Search

We analysed DNA methylation data from 30 datasets comprising 3474 individuals, 19 tissues and 8 ethnicities at CpGs covered by the Illumina450K array. We identified 4143 hypervariable CpGs (‘hvCpGs’) with methylation in the top 5% most variable sites across multiple tissues and ethnicities. hvCpG methylation was influenced but not determined by genetic variation, and was not linked to probe reliability, epigenetic drift, age, sex or cell heterogeneity effects. hvCpG methylation tended to covary across tissues derived from different germ-layers and hvCpGs were enriched for proximity to ERV1 and ERVK retrovirus elements. hvCpGs were also enriched for loci previously associated with periconceptional environment, parent-of-origin-specific methylation, and distinctive methylation signatures in monozygotic twins. Together, these properties position hvCpGs as strong candidates for studying how stochastic and/or environmentally influenced DNA methylation states which are established in the early embryo and maintained stably thereafter can influence life-long health and disease.

Induced pluripotent stem cells (iPSCs) with potential for therapeutic applications can be derived from somatic cells via ectopic expression of a set of limited and defined transcription factors. However, due to risks of random integration of the reprogramming transgenes into the host genome, the low efficiency of the process, and the potential risk of virally induced tumorigenicity, alternative methods have been developed to generate pluripotent cells using nonintegrating systems, albeit with limited success. Here, we show that c-KIT+ human first-trimester amniotic fluid stem cells (AFSCs) can be fully reprogrammed to pluripotency without ectopic factors, by culture on Matrigel in human embryonic stem cell (hESC) medium supplemented with the histone deacetylase inhibitor (HDACi) valproic acid (VPA). The cells share 82% transcriptome identity with hESCs and are capable of forming embryoid bodies (EBs) in vitro and teratomas in vivo. After long-term expansion, they maintain genetic stability, protein level expression of key pluripotency factors, high cell-division kinetics, telomerase activity, repression of X-inactivation, and capacity to differentiate into lineages of the three germ layers, such as definitive endoderm, hepatocytes, bone, fat, cartilage, neurons, and oligodendrocytes. We conclude that AFSC can be utilized for cell banking of patient-specific pluripotent cells for potential applications in allogeneic cellular replacement therapies, pharmaceutical screening, and disease modeling. ispartof: Molecular Therapy vol:20 issue:10 pages:1953-1967 ispartof: location:United States status: published

Summary Context Human growth hormone receptor (GHR) transcripts have two isoforms, full-length (GHRfl) or exon 3 deleted (GHRd3). An association of these isoforms has been found with small for gestational age (SGA) infants but does not influence adult height. The role of this polymorphism in the birth size spectrum in the general population is unclear. Objective To determine the association of maternal and infants GHR exon 3 polymorphism with antenatal growth, birth size and early postnatal growth in two large, normal white European birth cohorts. Study design Pregnant women from white European families were recruited by the University College London Foetal Growth Study (n = 774) and the Moore normal pregnancy cohort (n = 274). GHR variants, wild-type (fl) and deleted for exon 3 (d3) were analysed using multiplex PCR. Results There was a significant underrepresentation of infants wild-type fl/fl (36%) and overrepresentation of d3/d3 (14%) genotypes in the SGA infants within the cohorts (χ2 = 11·2, P = 0·003, df = 2). Fl/fl was overrepresented in large for gestational age (LGA) infants (χ2 = 6·1, P = 0·047, df = 2). There was a significant association of infants GHR isoforms with placental weight (P

The molecular requirements for neural tube closure are complex. This is illustrated by the occurrence of neural tube defects (NTDs) in many genetic mouse mutants, which implicate a variety of genes, pathways and cellular functions. NTDs are also prevalent birth defects in humans, affecting around 1 per 1000 pregnancies worldwide. In humans the causation is thought to involve the interplay of fetal genes and the effect of environmental factors. Recent studies on the aetiology of human NTDs, as well as analysis of mouse models, have raised the question of the possible involvement of epigenetic factors in determining susceptibility. A consideration of potential causative factors in human NTDs must now include both alterations in the regulation of gene expression, through mutation of promoter or regulatory elements, and the additional analysis of epigenetic regulation. Alterations in the epigenetic status can be directly modified by various environmental insults or maternal dietary factors.

