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Over 130 X-linked genes have been robustly associated with developmental disorders, and X-linked causes have been hypothesised to underlie the higher developmental disorder rates in males. Here, we evaluate the burden of X-linked coding variation in 11,044 developmental disorder patients, and find a similar rate of X-linked causes in males and females (6.0% and 6.9%, respectively), indicating that such variants do not account for the 1.4-fold male bias. We develop an improved strategy to detect X-linked developmental disorders and identify 23 significant genes, all of which were previously known, consistent with our inference that the vast majority of the X-linked burden is in known developmental disorder-associated genes. Importantly, we estimate that, in male probands, only 13% of inherited rare missense variants in known developmental disorder-associated genes are likely to be pathogenic. Our results demonstrate that statistical analysis of large datasets can refine our understanding of modes of inheritance for individual X-linked disorders., Developmental disorders (DDs) are more prevalent in males, thought to be due to X-linked genetic variation. Here, the authors investigate the burden of X-linked coding variants in 11,044 DD patients, showing that this contributes to ~6% of both male and female cases and therefore does not solely explain male bias in DDs.

Background Genome-wide association studies have reported more than 100 risk loci for rheumatoid arthritis (RA). These loci are shown to be enriched in immune cell-specific enhancers, but the analysis so far has excluded stromal cells, such as synovial fibroblasts (FLS), despite their crucial involvement in the pathogenesis of RA. Here we integrate DNA architecture, 3D chromatin interactions, DNA accessibility, and gene expression in FLS, B cells, and T cells with genetic fine mapping of RA loci. Results We identify putative causal variants, enhancers, genes, and cell types for 30–60% of RA loci and demonstrate that FLS account for up to 24% of RA heritability. TNF stimulation of FLS alters the organization of topologically associating domains, chromatin state, and the expression of putative causal genes such as TNFAIP3 and IFNAR1. Several putative causal genes constitute RA-relevant functional networks in FLS with roles in cellular proliferation and activation. Finally, we demonstrate that risk variants can have joint-specific effects on target gene expression in RA FLS, which may contribute to the development of the characteristic pattern of joint involvement in RA. Conclusion Overall, our research provides the first direct evidence for a causal role of FLS in the genetic susceptibility for RA accounting for up to a quarter of RA heritability. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02460-6.

Inorganic orthophosphate (Pi) is an essential nutrient for plant growth, and its availability strongly impacts crop yield. PHOSPHATE1 (PHO1) transfers Pi from root to shoot via Pi export into root xylem vessels. In this work, we demonstrate that an upstream open reading frame (uORF) present in the 5′ untranslated region of the Arabidopsis (Arabidopsis thaliana) PHO1 inhibits its translation and influences Pi homeostasis. The presence of the uORF strongly inhibited the translation of a PHO1 5′UTR-luciferase construct in protoplasts. A point mutation removing the PHO1 uORF (ΔuORF) in transgenic Arabidopsis resulted in increased association of its mRNA with polysomes and led to higher PHO1 protein levels, independent of Pi availability. Interestingly, deletion of the uORF led to higher shoot Pi content and was associated with improved shoot growth under low external Pi supply and no deleterious effects under Pi-sufficient conditions. We further show that natural accessions lacking the PHO1 uORF exhibit higher PHO1 protein levels and shoot Pi content. Increased shoot Pi content was linked to the absence of the PHO1 uORF in a population of F2 segregants. We identified the PHO1 uORF in genomes of crops such as rice (Oryza sativa), maize (Zea mays), barley (Hordeum vulgare), and wheat (Triticum aesativum), and we verified the inhibitory effect of the rice PHO1 uORF on translation in protoplasts. Our work suggests that regulation of PHO1 expression via its uORF might be a genetic resource useful—both in natural populations and in the context of genome editing—toward improving plant growth under Pi-deficient conditions.

