Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis

Nucleolar Essential Protein 1 (Nep1) is required for small subunit (SSU) ribosomal RNA (rRNA) maturation and is mutated in Bowen–Conradi Syndrome. Although yeast (Saccharomyces cerevisiae) Nep1 interacts with a consensus sequence found in three regions of SSU rRNA, the molecular details of the interaction are unknown. Nep1 is a SPOUT RNA methyltransferase, and can catalyze methylation at the N1 of pseudouridine. Nep1 is also involved in assembly of Rps19, an SSU ribosomal protein. Mutations in Nep1 that result in decreased methyl donor binding do not result in lethality, suggesting that enzymatic activity may not be required for function, and RNA binding may play a more important role. To study these interactions, the crystal structures of the scNep1 dimer and its complexes with RNA were determined. The results demonstrate that Nep1 recognizes its RNA site via base-specific interactions and stabilizes a stem-loop in the bound RNA. Furthermore, the RNA structure observed contradicts the predicted structures of the Nep1-binding sites within mature rRNA, suggesting that the Nep1 changes rRNA structure upon binding. Finally, a uridine base is bound in the active site of Nep1, positioned for a methyltransfer at the C5 position, supporting its role as an N1-specific pseudouridine methyltransferase

Methylation QTLs in the developing brain and their enrichment in schizophrenia risk loci

We characterized DNA methylation quantitative trait loci (mQTLs) in a large collection (n = 166) of human fetal brain samples spanning 56-166 d post-conception, identifying >16,000 fetal brain mQTLs. Fetal brain mQTLs were primarily cis-acting, enriched in regulatory chromatin domains and transcription factor binding sites, and showed substantial overlap with genetic variants that were also associated with gene expression in the brain. Using tissue from three distinct regions of the adult brain (prefrontal cortex, striatum and cerebellum), we found that most fetal brain mQTLs were developmentally stable, although a subset was characterized by fetal-specific effects. Fetal brain mQTLs were enriched amongst risk loci identified in a recent large-scale genome-wide association study (GWAS) of schizophrenia, a severe psychiatric disorder with a hypothesized neurodevelopmental component. Finally, we found that mQTLs can be used to refine GWAS loci through the identification of discrete sites of variable fetal brain methylation associated with schizophrenia risk variants

The landscape of tolerated genetic variation in humans and primates.

Personalized genome sequencing has revealed millions of genetic differences between individuals, but our understanding of their clinical relevance remains largely incomplete. To systematically decipher the effects of human genetic variants, we obtained whole-genome sequencing data for 809 individuals from 233 primate species and identified 4.3 million common protein-altering variants with orthologs in humans. We show that these variants can be inferred to have nondeleterious effects in humans based on their presence at high allele frequencies in other primate populations. We use this resource to classify 6% of all possible human protein-altering variants as likely benign and impute the pathogenicity of the remaining 94% of variants with deep learning, achieving state-of-the-art accuracy for diagnosing pathogenic variants in patients with genetic diseases

RELIABILITY OF CERVICAL EXTENSION AND ROTATION ISOMETRIC STRENGTH TESTING IN SYMPTOMATIC SUBJECTS

Objectives The purposes of this study were: 1) To assess the reliability of cervical extension and rotation isometric strength testing of subjects who were experiencing neck pain at the time of testing, and 2) To determine if there is an association between cervical strength and neck pain intensity, or level of neck disability, or fear of neck movement, or cervical range of motion. Design A reliability study of repeated measurements of isometric cervical extension and rotation strength and a correlational study to assess the association between strength and pain, disability, fear of movement, and range of motion of the cervical spine were conducted on a sample of symptomatic subjects. Participants Two groups (N = 60 & N = 55) of volunteers with neck pain were recruited by advertisements located in a private chiropractic clinic and a hospital bulletin board. The group for cervical extension strength testing consisted of 25 men (age = 38 ± 14 yr; disability = 28 ± 16%; pain = 29 ± 25mm) and 35 women (age = 36 ± 12 yr; disability = 26 ± 15%; pain = 31 ± 26 mm). The other group for cervical rotation strength testing consisted of 25 men (age = 40 ± 11 yr; disability = 25 ± 13%; pain = 22 ± 20mm) and 30 women (age = 37 ± 11 yr; disability = 29 ± 13%; pain = 31 ± 24mm). Main Outcome Measures: Cervical extension strength was measured on an isometric extension strength testing machine (MedXTM Cervical Extension Machine). Cervical rotation strength was measured on an isometric rotation strength testing machine (MedXTM Cervical Rotation Machine). Strength testing was carried out in 2 testing sessions (48 hours apart). Prior to each testing session all participants completed a visual analogue scale for neck pain and a neck disability questionnaire. In addition, individuals who took part in cervical rotation strength testing completed a visual analogue scale for fear of neck movement and had their cervical range of motion measured. Results Cervical extension strength testing (ICC = 0.949, 95% CI = 0.9477 - 0.9502) and cervical rotation strength testing (ICC = 0.965, 95% Cl = 0.9645 - 0.9663) were reliable. Standard error of measurement (SEM) values for cervical extension strength and cervical rotation strength were 23% and 6%, respectively. A multiple regression analysis did not reveal any significant association between cervical strength and neck pain intensity, or level of neck disability, or fear of neck movement, or cervical range of motion. Conclusion The reliability of both cervical extension and rotation strength measurements in subjects who are experiencing neck pain at the time of testing was good with a clinically acceptable level of precision. There was no association between cervical strength, neck pain intensity, fear of neck movement or cervical range of motion but the sample size for a multiple regression analysis was too small