Articles in 2016

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  • A defining characteristic of grasses, including major cereal crops, is the way in which flowers are arranged on an inflorescence. A new study finds that regulation of hormone levels during development is crucial for determining the arrangement of flowers on a barley inflorescence, opening new doors for increasing grain yield.

    • Scott A Boden
    News & Views
  • Our understanding of how DNA copy number changes contribute to disease, including cancer, has to a large degree been focused on the changes in gene dosage that they generate and has neglected the effects of the DNA rearrangements that lead to their formation. A new study reports an innovative analytical framework for copy number alterations that are oncogenic primarily owing to the genomic rearrangements that underlie them.

    • Rameen Beroukhim
    • Xiaoyang Zhang
    • Matthew Meyerson
    News & Views
  • A genome-wide study of fasting insulin, HDL cholesterol and triglycerides, designed to depict insulin resistance, identified 53 independent loci associated with a limited capacity to store fat in a healthy way. The increased power of this multitrait approach provides insights into an otherwise difficult-to-grasp phenotype.

    • Iris M Heid
    • Thomas W Winkler
    News & Views
  • Agriculture has depended since its Neolithic origins upon spontaneous or induced genetic variation. Human selection on naturally occurring variation in flowering is the most frequent source of domesticated crop plants. In the current era of rapid technological advance in reading and writing genomes, we advocate universal access to some safe modular variation in flower, leaf and color traits that can be operated without labs or restrictions by ordinary farmers and gardeners.

    Editorial
  • James Liley, John Todd and Chris Wallace present a statistical method for determining whether disease-associated variants have different effect sizes in phenotypically defined subgroups of disease cases. The test can be combined with existing methods to determine whether genetic heterogeneity is driven by population stratification or by different mechanisms of disease pathology.

    • James Liley
    • John A Todd
    • Chris Wallace
    Technical Report
  • Nir Hacohen, Bruce Walker, David Sabatini, Eric Lander and colleagues perform a CRISPR–Cas9-based screen for host factors that are required for HIV infection. They identify two known and three novel factors that are necessary for viral infection but that are not required for cell viability, making them potential targets for antiviral therapy.

    • Ryan J Park
    • Tim Wang
    • Bruce D Walker
    Article
  • 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.

    • Sun-Gou Ji
    • Brian D Juran
    • Carl A Anderson
    Letter
  • 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.

    • Jacqueline M Lane
    • Jingjing Liang
    • Richa Saxena
    Letter
  • Manju Kurian and colleagues report heterozygous variants in KMT2B in 27 unrelated individuals with a complex progressive childhood-onset dystonia, often associated with a typical facial appearance. Their findings highlight a clinically recognizable form of dystonia and demonstrate a crucial role for KMT2B in the physiological control of voluntary movement.

    • Esther Meyer
    • Keren J Carss
    • Manju A Kurian
    Article
  • Jaroslaw Maciejewski, Seishi Ogawa and colleagues examine the clonal dynamics of myelodysplastic syndromes (MDS) by analyzing whole-exome and targeted sequencing data from a large patient collection. They find that progression steps previously defined by pathologic criteria are accompanied by distinct molecular changes, and they show that driver genes can be classified into molecular subtypes differentially associated with low-risk MDS, high-risk MDS or secondary acute myeloid leukemia.

    • Hideki Makishima
    • Tetsuichi Yoshizato
    • Jaroslaw P Maciejewski
    Article
  • 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.

    • Benjamin Z Stanton
    • Courtney Hodges
    • Gerald R Crabtree
    Letter
  • Gerald Crabtree, Cigall Kadoch and colleagues report that BAF complexes oppose PRC by rapid, ATP-dependent eviction in the absence of Pol II occupancy, transcription or replication, leading to the formation of accessible chromatin. They also find that tumor-suppressor and oncogenic mutations in BAF subunits result in differential effects on PRC eviction.

    • Cigall Kadoch
    • Robert T Williams
    • Gerald R Crabtree
    Article
  • 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.

    • Xiaofeng Wang
    • Ryan S Lee
    • Charles W M Roberts
    Letter
  • 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.

    • Daria V Zhernakova
    • Patrick Deelen
    • Lude Franke
    Letter
  • 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.

    • Changwei Shao
    • Baolong Bao
    • Songlin Chen
    LetterOpen Access
  • 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.

    • Min-Tzu Lo
    • David A Hinds
    • Chi-Hua Chen
    Letter
  • 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.

    • Audrey Y Chu
    • Xuan Deng
    • Caroline S Fox
    Letter