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The Xist lncRNA mediates X chromosome inactivation (XCI). Here we show that Spen, an Xist-binding repressor protein essential for XCI , binds to ancient retroviral RNA, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen loss activates a subset of endogenous retroviral (ERV) elements in mouse embryonic stem cells, with gain of chromatin accessibility, active histone modifications, and ERV RNA transcription. Spen binds directly to ERV RNAs that show structural similarity to the A-repeat of Xist, a region critical for Xist-mediated gene silencing. ERV RNA and Xist A-repeat bind the RRM domains of Spen in a competitive manner. Insertion of an ERV into an A-repeat deficient Xist rescues binding of Xist RNA to Spen and results in strictly local gene silencing in cis. These results suggest that Xist may coopt transposable element RNA-protein interactions to repurpose powerful antiviral chromatin silencing machinery for sex chromosome dosage compensation. The genetic material inside cells is often packaged into thread-like structures called chromosomes. In humans, mice and other mammals, a pair of sex chromosomes determines the genetic or chromosomal sex of each individual. Those who inherit two “X” chromosomes are said to be chromosomally female, while chromosomal males have one “X” and one “Y” chromosome. This means females have twice as many copies of genes on the X chromosome as a male does, which turns out to be double the number that the body needs. To solve this problem, mammals have developed a strategy known as dosage compensation. The second X chromosome in females becomes “silent”: its DNA remains unchanged, but none of the genes are active. A long noncoding RNA molecule called Xist is responsible for switching off the extra X genes in female cells. It does this by coating the entirety of the second X chromosome. Normally, RNA molecules transmit the coded instructions in genes to the cellular machinery that manufactures proteins. “Noncoding” RNAs like Xist, however, are RNAs that have taken on different jobs inside the cell. Researchers believe that the ancestral Xist gene may have once encoded a protein but changed over time to produce only a noncoding RNA. Carter, Xu et al. therefore set out to find out how exactly this might have happened, and also how Xist might have acquired its ability to switch genes off. Initial experiments used mouse cells grown in the laboratory, in which a protein called Spen was deleted. Spen is known to help Xist silence the X chromosome. In female cells lacking Spen, the second X chromosome remained active. Other chromosomes in male and female cells also had stretches of DNA that became active upon Spen’s removal. These DNA sequences, termed endogenous retroviruses, were remnants of ancestral viral infections. In other words, Spen normally acted as an antiviral defense. Analysis of genetic sequences showed that Spen recognized endogenous retrovirus sequences resembling a key region in Xist, a region which was needed for Xist to work properly. Inserting fragments of endogenous retroviruses into a defective version of Xist lacking this region also partially restored its ability to inactivate genes, suggesting that X chromosome silencing might work by hijacking cellular defenses against viruses. That is, female cells essentially ‘pretend’ there is a viral infection on the second X chromosome by coating it with Xist (which mimics endogenous retroviruses), thus directing Spen to shut it down. This research is an important step towards understanding how female cells carry out dosage compensation in mammals. More broadly, it sheds new light on how ancient viruses may have shaped the evolution of noncoding RNAs in the human genome.

Cholesteryl ester transfer protein (CETP) shuttles various lipids between lipoproteins, resulting in the net transfer of cholesteryl esters from atheroprotective, high-density lipoproteins (HDL) to atherogenic, lower-density species. Inhibition of CETP raises HDL cholesterol and may potentially be used to treat cardiovascular disease. Here we describe the structure of CETP at 2.2-Å resolution, revealing a 60-Å-long tunnel filled with two hydrophobic cholesteryl esters and plugged by an amphiphilic phosphatidylcholine at each end. The two tunnel openings are large enough to allow lipid access, which is aided by a flexible helix and possibly also by a mobile flap. The curvature of the concave surface of CETP matches the radius of curvature of HDL particles, and potential conformational changes may occur to accommodate larger lipoprotein particles. Point mutations blocking the middle of the tunnel abolish lipid-transfer activities, suggesting that neutral lipids pass through this continuous tunnel.

N-myristoyl transferase (NMT) catalyzes the transfer of the fatty acid myristate from myristoyl-CoA to the N-terminal glycine of substrate proteins, and is found only in eukaryotic cells. The enzyme in this study is the 451 amino acid protein produced by Candida albicans , a yeast responsible for the majority of systemic infections in immuno-compromised humans. NMT activity is essential for vegetative growth, and the structure was determined in order to assist in the discovery of a selective inhibitor of NMT which could be developed as an anti-fungal drug. NMT has no sequence homology with other protein sequences and has a novel α/β fold which shows internal twofold symmetry, which may be a result of gene duplication. On one face of the protein there is a long, curved, relatively uncharged groove, at the center of which is a deep pocket. The pocket floor is negatively charged due to the vicinity of the C-terminal carboxylate and a nearby conserved glutamic acid residue, which separates the pocket from a cavity. These observations, considered alongside the positions of residues whose mutation affects substrate binding and activity, suggest that the groove and pocket are the sites of substrate binding and the floor of the pocket is the catalytic center.