BACKGROUND: Silver-Russell syndrome (SRS) is characterised by intrauterine growth restriction, poor postnatal growth, relative macrocephaly, triangular face and asymmetry. Maternal uniparental disomy (mUPD) of chromosome 7 and hypomethylation of the imprinting control region (ICR) 1 on chromosome 11p15 are found in 5-10% and up to 60% of patients with SRS, respectively. As many features are non-specific, diagnosis of SRS remains difficult. Studies of patients in whom the molecular diagnosis is confirmed therefore provide valuable clinical information on the condition.METHODS: A detailed, prospective study of 64 patients with mUPD7 (n=20) or ICR1 hypomethylation (n=44) was undertaken.RESULTS AND CONCLUSIONS: The considerable overlap in clinical phenotype makes it difficult to distinguish these two molecular subgroups reliably. ICR1 hypomethylation was more likely to be scored as 'classical' SRS. Asymmetry, fifth finger clinodactyly and congenital anomalies were more commonly seen with ICR1 hypomethylation, whereas learning difficulties and referral for speech therapy were more likely with mUPD7. Myoclonus-dystonia has been reported previously in one mUPD7 patient. The authors report mild movement disorders in three further cases. No correlation was found between clinical severity and level of ICR1 hypomethylation. Use of assisted reproductive technology in association with ICR1 hypomethylation seems increased compared with the general population. ICR1 hypomethylation was also observed in affected siblings, although recurrence risk remains low in the majority of cases. Overall, a wide range of severity was observed, particularly with ICR1 hypomethylation. A low threshold for investigation of patients with features suggestive, but not typical, of SRS is therefore recommended.

International audience; Imprinted genes play crucial roles in mammalian development and disruption of their expression is associated with many human disorders including tumourigenesis; yet, the actual number of imprinted genes in the human genome remains a matter of debate. Here, we report on the unexpected finding that the chromosome 19 microRNA cluster (C19MC), the largest human microRNA gene cluster discovered so far, is regulated by genomic imprinting with only the paternally inherited allele being expressed in the placenta. DNA methylation profiling identified a differentially methylated region (C19MC-DMR1) that overlaps an upstream CpG-rich promoter region associated with short tandem repeats. It displays a maternal-specific methylation imprint acquired in oocytes and generates a complex population of large, compartimentalized non-coding RNA (ncRNA) species retained in close proximity to the C19MC transcription site. This occurs adjacent to, but not within, a poorly characterized nuclear Alu-rich domain. Interestingly, C19MC maps near another imprinted gene, the maternally expressed ZNF331 gene, and therefore may define a novel, previously unrecognized large imprinted primate-specific chromosomal domain. Altogether, our study adds C19MC to the growing list of imprinted repeated small RNA gene clusters and further strengthens the potential involvement of small ncRNAs in the function and/or the evolution of imprinted gene networks.

The imprinted insulin-like growth factor 2 (IGF2) gene is expressed predominantly from the paternal allele. Loss of imprinting (LOI) associated with hypomethylation at the promoter proximal sequence (DMR0) of the IGF2 gene was proposed as a predisposing constitutive risk biomarker for colorectal cancer. We used pyrosequencing to assess whether IGF2 DMR0 methylation is either present constitutively prior to cancer or whether it is acquired tissue-specifically after the onset of cancer. DNA samples from tumour tissues and matched non-tumour tissues from 22 breast and 42 colorectal cancer patients as well as peripheral blood samples obtained from colorectal cancer patients [SEARCH (n=case 192, controls 96)], breast cancer patients [ABC (n=case 364, controls 96)] and the European Prospective Investigation of Cancer [EPIC-Norfolk (n=breast 228, colorectal 225, controls 895)] were analysed. The EPIC samples were collected 2-5 years prior to diagnosis of breast or colorectal cancer. IGF2 DMR0 methylation levels in tumours were lower than matched non-tumour tissue. Hypomethylation of DMR0 was detected in breast (33%) and colorectal (80%) tumour tissues with a higher frequency than LOI indicating that methylation levels are a better indicator of cancer than LOI. In the EPIC population, the prevalence of IGF2 DMR0 hypomethylation was 9.5% and this correlated with increased age not cancer risk. Thus, IGF2 DMR0 hypomethylation occurs as an acquired tissue-specific somatic event rather than a constitutive innate epimutation. These results indicate that IGF2 DMR0 hypomethylation has diagnostic potential for colon cancer rather than value as a surrogate biomarker for constitutive LOI.

