiological role of MAGE proteins has remained a mystery. Recent studies are now beginning to provide insights into MAGE gene function. Necdin acts as a cell cycle regulatory protein and plays a key role in the pathogenesis of Prader-Willi syndrome, a neurogenetic disorder. MAGE-D1, identified as a binding partner for the p75 neurotrophin receptor, the apoptosis inhibitory protein XIAP, and Dlx/MSX homeodomain proteins, blocks cell cycle progression and enhances apoptosis. This review provides an overview of the human MAGE genes and proteins, summarizes recent findings on their cellular roles, and provides a baseline for future studies on this intriguing gene family.

Genome organization, function, and imprinting in Prader-Willi and Angelman syndromes

The chromosomal region, 15q11-q13, involved in Prader-Willi and Angelman syndromes (PWS and AS) represents a paradigm for understanding the relationships between genome structure, epigenetics, evolution, and function. The PWS/AS region is conserved in organization and function with the homologous mouse chromosome 7C region. However, the primate 4 Mb PWS/AS region is bounded by duplicons derived from an ancestral HERC2 gene and other sequences that may predispose to chromosome rearrangements. Within a 2 Mb imprinted domain, gene function depends on parental origin. Genetic evidence suggests that PWS arises from functional loss of several paternally expressed genes, including those that function as RNAs, and that AS results from loss of maternal UBE3A brain-specific expression. Imprinted expression is coordinately controlled in cis by an imprinting center (IC), a genetic element functional in germline and/or early postzygotic development that regulates the establishment of parental specific allelic differences in replication timing, DNA methylation, and chromatin structure.

A necdin/MAGE-like gene in the chromosome 15 autism susceptibility region: expression, imprinting, and mapping of the human and mouse orthologues

BACKGROUND

Proximal chromosome 15q is implicated in neurodevelopmental disorders including Prader-Willi and Angelman syndromes, autistic disorder and developmental abnormalities resulting from chromosomal deletions or duplications. A subset of genes in this region are subject to genomic imprinting, the expression of the gene from only one parental allele.

RESULTS

We have now identified the NDNL2 (also known as MAGE-G) gene within the 15q autistic disorder susceptibility region and have mapped its murine homolog to the region of conserved synteny near necdin (Ndn) on mouse Chr 7. NDNL2/MAGE-G is a member of a large gene family that includes the X-linked MAGE cluster, MAGED1 (NRAGE), MAGEL2 and NDN, where the latter two genes are implicated in Prader-Willi syndrome. We have now determined that NDNL2/Ndnl2 is widely expressed in mouse and human fetal and adult tissues, and that it is apparently not subject to genomic imprinting by the PWS/AS Imprinting Center.

CONCLUSION

Although NDNL2/MAGE-G in the broadly defined chromosome 15 autistic disorder susceptibility region, it is not likely to be pathogenic based on its wide expression pattern and lack of imprinted expression.

[Rectal self-mutilation, rectal bleeding and Prader-Willi syndrome]

Prader-Willi syndrome is a genetic disorder characterized by infantile hypotonia, obesity, hypogonadism and mental retardation. Individuals with Prader-Willi syndrome manifest a severe skin picking behavior, including rectal picking.

CASE REPORT

We report the case of a girl (12 years old) with this syndrome in whom rectal picking resulted in rectal bleeding and solitary rectal ulcer.

CONCLUSION

Caregivers of children with Prader-Willi syndrome should be aware of a potential rectal picking behavior, which results in significant bleeding. Early recognition of such a behavior helps to avoid misdiagnosis.

Imprinted genes and mental dysfunction

There is a rapidly accumulating body of evidence from family, adoption and twin studies suggestive of a genetic component to many common mental disorders. In some cases, the transmission of abnormalities has been shown to be dependent upon the sex of the parent from whom they are inherited. Such 'parent-of-origin effects' may be explained by a number of genetic mechanisms, one of which is 'genomic imprinting'. In imprinted genes one allele is silenced according to its parental origin. This in turn means that imprinted traits are passed down the maternal or paternal line, in contrast to the more frequent Mendelian mode of inheritance that is indifferent to the parental origin of the allele. In the present review, we survey the evidence for the influence of imprinted genes on a number of mental disorders, ranging from explicit imprinted conditions, where in some cases abnormalities have been mapped to particular gene candidates, to examples where the evidence for parent-of-origin effects is less strong. We also consider, briefly, the wider implications of imprinted effects on mental dysfunction, in particular with respect to evolutionary pressures on mammalian brain development and function.

Cloning of dexamethasone-induced transcript: a novel glucocorticoid-induced gene that is upregulated in emphysema

To identify changes in gene expression associated with emphysema, we used differential display to compare RNA extracted from emphysematous lungs with that of unused donor tissues taken at the time of transplant. A differentially expressed sequence was identified corresponding to the 3' end of a novel human complementary DNA (cDNA) of unknown function. The human and mouse cDNA sequences were completed by 5' rapid amplification of cDNA ends. We have named it DEXI for dexamethasone-induced transcript. DEXI messenger RNA (mRNA) was upregulated 147% in emphysematous tissue compared with donor tissue. DEXI mRNA was also upregulated 230% by dexamethasone treatment of A549. The increase in expression of DEXI found in emphysema patients' tissues may be owing to their known treatment with corticosteroids. The human DEXI gene is intronless and the predicted open reading frame encodes a 95-residue acidic protein. Database searches revealed the presence of homologues only in mammals, and a human pseudogene. The protein has a predicted central transmembrane domain and a carboxy-terminal leucine zipper. The human mRNA has a single 1.3-kb transcript. We suggest that the increased expression of DEXI in emphysema may either be relevant to disease progression or be indicative of glucocorticoid responsiveness in treated patients.