Next-generation sequencing is a powerful tool for the discovery of genes related to neurodevelopmental disorders (NDDs). Here, we report the identification of a distinct syndrome due to de novo or inherited heterozygous mutations in Tousled-like kinase 2 (TLK2) in 38 unrelated individuals and two affected mothers, using whole-exome and whole-genome sequencing technologies, matchmaker databases, and international collaborations. Affected individuals had a consistent phenotype, characterized by mild-borderline neurodevelopmental delay (86%), behavioral disorders (68%), severe gastro-intestinal problems (63%), and facial dysmorphism including blepharophimosis (82%), telecanthus (74%), prominent nasal bridge (68%), broad nasal tip (66%), thin vermilion of the upper lip (62%), and upslanting palpebral fissures (55%). Analysis of cell lines from three affected individuals showed that mutations act through a loss-of-function mechanism in at least two case subjects. Genotype-phenotype analysis and comparison of computationally modeled faces showed that phenotypes of these and other individuals with loss-of-function variants significantly overlapped with phenotypes of individuals with other variant types (missense and C-terminal truncating). This suggests that haploinsufficiency of TLK2 is the most likely underlying disease mechanism, leading to a consistent neurodevelopmental phenotype. This work illustrates the power of international data sharing, by the identification of 40 individuals from 26 different centers in 7 different countries, allowing the identification, clinical delineation, and genotype-phenotype evaluation of a distinct NDD caused by mutations in TLK2.

Next-generation sequencing is a powerful tool for the discovery of genes related to neurodevelopmental disorders (NDDs). Here, we report the identification of a distinct syndrome due to de novo or inherited heterozygous mutations in Tousled-like kinase 2 (TLK2) in 38 unrelated individuals and two affected mothers, using whole-exome and whole-genome sequencing technologies, matchmaker databases, and international collaborations. Affected individuals had a consistent phenotype, characterized by mild-borderline neurodevelopmental delay (86%), behavioral disorders (68%), severe gastro-intestinal problems (63%), and facial dysmorphism including blepharophimosis (82%), telecanthus (74%), prominent nasal bridge (68%), broad nasal tip (66%), thin vermilion of the upper lip (62%), and upslanting palpebral fissures (55%). Analysis of cell lines from three affected individuals showed that mutations act through a loss-of-function mechanism in at least two case subjects. Genotype-phenotype analysis and comparison of computationally modeled faces showed that phenotypes of these and other individuals with loss-of-function variants significantly overlapped with phenotypes of individuals with other variant types (missense and C-terminal truncating). This suggests that haploinsufficiency of TLK2 is the most likely underlying disease mechanism, leading to a consistent neurodevelopmental phenotype. This work illustrates the power of international data sharing, by the identification of 40 individuals from 26 different centers in 7 different countries, allowing the identification, clinical delineation, and genotype-phenotype evaluation of a distinct NDD caused by mutations in TLK2.

The global rise in metabolic diseases can be attributed to a complex interplay between biology, behavior and environmental factors. This article reviews the current literature concerning DNA methylation-based epigenetic inheritance (intergenerational and transgenerational) of metabolic diseases through the male germ line. Included are a presentation of the basic principles for DNA methylation in developmental programming, and a description of windows of susceptibility for the inheritance of environmentally induced aberrations in DNA methylation and their associated metabolic disease phenotypes. To this end, escapees, genomic regions with the intrinsic potential to transmit acquired paternal epigenetic information across generations by escaping the extensive programmed DNA demethylation that occurs during gametogenesis and in the zygote, are described. The ongoing descriptive and functional examinations of DNA methylation in the relevant biological samples, in conjugation with analyses of non-coding RNA and histone modifications, hold promise for improved delineation of the effect size and mechanistic background for epigenetic inheritance of metabolic diseases.

J. Lönnqvist on työryhmän Psychiat Genomics Consortium jäsen. Genetic correlation is a key population parameter that describes the shared genetic architecture of complex traits and diseases. It can be estimated by current state-of-art methods, i.e., linkage disequilibrium score regression (LDSC) and genomic restricted maximum likelihood (GREML). The massively reduced computing burden of LDSC compared to GREML makes it an attractive tool, although the accuracy (i.e., magnitude of standard errors) of LDSC estimates has not been thoroughly studied. In simulation, we show that the accuracy of GREML is generally higher than that of LDSC. When there is genetic heterogeneity between the actual sample and reference data from which LD scores are estimated, the accuracy of LDSC decreases further. In real data analyses estimating the genetic correlation between schizophrenia (SCZ) and body mass index, we show that GREML estimates based on similar to 150,000 individuals give a higher accuracy than LDSC estimates based on similar to 400,000 individuals (from combinedmeta-data). A GREML genomic partitioning analysis reveals that the genetic correlation between SCZ and height is significantly negative for regulatory regions, which whole genome or LDSC approach has less power to detect. We conclude that LDSC estimates should be carefully interpreted as there can be uncertainty about homogeneity among combined meta-datasets. We suggest that any interesting findings from massive LDSC analysis for a large number of complex traits should be followed up, where possible, with more detailed analyses with GREML methods, even if sample sizes are lesser.