Growth is defined as the progressive increase in size and is listed as one of the eight main characteristics of life. In human gestation the most rapid growth phase is from 16 to 32 weeks when first there is both cell number and size increase and then from 32 weeks onwards there is continued size increase (Pollack and Divon, 1992). The mechanism of growth in utero is of fundamental interest to clinicians and scientists because of its implications for neonatal health. Growth is multifactorial in origin with both genetics and environment contributing equally large parts. Despite this complexity analysis of the candidate genes involved is possible using simple tissue biopsies at the relevant stages of development. Of particular interest in understanding fetal growth is the analysis of a group of genes that show a parent-of-origin effect known as genomic imprinting. Imprinted genes are not only found in eutherian (placental) and metatherian (marsupial) mammals but surprisingly also in plants. Nevertheless, their evolution in mammals appears to be linked primarily to placentation. It is thought to result from a potential conflict between the parents in terms of the drive to successfully propagate their own separate genes and the mother’s added drive for her survival through the pregnancy to reproduce again. This means that the mother wants to restrict fetal growth and the father to enhance it.

Mouse distal chromosome 2 was one of the earliest described imprinting regions. Maternal and paternal inheritance of the region is associated with opposite phenotypes affecting growth, development and behaviour. Mis-expression of proteins determined by the imprinted Gnas locus can account for the phenotypes. The imprinting domain in mouse distal chromosome 2 is small, comprising the Gnas locus. This locus is unusually complex, containing biallelic, maternally and paternally expressed transcripts that share exons. It also contains two germline differentially methylated regions that have the characteristics of imprinting control regions. One of these specifically controls the tissue-specific imprinting of the Gnas exon 1 transcript but does not affect the imprinting of other transcripts. Imprinting of other transcripts may be controlled by the other germline differentially methylated region by a mechanism involving antisense RNA.

Growth is a complex process which is in part genetically determined. Among other genetic causes, uniparental disomy (UPD), the exceptional inheritance of two homologous chromosomes from only one parent, may occasionally be detected. Recent insights have revealed that the molecular basis for the clinical features of UPD are specific human genes that are only monoallelically active, depending on whether they are located on the paternal or maternal chromosome. UPD will lead to an imbalanced expression of these imprinted genes and cause abnormal development. Meanwhile, specific syndromes have been found to be associated with UPD, these include Prader-Willi syndrome (maternal UPD15/mUPD15), Angelman syndrome (paternal UPD15/pUPD15), (transient) neonatal diabetes mellitus (pUPD6), Silver-Russell syndrome (mUPD7), Beckwith-Wiedemann syndrome (pUPD11) and the mUPD14 syndrome. Among other features, most of these syndromes are also characterised by growth restriction. Additionally, UPDs of further chromosomes have been described in growth restricted patients without additional phenotypic abnormalities; however, a conclusive association between the UPD and the clinical features remains to be investigated. Conclusion: in this review we propose a set of reasons for testing of specific uniparental disomies other than 15 in growth restricted patients.

The finding of maternal uniparental disomy for chromosome 7 (matUPD7) in approximately 7% of Silver-Russell syndrome (SRS) cases has lead to the assumption that imprinted gene(s) on chromosome 7 are responsible for at least some cases. However, the observation in a familial case that both maternal and paternal inheritance of proximal 7p results in an SRS-like phenotype suggests that the causative genes may not be imprinted, and that an extra copy of genes within this region cause SRS. As all cases of complete matUPD7 could have arisen by trisomy rescue, it is possible that undetected trisomy 7 mosaicism contributes towards the phenotype of SRS, and that the matUPD7 seen in some cases is a consequence of trisomy rescue. Previous studies in cases of trisomy rescue for a number of autosomes have shown a strong association with skewed X inactivation in diploid tissues. Thus, we hypothesised that if trisomy mosaicism was involved in SRS, the frequency of skewed X inactivation should be increased in a population of non-matUPD7 SRS patients. Consistent with this hypothesis, results showed a significant increase in the frequency of completely skewed X inactivation in SRS patients (three of 29) when compared to controls (three of 270), suggesting the possible presence of undetected trisomy 7 in SRS patients and/or their placentas.

