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Konstantinos Lazaridis, Carl Anderson and colleagues report results of a genome-wide association study of primary sclerosing cholangitis (PSC). They identify four new susceptibility loci for PSC and quantify the correlation of common genetic variation shared between PSC and inflammatory bowel diseases.
Richa Saxena and colleagues report genome-wide association analyses of sleep disturbance traits in the UK Biobank cohort. They discover loci associated with insomnia symptoms and excessive daytime sleepiness and identify genetic correlations with several neuropsychiatric and metabolic traits.
Gerald Crabtree, Keji Zhao and colleagues report that recurrent disease-associated mutations in SMARCA4 result in increased PRC1 deposition and activity. Using an in cellula assay, they find that the BAF (mSWI/SNF) complex directly evicts PRC from chromatin via an ATP-dependent mechanism and that this occurs within minutes of BAF occupancy.
Charles Roberts and colleagues show that deletion of Arid1a from mouse intestinal epithelium results in invasive adenocarcinomas resembling human colorectal cancer. They further show that ARID1A loss impairs SWI/SNF targeting and enhancer-mediated gene regulation.
Charles Roberts, Peter Park, Bradley Bernstein and colleagues examine the consequences of SMARCB1 loss on enhancer landscapes in human rhabdoid tumors. They show that SMARCB1 is essential for the integrity and abundance of SWI/SNF complexes and facilitates their targeting to appropriate enhancers.
Bastiaan Heijmans, Peter ’t Hoen, Lude Franke and colleagues describe a strategy to identify context-dependent expression quantitative trait loci (eQTLs). They apply their method to peripheral blood RNA–seq data from 2,116 unrelated individuals and discover 23,060 significant cis-regulated genes, of which 12% showed context-dependent eQTL effects.
Songlin Chen, Manfred Schartl, Qingyin Wang, Deborah M. Power and colleagues analyze the genome of the Japanese flounder and its transcriptome dynamics during metamorphosis. They report a role for thyroid hormone and retinoic acid signaling, as well as phototransduction pathways, in the regulation of craniofacial asymmetry.
Chi-Hua Chen and colleagues report a GWAS for five personality traits and identify four loci associated with extraversion and two associated with neuroticism at genome-wide significance. They find that the five personality traits are genetically correlated and identify genetic correlations between personality traits and psychiatric disorders.
Audrey Chu, Matthew Steinhauser, Caroline Fox and colleagues report results of genome-wide association meta-analyses of ectopic-fat traits in individuals of European, African, Hispanic and Chinese ancestry. They identify seven new loci associated with ectopic-fat traits and present functional studies suggesting physiological roles for ATXN1 and UBE2E2 in adipogenesis.
Peter 't Hoen, Lude Franke, Bastiaan Heijmans and colleagues present a combined analysis of methylome and transcriptome data from a large collection of whole-blood samples to infer the downstream effects of disease-associated variants. They identify a large number of trait-associated SNPs influencing methylation of CpG sites in trans, providing insights into the downstream functional effects of many disease-associated variants.
Zachary Lippman, José Jiménez-Gómez and colleagues show that cultivated tomatoes have lost day-length-sensitive flowering, compared to their wild relatives, as a result of cis-regulatory variation affecting expression of SP5G, a paralog of the florigen gene SFT. They engineered SP5G loss-of-function mutant plants, resulting in rapid flowering and early yield.
Yoshitaka Fukada, Hikari Yoshitane and colleagues report that rhythmic expression of ADARB1, an RNA-editing enzyme that catalyzes adenosine-to-inosine conversion, controls mRNA oscillations in the mouse liver. Mice with Adarb1 mutations exhibit short-period rhythms in locomotor activity and gene expression.
Thorsten Schnurbusch, Helmy Youssef and colleagues show that VRS2, a transcription factor of the SHI family, regulates floral organ patterning and phase duration during spike development in barley. Their data establish a link between the SHI protein family and sucrose metabolism during organ growth and development.
Pim van der Harst and colleagues report a genome-wide association study for resting heart rate in individuals of European ancestry and identify 64 associated loci, 46 of which have not been previously reported. A genetic risk score constructed using the associated variants is significantly associated with increased mortality risk.
Lars Bullinger, Jinghui Zhang, Jeffery Klco, James Downing and colleagues report a detailed genomic analysis of pediatric and adult core-binding factor acute myeloid leukemias (CBF-AMLs). They identify recurrent mutations in CCND2, MGA, DHX15 and ZBTB7A and highlight dramatic differences in the landscape of cooperating mutations between different CBF-AML subtypes.
Bikram Gill and colleagues report map-based cloning of Fhb1, which confers resistance to Fusarium head blight in wheat. They show that the PFT gene at Fhb1 confers resistance and encodes a chimeric lectin with agglutinin domains and a pore-forming toxin domain, identifying a new type of durable plant-resistance gene.
Joshua Milner and colleagues show that increased TPSAB1 copy number causes a multisystem disorder marked by elevated basal serum tryptase levels. Shared symptoms in affected individuals include irritable bowel syndrome, cutaneous flushing and pruritus, connective tissue abnormalities and dysautonomia.
Paul Brennan and colleagues perform genome-wide association analysis for oral cavity and pharyngeal cancer in trans-ancestry populations. They find seven new loci across different cancer subtypes, including a protective association in the HLA region that has a stronger effect in patients with human papillomavirus–positive cancers.
Amit Majithia and colleagues employ a pooled assay in human macrophages to assess the functional effects of all possible missense variants in PPARG. Their study shows the value of saturation mutagenesis and prospective experimental characterization to support diagnostic interpretation of newly discovered missense variants in disease-related genes.
Richard Spritz and colleagues present a genome-wide association study of autoimmune vitiligo in 4,680 cases and 39,586 controls and report 23 new risk loci. Their results highlight specific pathways, including immune response, apoptosis and melanocyte function, that may be important in the pathobiology of autoimmune vitiligo.