Little is known about the inheritance of very low heteroplasmy mitochondria DNA (mtDNA) variations. Even with the development of new next-generation sequencing methods, the practical lower limit of measured heteroplasmy is still about 1% due to the inherent noise level of the sequencing. In this study, we sequenced the mitochondrial genome of 44 individuals using Illumina high-throughput sequencing technology and obtained high-coverage mitochondria sequencing data. Our study population contains many mother-offspring pairs. This unique study design allows us to bypass the usual heteroplasmy limitation by analyzing the correlation of mutation levels at each position in the mtDNA sequence between maternally related pairs and non-related pairs. The study showed that very low heteroplasmy variants, down to almost 0.1%, are inherited maternally and that this inheritance begins to decrease at about 0.5%, corresponding to a bottleneck of about 200 mtDNA.

Die nicht-Mendelsche Vererbung des t-Haplotyps von heterozygoten Mausmännchen an ihre Nachkommen ist unter der Bezeichnung Transmission Ratio Distortion bekannt. Der t-Haplotyp, eine abweichende Form des t-Komplexes, erstreckt sich über fast ein Drittel des Mauschromosoms 17 und codiert mehrere Distortergene und ein Respondergen, die in der Spermatogenese zur Ausbildung von zwei verschiedenen Spermienpopulationen führen. Die früh exprimierten Distorter wirken auf Signalkaskaden einer Spermienmotilitätskinase, Smok1, und haben eine negative Wirkung auf die Motilität aller Spermien, während der Responder diese Situation nur in Spermien, die das Respondergen tragen, wieder ausgleicht. Dies verschafft den sogenannten t-Spermien einen Vorteil bei der Befruchtung und führt zu der ungewöhnlich hohen Vererbung. Vorangegangene Arbeiten haben gezeigt, dass ein responderbasiertes Transgen haploidspezifische Transkriptexpression aufweist, das heißt, die mRNA ist haploidspezifisch auf die Hälfte der runden Spermatiden begrenzt, obwohl diese Zellen durch Zellbrücken miteinander verbunden sind und ein Austausch von Genprodukten stattfinden kann. Außerdem ist das Responderprotein nur im Flagellum elongierter Spermien detektierbar, das heißt, die Translation findet erst in späten Spermatogenesestadien statt. Dies zeigt, dass translationelle Regulation in der Expression des Respondergens involviert ist und eine datenbankbasierte Analyse konnte bereits mögliche, regulatorische Elemente der translationellen Kontrolle in der 5’- untranslatierten Region (5’-UTR) des Respondertranskripts aufdecken. Im Rahmen dieser Arbeit wurden verschiedene, responderbasierte Transgene kloniert, aus denen transgene Mäuse generiert wurden, um die Haploidspezifität der t-Komplex Responders in vivo auf Transkript- und Proteinebene durch in situ Hybridisierung und Immunhistochemie sowie funktionell in einem Vererbungstest zu untersuchen. Um die Bedeutung von regulatorischen Elementen der 5’-UTR für die Responderexpression zu klären, wurden unterschiedliche Deletionskonstrukte generiert und die Expressionsanalyse in vivo zeigte, dass die 5’-UTR tatsächlich in der Transkriptlokalisation involviert war. Sobald die selben 5’-UTR-Deletionen in Kombination mit der codierenden Region des Responders verwendet wurden, konnte gezeigt werden, dass die codierende Sequenz für die Transkriptstabilität und erfolgreiche Translation wichtig war, allerdings nur zusammen mit mindestens dem letzten Drittel der 5’-UTR. Schließlich konnte bei Untersuchungen der spezifischen Subdomänen innerhalb der codierenden Region des Responders durch Verwendung von Deletionskonstrukten in dieser Region verdeutlicht werden, dass eine erfolgreiche Translation des Gens von dem Vorhandensein der regulatorischen Subdomäne in der codierenden Sequenz abhängig war. Um das Ergebnis der Deletionsuntersuchungen auch funktionell zu bestätigen, wurden transgene Mäuse mit den Deletionen in der codierenden Region in einem Transmissionstest eingesetzt, bei dem die jeweilige Vererbungsrate des Transgens in Anwesenheit von Distortern erfasst wurde. Im Hinblick auf Transmission Ratio Distortion war dieser Vererbungstest nicht sehr aussagekräftig und damit nicht ausreichend, um zu beantworten, welche Responderuntereinheit allein ausreichende Responderaktivität hat. Zusätzlich offenbarte der Test, dass die gewählte Integrationsstrategie für Transgene möglicherweise Defizite aufweist. Zur Generierung von transgenen Mäusen wurde ein Rekombinase vermittelter Kassettenaustausch transgener Konstrukte als Einzelkopie in den ColA1 -Locus von embryonalen Stammzellen verwendet, aber der Integrationsort selbst zeigte im Verlauf dieser Arbeit jedoch unerwartete Positionseffekte, die zu niedriger oder komplett abwesender Expression der Transgene führten und die Ergebnisse der in situ Hybridisierung, der Immunhistochemie und des Transmissionstests beeinflussten. Das Vorhaben der Arbeit war die regulatorischen