The main features of Silver-Russell syndrome (SRS) are pre- and postnatal growth restriction and a characteristic small, triangular face. SRS is also accompanied by other dysmorphic features including fifth finger clinodactyly and skeletal asymmetry. The disorder is clinically and genetically heterogeneous, and various modes of inheritance and abnormalities involving chromosomes 7, 8, 15, 17, and 18 have been associated with SRS and SRS-like cases. However, only chromosomes 7 and 17 have been consistently implicated in patients with a strict clinical diagnosis of SRS. Two cases of balanced translocations with breakpoints in 17q23.3-q25 and two cases with a hemizygous deletion of the chorionic somatomammatropin gene (CSH1) on 17q24.1 have been associated with SRS, strongly implicating this region. Maternal uniparental disomy for chromosome 7 (mUPD(7)) occurs in up to 10% of SRS patients, with disruption of genomic imprinting underlying the disease status in these cases. Recently, two SRS patients with a maternal duplication of 7p11.2-p13, and a single proband with segmental mUPD for the region 7q31-qter, were described. These key patients define two separate candidate regions for SRS on both the p and q arms of chromosome 7. Both the 7p11.2-p13 and 7q31-qter regions are subject to genomic imprinting and the homologous regions in the mouse are associated with imprinted growth phenotypes. This review provides an overview of the genetics of SRS, and focuses on the newly defined candidate regions on chromosome 7. The analyses of imprinted candidate genes within 7p11.2-p13 and 7q31-qter, and gene candidates on distal 17q, are discussed. Keywords: Silver-Russell syndrome; imprinting; mUPD(7); candidates

The twisted gastrulation gene (tsg) encodes a secreted protein required for the correct specification of dorsal midline cell fate during gastrulation in Drosophila. We report that tsg homologs from human, mouse, zebrafish, and Xenopus share 72-98% identity at the amino acid level and retain all 24 cysteine residues from Drosophila. In contrast to Drosophila where tsg expression is limited to early embryos, expression is found throughout mouse and human development. In Drosophila, tsg acts in synergy with decapentaplegic (dpp), a member of the TGF-beta family of secreted proteins. The vertebrate orthologs of dpp, BMP-2 and -4, are crucial for gastrulation and neural induction, and aberrant signaling by BMPs and other TGF-beta family members results in developmental defects including holoprosencephaly (HPE). Interestingly, human TSG maps to the HPE4 locus on Chromosome 18p11.3, and our analysis places the gene within 5 Mbp of TG-interacting factor (TGIF).

Cleft palate most commonly occurs as a sporadic multifactorial disorder with a clear but difficult to define genetic component. As a semi-dominant disorder, X-linked cleft palate (CPX) provides a useful model to investigate a congenital defect that is little influenced by non-genetic factors. By using an Icelandic kindred, CPX has been localised between DXS1196 and DXS1217 and mapped, in a 3-Mb yeast artificial chromosome contig, at Xq21.3. Markers generated from this physical map have now been used to construct a contig of P1 and bacterial artificial chromosome clones for genomic DNA sequencing. Genomic DNA sequence analysis has revealed two novel expressed genes and two pseudogenes in the order Cen-KLHL4-LAMRL5-CAPZA1P-CPXCR1-Tel. KLHL4 and CPXCR1 are widely expressed in fetal tissues, including the tongue, mandible and palate. DNA mutation screening of CPXCR1 has revealed several sequence variants present on all affected CPX chromosomes. However, these variants have also been detected at a lower frequency on unaffected chromosomes, indicating that they are polymorphisms that are unlikely to cause the CPX phenotype.

The GRB10 gene encodes a growth suppressor and maps to human chromosome 7p11.2-p13. Maternal duplication (matdup) of this region has recently been associated with Silver-Russell syndrome (SRS), which is characterised by pre- and postnatal growth restriction, craniofacial dysmorphism and lateral asymmetry. Maternal uniparental disomy for chromosome 7 (mUPD7) occurs in approximately 7% of SRS patients. Exposure of a recessive allele due to isodisomy has been ruled out in five mUPD7 cases, suggesting genomic imprinting as the basis for disease. Assuming SRS patients with matdup of 7p11.2-p13 and mUPD7 share a common aetiology, this would implicate a maternally expressed gene from this interval, which is involved in growth inhibition. Murine Grb10 was identified as a maternally expressed gene by subtractive hybridisation using normal and androgenetic mouse embryos. Grb10 maps to the homologous region of proximal mouse chromosome 11, for which mUPD incurs reduced birthweight. A role for GRB10 in SRS was evaluated by determining its imprinting status in multiple human foetal tissues using expressed polymorphisms, and by screening the coding region for mutations in 18 classic non-mUPD7 SRS patients. Maternal repression of GRB10 was observed specifically in the developing central nervous system including brain and spinal cord, with biallelic expression in peripheral tissues. This is in contrast to mouse Grb10, and represents the first example of opposite imprinting in human and mouse homologues. While a role for GRB10 in mUPD7 SRS cases can not be ruled out on the basis of imprinting status, no mutations were identified in the patients screened.