Analysis of DEXI/Dexi refines the organization of the mouse 7C and human 15q11-->q13 imprinting clusters

Identification of imprinted genes in the Prader-Willi/Angelman syndrome deletion region is complicated by the presence of large flanking repeats. While inactive copies of DEXI are located within the repeats, we have now localized the active DEXI gene to 15q11-->q13 outside the PWS/AS deletion and Dexi to mouse chromosome 16, suggesting complex evolution of this genomic region in both species.

The role of genomic imprinting in human developmental disorders: lessons from Prader-Willi syndrome

Normal human development involves a delicate interplay of gene expression in specific tissues at narrow windows of time. Temporally and spatially regulated gene expression is controlled both by gene-specific factors and chromatin-specific factors. Genomic imprinting is the expression of specific genes primarily from only one allele at particular times during development, and is one mechanism implicated in the intricate control of gene expression. Two human genetic disorders, Prader-Willi syndrome (PWS, MIM 176270) and Angelman syndrome (AS, MIM 105830), result from rearrangements of chromosome 15q11-q13, an imprinted region of the human genome. Despite their rarity, disorders such as PWS and AS can give focused insight into the role of genomic imprinting and imprinted genes in human development.

The imprinted gene and parent-of-origin effect database

The database of imprinted genes and parent-of-origin effects in animals (http://www.otago.ac.nz/IGC ) is a collation of genes and phenotypes for which parent-of-origin effects have been reported. The database currently includes over 220 entries, which describe over 40 imprinted genes in human, mouse and other animals. In addition a wide variety of other parent-of-origin effects, such as transmission of human disease phenotypes, transmission of QTLs, uniparental disomies and interspecies crosses are recorded. Data are accessed through a search engine and references are hyperlinked to PubMed.

Mechanisms of genomic imprinting

Imprinted genes represent a curious defiance of normal Mendelian genetics. Mammals inherit two complete sets of chromosomes, one from the mother and one from the father, and most autosomal genes will be expressed from both the maternal and the paternal alleles. Imprinted genes, however, are expressed from only one chromosome, in a parent-of-origin-dependent manner. Because silent and active promoters are present in a single nucleus, the differences in activity cannot be explained by transcription-factor abundance. Thus, transcription of imprinted genes represents a clear situation in which epigenetic mechanisms restrict gene expression and, therefore, offers a model for understanding the role of DNA modifications and chromatin structure in maintaining appropriate patterns of expression. Furthermore, because of their parent-of-origin-restricted expression, phenotypes determined by imprinted genes are susceptible not only to genetic alterations in the genes but also to disruptions in the epigenetic programs controlling regulation. Imprinted genes are often associated with human diseases, including disorders affecting cell growth, development, and behavior.

The novel gene, gamma2-COP (COPG2), in the 7q32 imprinted domain escapes genomic imprinting

The gene MEST (or PEG1) on chromosome 7q32 is paternally expressed in human fetal tissues as a result of genomic imprinting. Since some imprinted genes are clustered, we speculated that an imprinted gene cluster might exist at 7q32. We have sought to isolate additional human genes close to MEST and to characterize their allelic expression patterns. Here, we report the biallelic expression of the gene, gamma2-COP (coatomer protein complex, subunit gamma 2, HUGO-approved symbol COPG2), and monoallelic expression of the transcript, CIT1, which is located in intron 20 of gamma2-COP. Recently, gamma2-COP was reported to be a novel imprinted gene that overlaps the 3'-untranslated region (3'-UTR) of MEST in a tail-to-tail orientation. However, our results revealed biallelic expression in all fetal tissues and adult blood lymphocytes. On the other hand, CIT1 was an antisense transcript of gamma2-COP intron 20 and was expressed from the paternal allele in all fetal tissues examined. Adult blood lymphocytes showed biallelic expression. We identified additional MEST 3'-UTR sequence, which overlaps the last four exons and introns of gamma2-COP. This additional MEST 3'-UTR may complicate analysis of gamma2-COP imprinting. Our data indicate that the region containing MEST at 7q32 is an imprinted domain, but gamma2-COP adjacent to MEST escapes genomic imprinting.

Prader-Willi Syndrome: Clinical and Genetic Findings

Since the initial medical description by Prader, Labhart and Willi in 1956 of individuals with overlapping features, the Prader-Willi syndrome has become recognized as a classical but sporadic genetic syndrome. Prader-Willi syndrome is the most common genetic cause of life-threatening obesity in humans. It is estimated that there are 350,000-400,000 people with this syndrome worldwide. Prader-Willi Syndrome Association USA knows of more than 3,400 persons with Prader-Willi syndrome in the USA out of an approximate 17,000-22,000. Prader-Willi syndrome with an incidence of 1 in 10,000 to 25,000 individuals and Angelman syndrome, an entirely different clinical condition, were the first examples in humans of genetic imprinting. Genetic imprinting or the differential expression of genetic information depending on the parent of origin plays a significant role in other conditions including malignancies.