Elemente des Respondertranskripts zu identifizieren, die bedeutsam für die spezielle Expression diese Gens sind, um diese bei der Manipulation der Expression anderer Gene in der Maus oder anderen Spezies einsetzen zu können. Diese Arbeit konnte zeigen, dass die 5’-UTR des Respondergens in der Transkriptlokalisation involviert ist, während die codierende Region, allerdings nur in Kombination mit der 5’-UTR, die Transkriptstabilität und Translation kontrolliert. Somit verdeutlichen die Ergebnisse dieser Arbeit, dass die posttranskriptionelle Regulation des Responders sehr komplex ist und auf verschiedene regulatorische Elemente innerhalb des Transkripts angewiesen ist und dies erschwert eine mögliche Anwendung deutlich., Non-Mendelian inheritance of the t-haplotype from heterozygous male mice to their offspring is also known as transmission ratio distortion. The t-haplotype, a variant form of the t-complex, spans nearly one third of mouse chromosome 17 and encodes several distorter genes and one responder gene, which lead to formation of two different sperm populations during spermatogenesis. Early expressed distorters activate signalling cascades of the sperm motility kinase, smok1, resulting in a negative effect on the motility of all sperm, while the responder counterbalances this situation only in sperm carrying the responder gene. This gives these so called t-sperm an advantage during fertilisation, and leads to an abnormally high inheritance. Previous work has demonstrated that a responder-based transgene shows haploid- specific transcript expression, which means that the mRNA is restricted to only half of all round spermatids, although these cells are connected via cellular bridges and thus exchange of gene products can occur. Furthermore, the responder protein is detectable only in the flagellum of elongated sperm, which means its translation takes place during late stages of spermatogenesis. This shows that translational regulation might be involved in responder gene expression and in silico analysis revealed already possible regulatory elements for translational control of the responder within the 5’-untranslated region (5’UTR) of the responder transcript. In the context of this work different responder-based transgenes were cloned to generate transgenic mice and to investigate the haploid specificity of the t-complex responder in vivo on transcript and protein level by using in situ hybridization and immunohistochemistry and functionally in a transmission ratio distortion test. In order to address the importance of regulatory elements of the 5’-UTR in responder expression several deletion constructs were generated and expression analyses in vivo revealed that the 5’-UTR was indeed involved in transcript localisation. When the same 5’-UTR deletions were examined in combination with the responder coding sequence, it was demonstrated that the coding region was necessary for transcript stability and successful translation, along with at least the last third of the 5’-UTR region. Additionally, analysis of specific subdomains within the coding region of the responder using deletion constructs within this region, revealed that successful translation of this gene was dependent on the presence of at least the regulatory subdomain in the coding sequence. In order to functionally verify observations from the deletion studies, transgenic mice harbouring the coding region deletions were used in a transmission ratio distortion test, which measured the rate of transgene inheritance in the presence of distorters. In terms of transmission ratio distortion this test was inconclusive, and was thus insufficient to answer the question of which responder subdomain has adequate responder activity. The test further revealed possible shortfalls in the transgene integration strategy chosen. A strategy using recombinase-mediated cassette exchange of transgenic constructs integrated as a single copy in the ColA1 locus was used to generate mice, but within this work the locus itself revealed some unexpected positional effects resulting in low or completely absent expression, thereby impacting the outcome of in situ hybridization analyses, immunohistochemistry, and of the transmission test. The intention of this work was to identify regulatory elements in the responder transcript which are important for the special expression of this gene and which might be used to manipulate other genes in the mouse or in other species. This work demonstrated that the 5’-UTR of the responder is involved in transcript localization while the coding region only in combination with the 5’-UTR is controlling transcript stability and translation. Therefore the results of this work revealed that post-transcriptional regulation of the responder is quite complex and depends on different regulatory elements within the transcript and this makes a possible application significantly difficult.