Summary Silver-Russell syndrome (SRS) is characterized by pre- and postnatal growth failure and other dysmorphic features. The syndrome is genetically heterogenous, but maternal uniparental disomy of chromosome 7 has been demonstrated in ∼7% of cases. This suggests that at least one gene on chromosome 7 is imprinted and involved in the pathogenesis of SRS. We have identified a de novo duplication of 7p11.2-p13 in a proband with features characteristic of SRS. FISH confirmed the presence of a tandem duplication encompassing the genes for growth factor receptor–binding protein 10 ( GRB10 ) and insulin-like growth factor–binding proteins 1 and 3 ( IGFBP1 and - 3 ) but not that for epidermal growth factor–receptor ( EGFR ). Microsatellite markers showed that the duplication was of maternal origin. These findings provide the first evidence that SRS may result from overexpression of a maternally expressed imprinted gene, rather than from absent expression of a paternally expressed gene. GRB10 lies within the duplicated region and is a strong candidate, since it is a known growth supressor. Futhermore, the mouse homologue ( Grb10/Meg1 ) is reported to be maternally expressed and maps to the imprinted region of proximal mouse chromosome 11 that demonstrates prenatal growth failure when it is maternally disomic. We have demonstrated that the GRB10 genomic interval replicates asynchronously in human lymphocytes, suggestive of imprinting. An additional 36 SRS probands were investigated for duplication of GRB10 , but none were found. However, it remains possible that GRB10 and/or other genes within 7p11.2-p13 are responsible for some cases of SRS.

Intrauterine growth retardation (IUGR) is defined as growth retarded to be below the tenth centile. The insulin-like growth factors and their receptors are implicated in pre- and postnatal growth and development, and it is believed that alteration in their activity may contribute to IUGR. In this study nine normal and nine intrauterine growth retarded births were followed and term placentas examined for expression of the insulin-like growth factors and their receptors. It was found that the expression of insulin-like growth factor 1 (IGF1), insulin-like growth factor 2 (IGF2), and the insulin, IGF1 and IGF2 receptor transcripts (IGF1R and IGF2R, respectively) was present in all term placentas examined. Expression of insulin was not detected. Quantitative polymerase chain reaction (PCR) was used to compare transcription levels in term placentas from normal with IUGR births. There was no significant difference in the levels of transcripts for IGF1, insulin receptor, or IGF2R between normal and IUGR term placentas. However, the IUGR term placentas had significantly higher levels of IGF2 and IGF1R expression compared with the normal term placentas. The increase in the transcription of IGF2 and IGF1R in IUGR term placentas may represent a counter regulatory mechanism in response to the growth retardation.

Insulin, insulin-like growth factor-I (Igf-I), and insulin-like growth factor-II (Igf-II) are known to enhance growth in mouse preimplantation embryos. The addition of insulin, Igf-I, and Igf-II to mouse embryos in culture results in an increase in protein synthesis, cell number, and the proportion of embryos developing to the blastocyst stage. To study the role of the insulin-like growth factors in early human development, the timing of gene expression of insulin, IGF1, IGF2, and their receptors was analysed. Reverse transcription polymerase chain reaction (RT-PCR) was used to examine the presence of transcripts in preimplantation embryos. Following reverse transcription, strategically designed nested primers were used for amplification from cDNA. Transcripts for all three receptors (insulin receptor, IGF1R, IGF2R) were present in human oocytes and preimplantation embryos. However, of the ligands, only IGF2 transcripts were detected. This is consistent with expressed patterns seen in the mouse. As in the human, mouse Igf2 is the only ligand in the family expressed and has been shown to have an autocrine effect on preimplantation development. It has previously been shown that insulin and Igf-I are produced by the mouse maternal reproductive tract and have a paracrine effect on the preimplantation embryo. We speculate that a similar relationship exists in the human and that preimplantation development may be regulated by IGFs from both embryonic (IGF-II) and maternal (insulin and IGF-I) sources.

Silver-Russell syndrome (SRS) is characterised by intrauterine and postnatal growth failure accompanied by a variable number of dysmorphic features. It is usually sporadic although a few familial cases have been described. In a prospective study of 33 patients with sporadic SRS, we have studied the parent of origin of chromosome 7 using variable number tandem repeat (VNTR) or microsatellite repeat markers and have identified two patients with maternal uniparental disomy of chromosome 7 (mUPD7). In one family, inconsistent inheritance of paternal alleles of markers on chromosomes other than 7 led to their exclusion from further study. The probands were clinically mild and symmetrical, but showed no gross clinical differences from the 30 patients with chromosome 7 derived from both parents.