Dosage compensation between the sexes has emerged independently multiple times during evolution, often harnessing long noncoding RNAs (lncRNAs) to alter gene expression on the sex chromosomes. In eutherian mammals, X chromosome inactivation (XCI) in females proceeds via the lncRNA Xist, which coats one of the two X chromosomes and recruits repressive proteins to epigenetically silence gene expression in cis. How Xist evolved new functional RNA domains to recruit ancient, pleiotropic protein partners is of great interest. Here we show that Spen, an Xist-binding repressor protein essential for XCI, binds to ancient retroviral RNA, performing a surveillance role to recruit chromatin silencing machinery to these parasitic loci. Spen inactivation leads to de- repression of a subset of endogenous retroviral (ERV) elements in embryonic stem cells, with gain of chromatin accessibility, active histone modifications, and ERV RNA transcription. Spen binds directly to ERV RNAs that show structural similarity to the A- repeat of Xist, a region critical for Xist-mediated gene silencing. ERV RNA and Xist A- repeat bind the RRM3 domain of Spen in a competitive manner. Insertion of an ERV into an A-repeat deficient Xist rescues binding of Xist RNA to Spen and results in local gene silencing in cis. These results suggest that insertion of an ERV element into proto-Xist may have been a critical evolutionary event, which allowed Xist to coopt transposable element RNA-protein interactions to repurpose powerful antiviral chromatin silencing machinery for sex chromosome dosage compensation.

Altered extrahepatic bile ducts, gut, and cardiovascular anomalies constitute the variable phenotype of biliary atresia (BA). To identify potential susceptibility loci, Caucasian children, normal (controls) and with BA (cases) at two US centers were compared at >550000 SNP loci. Systems biology analysis was carried out on the data. In order to validate a key gene identified in the analysis, biliary morphogenesis was evaluated in 2-5-day post-fertilization zebrafish embryos after morpholino-antisense oligonucleotide knockdown of the candidate gene ADP ribosylation factor-6 (ARF6, Mo-arf6). Among 39 and 24 cases at centers 1 and 2, respectively, and 1907 controls, which clustered together on principal component analysis, the SNPs rs3126184 and rs10140366 in a 3' flanking enhancer region for ARF6 demonstrated higher minor allele frequencies (MAF) in each cohort, and 63 combined cases, compared with controls (0.286 vs. 0.131, P = 5.94x10-7, OR 2.66; 0.286 vs. 0.13, P = 5.57x10-7, OR 2.66). Significance was enhanced in 77 total cases, which included 14 additional BA genotyped at rs3126184 only (p = 1.58x10-2, OR = 2.66). Pathway analysis of the 1000 top-ranked SNPs in CHP cases revealed enrichment of genes for EGF regulators (p<1 x10-7), ERK/MAPK and CREB canonical pathways (p<1 x10-34), and functional networks for cellular development and proliferation (p<1 x10-45), further supporting the role of EGFR-ARF6 signaling in BA. In zebrafish embryos, Mo-arf6 injection resulted in a sparse intrahepatic biliary network, several biliary epithelial cell defects, and poor bile excretion to the gall bladder compared with uninjected embryos. Biliary defects were reproduced with the EGFR-blocker AG1478 alone or with Mo-arf6 at lower doses of each agent and rescued with arf6 mRNA. The BA-associated SNPs identify a chromosome 14q21.3 susceptibility locus encompassing the ARF6 gene. arf6 knockdown in zebrafish implicates early biliary dysgenesis as a basis for BA, and also suggests a role for EGFR signaling in BA pathogenesis.

Astroblastomas (ABs) are rare brain tumors of unknown origin. We performed an integrative genetic and epigenetic analysis of AB-like tumors. Here, we show that tumors traceable to neural stem/progenitor cells (radial glia) that emerge during early to later brain development occur in children and young adults, respectively. Tumors with MN1 - BEND2 fusion appear to present exclusively in females and exhibit overexpression of genes expressed prior to 25 post-conception weeks (pcw), including genes enriched in early ventricular zone radial glia and ependymal tumors. Other, histologically classic ABs overexpress or harbor mutations of mitogen-activated protein kinase pathway genes, outer and truncated radial glia genes, and genes expressed after 25 pcw, including neuronal and astrocyte markers. Findings support that AB-like tumors arise in the context of epigenetic and genetic changes in neural progenitors. Selective gene fusion, variable imprinting and/or chromosome X-inactivation escape resulting in biallelic overexpression may contribute to female predominance of AB molecular subtypes. Astroblastoma (AB) is an uncommon brain tumour and its origin remains unknown. Here, the authors perform integrative molecular analysis of 35 AB-like tumours and provide evidence that these arise in the context of epigenetic and genetic changes in neural progenitors occurring during brain development.