Loss-of-function mutations of MECP2 are responsible for Rett syndrome (RTT), an X-linked neurodevelopmental disorder affecting mainly girls. The availability of MECP2 testing has led to the identification of such mutations in girls with atypical RTT features and the recognition of milder forms. Furthermore, duplication of the entire gene has recently been described in boys with mental retardation and recurrent infections. We describe a girl with a heterozygous de novo MECP2 duplication. The patient, at the age of 19, has mental retardation with no autistic features. She is friendly but gets frequently anxious. She has neither dysmorphic features nor malformations. Her motor development was delayed with walking at 20 months. Speech is fluid with good pronunciation but is simple and repetitive. Diagnosis was made after single-strand conformation analysis (SSCA) and multiplex ligation-dependent probe amplification (MLPA) analysis of MECP2. Array comparative genomic hybridization (aCGH) analysis showed a duplication of 29 kb including MECP2 and part of IRAK1. Fluorescent in situ hybridization (FISH) has revealed that the duplicated region is inserted near the telomere of the short arm of chromosome 10. X-chromosome inactivation in leukocyte DNA was not skewed. We conclude that it is likely that this MECP2 duplication is responsible for the mental retardation in this patient. This case broadens the phenotypic spectrum of MECP2 abnormalities with consequent implication in diagnosis and genetic counselling of girls with non-syndromic mental retardation.

Obesity has become a major worldwide challenge to public health, owing to an interaction between the Western 'obesogenic' environment and a strong genetic contribution. Recent extensive genome-wide association studies (GWASs) have identified numerous single nucleotide polymorphisms associated with obesity, but these loci together account for only a small fraction of the known heritable component. Thus, the 'common disease, common variant' hypothesis is increasingly coming under challenge. Here we report a highly penetrant form of obesity, initially observed in 31 subjects who were heterozygous for deletions of at least 593 kilobases at 16p11.2 and whose ascertainment included cognitive deficits. Nineteen similar deletions were identified from GWAS data in 16,053 individuals from eight European cohorts. These deletions were absent from healthy non-obese controls and accounted for 0.7% of our morbid obesity cases (body mass index (BMI) >or= 40 kg m(-2) or BMI standard deviation score >or= 4; P = 6.4 x 10(-8), odds ratio 43.0), demonstrating the potential importance in common disease of rare variants with strong effects. This highlights a promising strategy for identifying missing heritability in obesity and other complex traits: cohorts with extreme phenotypes are likely to be enriched for rare variants, thereby improving power for their discovery. Subsequent analysis of the loci so identified may well reveal additional rare variants that further contribute to the missing heritability, as recently reported for SIM1 (ref. 3). The most productive approach may therefore be to combine the 'power of the extreme' in small, well-phenotyped cohorts, with targeted follow-up in case-control and population cohorts.