Paternal duplications of chromosome 6q24, a region that contains the imprinted PLAGL1 and HYMAI transcripts, are associated with transient neonatal diabetes mellitus. A common feature of imprinted genes is that they tend to cluster together, presumably as a result of sharing common cis-Acting regulatory elements. To determine the extent of this imprinted cluster in human and mouse, we have undertaken a systematic analysis of allelic expression and DNA methylation of the genes mapping within an ∼1.4-Mb region flanking PLAGL1/Plagl1. We confirm that all nine neighbouring genes are biallelically expressed in both species. In human we identify two novel paternally expressed PLAGL1 coding transcripts that originate from unique promoter regions. Chromatin immunoprecipitation for CTCF and the cohesin subunits RAD21 and SMC3 reveals evolutionarily conserved binding sites within unmethylated regions ∼ 5 kb downstream of the PLAGL1 differentially methylated region and within the PLAGL1 30 untranslated region (UTR). Higher-order chromatin looping occurs between these regions in both expressing and non-expressing tissues, forming a non-Allelic chromatin loop around the PLAGL1/Plagl1 gene. In placenta and brain tissues, we identify an additional interaction between the PLAGL1 P3/P4 promoters and the unmethylated element downstream of the PLAGL1 differentially methylated region that we propose facilitates imprinted expression of these alternative isoforms. © The Author(s) 2013.

OBJECTIVE: Our purpose was to compare the level of expression of both type 1 and type 2 cyclooxygenase genes before and after labor and to localize their expression within the fetal membranes. STUDY DESIGN: The sites of type 2 and type 1 cyclooxygenase messenger ribonucleic acid synthesis were identified with in situ hybridization. Expression of both types 1 and 2 cyclooxygenase was studied by reverse transcriptase polymerase chain reaction. RESULTS: Cyclooxygenase type 2 and type 1 expression was localized within the amniotic epithelium and amniotic mesoderm. Type 1 but not type 2 enzyme was also expressed in the chorionic mesoderm. Expression of the type 2 enzyme was significantly increased with the onset of labor. Type 1 enzyme expression did not significantly change with labor. CONCLUSION: It is most likely that it is the inducible type 2 cyclooxygenase enzyme that mediates the increase in prostaglandin synthesis in amnion with the onset of labor.

Two severely growth-retarded fetuses found to have maternal uniparental disomy (UPD) for chromosome 16 and trisomy 16 placental mosaicism both had an unfavourable outcome. Antenatally, the first case was complicated by an unexplained raised maternal serum alpha-fetoprotein concentration, preterm premature rupture of the membranes, and growth retardation detectable at 21 weeks' gestation, whilst the other had an unexplained raised maternal serum human chorionic gonadotrophin level, a two-vessel cord on ultrasound, and cessation of growth at 25 weeks. At post-mortem, both babies had an imperforate anus. Fetal maternal UPD may explain the poor outcome that occurs in some cases of confined placental mosaicism for chromosome 16 and is also associated with specific fetal abnormalities.

As many as 16% of all recognized pregnancies may be anembryonic, with failure of the embryo at a very early stage of development leaving only the extraembryonic components of the conceptus to proliferate. Studies in the mouse have shown that the maternal and paternal contributions to the genome of the zygote are not functionally equivalent, due to parental genomic imprinting. Uniparental disomy can reveal imprinting effects, as in this phenomenon both members of a chromosome pair are inherited from the same parent. We have carried out a systematic search for uniparental disomy in tissues from 23 cases of early embryonic failure, using variable number tandem repeat (VNTR) analysis and PCR amplification of polymorphic short sequence repeats. Two cases of maternal uniparental heterodisomy for chromosome 21 were identified. One case occurred in conjunction with trisomy for chromosomes 7 and 9, but in the other case maternal uniparental heterodisomy for chromosome 21 was the only chromosomal abnormality found. We therefore postulate that there may be developmentally important genes on human chromosome 21 which are imprinted such that both parental copies are essential for normal embryogenesis.