The structural and luminescence properties of akermanite type compound Sr 2 MgSi 2 O 7 :Sm 3+ have been investigated. The crystal structure of Sr 2 MgSi 2 O 7 has been obtained from the X-ray diffraction data. Sr 2 MgSi 2 O 7 possesses tetragonal symmetry with space group P 4 ¯ 2 1  m (No. 113). Judd Ofelt (J-O) analysis of akermanite structured Sm 3+ -doped Sr 2 MgSi 2 O 7 phosphor synthesized by combustion synthesis followed by a solid-state reaction process is presented. SEM confirms the morphology. The photoluminescence emission (PL) spectra indicate that the phosphor gives orange red emission at 601 nm attributed to transitions 4 G 5/2 → 6 H 5/2 . Optimum concentration is found to be 7.0 mol.%. The CIE chromaticity coordinates are (0.57, 0.43). The branching ratio for the transition, 4 G 5/2 → 6 H 7/2 , is found to be around 53%, suggesting it as a potential laser material in addition to its use for fabrication of white LED phosphors.

BackgroundSickle cell disease (SCD) with vaso-occlusive pain crisis (VOC) has a major impact on healthcare resource utilisation and poses a significant financial burden for the patients. This study examines the economic implications of managing VOC in individuals with SCD in India, from the perspectives of patients, healthcare system and society.MethodsThis cross-sectional, observational study included 1000 patients with SCD across 14 centres enrolled from November 2021 to June 2022. Data were collected systematically using a structured electronic case record form. Employing a cost-of-illness approach, the study assessed the economic impact of SCD and VOC management, including assessing patient/caregiver costs, healthcare provider costs and societal burdens extrapolated to the larger SCD population in India.FindingsPatients incurred substantial out-of-pocket expenses, with a median (IQR) annual expenditure of INR 22 080/US$267 (IQR: INR 36 990/US$447.7), representing 14.65% (26.53) of their annual household income. Overall, catastrophic healthcare expenditure (CHE) for total annual average SCD care with VOC management was experienced by 624 patients (62.40%). Moreover, 334 patients (33.4%) experienced CHE of >25% of the annual household income. Patients with SCD with VOC had significantly higher median annual healthcare expenditures and used a higher median percentage of their yearly household income on healthcare compared with those without VOC (19.82% vs 6.08%; p<0.001). Cost incurred by healthcare providers for VOC management in different healthcare facilities (outpatient department/emergency department/intensive care unit) was similar across different reimbursed facilities (government tertiary care hospitals, non-governmental organisation-operated healthcare centres and government-subsidised healthcare setups). The estimated societal burden for VOC management in 1 year for 1000 patients visiting different healthcare facilities was around INR 35 119 074 (~US$0.42 million).InterpretationThese findings highlight the considerable economic strain on both patients and healthcare providers in SCD and VOC management, which is similar to the other non-communicable diseases emphasising the urgent need for targeted interventions to improve financial hardships among patients.FundingThe study was funded by Novartis Healthcare Private Limited.

IntroductionAtrial Fibrillation (AF) is the most common arrhythmia worldwide affecting an estimated 5% of people over the age of 65 and is a leading cause of stroke and heart failure. Identification of patients at risk allows preventative measures and treatment before these complications occur. Conventional risk prediction models are static, do not have flexibility to incorporate dynamic risk factors and possess only modest predictive value. Artificial intelligence and machine learning-powered health virtual twin technology offer transformative methods for risk prediction and guiding clinical decisions.Methods and analysisIn this prospective observational study, 1200 patients will be recruited in two tertiary centres. Patients hospitalised with acute illnesses (sepsis, heart failure, respiratory failure, stroke or critical illness) and patients having undergone high-risk surgery (major vascular surgery, upper gastrointestinal surgery and emergency surgery) will be monitored with a patch-based remote wireless monitoring system for up to 14 days. Clinical and electrocardiographic data will be used for modelling the risk of new-onset AF. The primary outcome is episodes of AF >30 s and will be described as ratio of episodes/patient and as percentage of patients having episodes of AF. Secondary outcomes include 30-day and 90-day readmission rates and complications of AF.The aim of this study is to generate data for the development and validation of health virtual twins predicting onset of AF in an at-risk population. The intelligent monitoring to predict atrial fibrillation (NOTE-AF) study is part of the TARGET project, a Horizon Europe funded programme which includes risk prediction, diagnosis and management of AF-related stroke (https://target-horizon.eu/).Ethics and disseminationThe study has received approval by the Health Research Authority and the National Research Ethics Service (REC reference 24/NW/0170, IRAS project ID: 342528) in the UK and has been registered on clinicaltrials.gov (NCT06600620). Results will be disseminated as outlined in the TARGET protocol to communicate project ideas, activities and results to diverse audiences.Trial registration numberNCT06600620.