Clinical definition of Silver–Russell sydrome In 1953 the American pediatrician Henry Silver reported two children with low birthweight, postnatal growth restriction and growth asymmetry [1]. Without knowing of these two cases, in the following year, Alexander Russell from the UK described five similar cases [2]. This group of patients became known as having Silver–Russell syndrome (SRS) or, in the US, Russell–Silver syndrome [OMIM: 180860]. Since these initial reports, several hundred cases have been described in the literature. A predominantly sporadic condition, common features include preand post-natal growth restriction, relative macrocephaly, growth asymmetry and a characteristic facial appearance. The condition is phenotypically variable, making confident clinical diagnosis difficult in some cases [3,4]. Thus in 1999, based on their ana lysis of 57 cases, Price and colleagues proposed a set of clinical diagnostic criteria, at least four of which should be present for a diagnosis of ‘classical SRS’: birthweight >2 SD below the mean, short stature at the time of diagnosis, weight >2 SD below the mean; limb, body or facial asymmetry and fifth finger clinodactyly [5].

Background Mutations in the T-box transcription factor gene TBX22 are found in patients with X-linked cleft palate and ankyloglossia (CPX), and are reported in approximately 5% of all non-syndromic cleft palate patients. Clinical variability in CPX ranges from a mild or occult submucous cleft palate to a severe, complete cleft of the secondary palate. Aims To explore the possibility that mutations lying outside of the TBX22 coding region might contribute to the phenotype, a non-coding upstream exon and its upstream regulatory region were investigated. Methods and results We sequenced 137 patients with cleft palate without coding region mutations and 295 controls. While no unique mutations were identified, seven single nucleotide polymorphisms (SNPs) were noted. These variants segregate into four distinct haplotypes. Individually, two of the SNPs associate significantly with cleft palate, as does the haplotype containing the rare allele of both SNPs. Analysis of the patient cohorts stratified for the presence of ankyloglossia significantly increases these associations. Reporter assays were used to analyse each of these haplotypes and the impact of individual SNPs. An important functional role for rs41307258 results in a decreased promoter activity of up to 50%. Conclusions CPX-like patients harbouring this promoter haplotype are therefore associated with decreased TBX22 transcriptional activity. The risk haplotype, in concert with additional genetic and/or environmental factors, may contribute to the phenotypic variation observed and provide a novel causative mechanism for cleft palate, especially in patients with ankyloglossia.

Uniparental disomy (UPD) is the inheritance of both copies of a given chromosome from the same parent (Warburton, 1988; Anon., 1991). The exact disease associations of UPD of individual chromosomes have yet to be fully elucidated and the question of whether UPD of some chromosomes may be regarded as a benign finding remains unanswered. We report an infant with uniparental maternal disomy 16, the only such infant identified at King's College Hospital. The infant had intrauterine growth retardation and minor congenital heart disease.

Imprinted gene(s) on human chromosome 7q32-qter have been postulated to be involved in intrauterine growth restriction associated with Silver-Russell syndrome (SRS) as 7–10% of patients have mUPD(7). Three imprinted genes, MEST, MESTIT1, and COPG2IT1 on chromosome 7q32, are unlikely to cause SRS since epigenetic and sequence mutation analyses have not shown any changes. One hundred kilobases proximal to MEST lies a group of four carboxypeptidase A (CPA) genes. Since most imprinted genes are found in clusters, this study focuses on analysing these CPAs for imprinting effects based on their proximity to an established imprinted domain. Firstly, a replication timing study across 7q32 showed that an extensive genomic region including the CPAs, MEST, MESTIT1, and COPG2IT1 replicates asynchronously. Subsequently, SNP analysis by sequencing RT-PCR products of CPA1, CPA2, CPA4, and CPA5 indicated preferential expression of CPA4. Pyrosequencing was used as a quantitative approach, which confirmed predominantly preferential expression of the maternal allele and biallelic expression in brain. CPA5 expression levels were too low to allow reliable evaluation of allelic expression, while CPA1 and CPA2 both showed biallelic expression. CPA4 was the only gene from this family in which an imprinting effect was shown despite the location of this family of genes next to an imprinted cluster. As CPA4 has a potential role in cell proliferation and differentiation, two preferentially expressed copies in mUPD patients with SRS syndrome would result in excess expression and could alter the growth profiles of these subjects and give rise to intrauterine growth restriction.

In man high levels of aneuploidy are seen in spontaneous abortions. Very few autosomal trisomies survive to birth, the three most common being those for chromosome 13, 18 and 21 giving rise to the syndromes named Patau, Edwards and Down respectively. Since the majority of these spontaneously abort, what makes the survivors different from the aborters? Could it be that they have tissue specific mosaicism with the additional normal cell line supporting survival? In this study fluorescence in situ hybridisation was used as a convenient way to detect trisomy in interphase cells. To study the level of mosaicism across gestation, different tissues from 21 trisomic foetuses were analysed using probes for chromosome 13, 18, 21, X and Y. Two trisomy 18 foetuses exhibited mosaicism. Two others, one trisomy 13 and one trisomy 18 had mosaic placentas. There was no clear association between the limited mosaicism seen and severity of the phenotype. We conclude that at least for this sample set, tissue-specific mosaicism was not likely to be responsible for potential survival to birth.

The pathologic changes in myotonic dystrophy (DM) skeletal muscle biopsies have been analyzed at both the histochemical and molecular level. A histochemical stain for pretyping single fibers in conjunction with sodium dodecyl sulphate-polyacrylamide gel electrophoresis allowed biochemical differences to be pinpointed in specific histochemical fiber types. These biochemical differences can be related to histochemical changes in fiber type observed in cross-section of the DM biopsies. Such changes included specific fiber type atrophy, hypertrophy, and disproportion. The pathogenesis of DM appears to be characterized by a large increase in the number of promiscuous fibers, that is, those fibers that express both fast and slow myosins. This promiscuity, which is rare in control muscle (less than 2%), is also prevalent at high levels in some family members at risk for DM. The observed promiscuity, although probably not a primary effect of DM, appears to be linked to the histochemical changes in fiber type observed in the DM biopsies.

Intellectual disability and cerebellar atrophy occur together in a large number of genetic conditions and are frequently associated with microcephaly and/or epilepsy. Here we report the identification of causal mutations in Sorting Nexin 14 (SNX14) found in seven affected individuals from three unrelated consanguineous families who presented with recessively inherited moderate-severe intellectual disability, cerebellar ataxia, early-onset cerebellar atrophy, sensorineural hearing loss, and the distinctive association of progressively coarsening facial features, relative macrocephaly, and the absence of seizures. We used homozygosity mapping and whole-exome sequencing to identify a homozygous nonsense mutation and an in-frame multiexon deletion in two families. A homozygous splice site mutation was identified by Sanger sequencing of SNX14 in a third family, selected purely by phenotypic similarity. This discovery confirms that these characteristic features represent a distinct and recognizable syndrome. SNX14 encodes a cellular protein containing Phox (PX) and regulator of G protein signaling (RGS) domains. Weighted gene coexpression network analysis predicts that SNX14 is highly coexpressed with genes involved in cellular protein metabolism and vesicle-mediated transport. All three mutations either directly affected the PX domain or diminished SNX14 levels, implicating a loss of normal cellular function. This manifested as increased cytoplasmic vacuolation as observed in cultured fibroblasts. Our findings indicate an essential role for SNX14 in neural development and function, particularly in development and maturation of the cerebellum.

The gene involved in an X-linked form of cleft palate has been finely mapped using 14 restriction fragment length polymorphic (RFLP) markers that cover the long arm of the X chromosome. By the combination of deletion mapping and linkage analysis, the gene has been localized between the anonymous DNA markers DXYS12 on the proximal side, and DXS17 distally.

The identification of genes that regulate fetal growth will help establish the reasons for intrauterine growth restriction. Most autosomal genes are expressed biallelically, but some are imprinted, expressed only from one parental allele. Imprinted genes are associated with fetal growth and development. The growth of the fetus in utero relies on effective nutrient transfer from the mother to the fetus via the placenta. Some current research on the genetic control of fetal growth has focused on genes that display imprinted expression in utero. The expression levels of four imprinted genes, the paternally expressed insulin growth factor 2 (IGF2), the mesoderm-specific transcript isoform 1 (MEST); the maternally expressed pleckstrin homology-like domain, family A, member 2 (PHLDA2); and the polymorphically imprinted insulin-like growth factor 2 (IGF2R) gene are all known to have roles in fetal growth and were studied in the placentae of 200 white European, normal term babies. The quantitative expression analysis with real-time PCR showed the maternally expressing PHLDA2 but not the paternally expressing IGF2 and MEST, nor the polymorphic maternally expressing IGF2R placental levels to have a statistically significant effect on birth weight. PHLDA2 expression levels are negatively correlated with size at birth. These data implicate PHLDA2 as an imprinted gene important in fetal growth and also as a potential marker of fetal growth.