Nature Genetics Contents: January 2017 pp 1 - 168

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Advertisement nature.com webcasts Springer Nature presents a custom webcast on: Liquid biopsy: CTC-based classifier predicts chemo resistance in lung cancer Date: Thursday January 19 2017 Time: 8AM PST, 11AM EST, 4PM GMT, 5PM CET  Register for FREE Sponsored by:  Menarini Silicon Biosystems   TABLE OF CONTENTS January 2017 Volume 49, Issue 1 Editorial Correspondence News and Views Analysis Articles Letters Advertisement January 2017 marks the 2nd anniversary of Nature Plants! Visit the journal to see what’s been publishing and submit your research. Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement nature.com webcasts Springer Nature presents a custom webcast on: CRISPR/Cas9 strategies for disease modeling and drug discovery Date: Tuesday, 24 January 2017 Time: 8AM PST, 11AM EST, 4PM GMT, 5PM CST  Register for FREE  Sponsored by:  The Jackson Laboratory     Advertisement CRISPR Calendar 2017 To celebrate the continuing rise to fame of the CRISPR system, the Nature Reviews Genetics 2017 CRISPR calendar highlights the underlying biology of CRISPR, as well as its diverse range of exciting potential applications in genetic research, biotechnology and therapeutics. Download the calendar free online Produced with support from  OriGene   Editorial Top Finally accepting plant domestication   p1 doi:10.1038/ng.3770 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. Correspondence Top Is a super-enhancer greater than the sum of its parts?   pp2 - 3 Noah Dukler, Brad Gulko, Yi-Fei Huang and Adam Siepel doi:10.1038/ng.3759 News and Views Top Copy number alterations unmasked as enhancer hijackers   pp5 - 6 Rameen Beroukhim, Xiaoyang Zhang and Matthew Meyerson doi:10.1038/ng.3754 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. See also: Article by Weischenfeldt et al. A multitrait GWAS sheds light on insulin resistance   pp7 - 8 Iris M Heid and Thomas W Winkler doi:10.1038/ng.3758 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. See also: Article by Lotta et al. How hormones regulate floral architecture in barley   pp8 - 9 Scott A Boden doi:10.1038/ng.3750 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. See also: Letter by Youssef et al. Genetics JOBS of the week Professor & Chair, Genetics UNC School of Medicine Postdoctoral Fellow – Cancer Genetics and Epigenetics City of Hope Director of the Primate Genetics Research Section Oregon Health & Science University and Knight Cancer Institute Postdoctoral Fellow University of Utah Department of Biochemistry Staff Scientist Wellcome Trust Sanger Institute More Science jobs from Analysis Top Tumor-suppressor genes that escape from X-inactivation contribute to cancer sex bias   pp10 - 16 Andrew Dunford, David M Weinstock, Virginia Savova, Steven E Schumacher, John P Cleary et al. doi:10.1038/ng.3726 Andrew Lane and colleagues analyze somatic alterations across 21 tumor types for evidence of sex bias. They find that an excess of genes on the non-pseudoautosomal region of the X chromosome harbor loss-of-function mutations more frequently in males, suggesting that biallelic expression of these genes in females contributes to reduced cancer incidence in females across a variety of tumor types. Advertisement Environmental Microbial Biofilms and Human Microbiomes: Drivers of Future Sustainability  February 12-15, 2017 | Nanyang Executive Centre, Singapore Presented by: Nanyang Technological University (NTU) | Singapore Centre for Environmental Life Sciences Engineering (SCELSE) | npj Biofilms and Microbiomes  Register now!    Articles Top Integrative genomic analysis implicates limited peripheral adipose storage capacity in the pathogenesis of human insulin resistance   pp17 - 26 Luca A Lotta, Pawan Gulati, Felix R Day, Felicity Payne, Halit Ongen et al. doi:10.1038/ng.3714 Luca Lotta, Robert Scott, Stephen O'Rahilly, Claudia Langenberg, David Savage, Nicholas Wareham, Ines Barroso and colleagues identify 53 genomic regions associated with insulin resistance phenotypes. Their findings suggest that limited storage capacity of peripheral adipose tissue is an important etiological component in insulin-resistant cardiometabolic disease and highlight genes and mechanisms underpinning this link. See also: News and Views by Heid & Winkler Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects   pp27 - 35 CNV and Schizophrenia Working Groups of the Psychiatric Genomics Consortium doi:10.1038/ng.3725 The CNV analysis group of the Psychiatric Genomic Consortium analyzes a large schizophrenia cohort to examine genomic copy number variants (CNVs) and disease risk. They find an enrichment of CNV burden in cases versus controls and identify 8 genome-wide significant loci as well as novel suggestive loci conferring either risk or protection to schizophrenia. The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies   pp36 - 45 Claire Redin, Harrison Brand, Ryan L Collins, Tammy Kammin, Elyse Mitchell et al. doi:10.1038/ng.3720 Michael Talkowski and colleagues analyze balanced chromosomal abnormalities in 273 individuals by whole-genome sequencing. Their findings suggest that sequence-level resolution improves prediction of clinical outcomes for balanced rearrangements and provides insight into pathogenic mechanisms such as altered gene regulation due to changes in chromosome topology. Titin-truncating variants affect heart function in disease cohorts and the general population   pp46 - 53 Sebastian Schafer, Antonio de Marvao, Eleonora Adami, Lorna R Fiedler, Benjamin Ng et al. doi:10.1038/ng.3719 Stuart Cook and colleagues study the role of TTN (titin)-truncating variants using a combination of heart physiology experiments in rats and genomic analysis in humans. Their data show that TTN variants are associated with a range of cardiac phenotypes in healthy individuals and in patients with dilated cardiomyopathy. Genome-wide association analyses using electronic health records identify new loci influencing blood pressure variation   pp54 - 64 Thomas J Hoffmann, Georg B Ehret, Priyanka Nandakumar, Dilrini Ranatunga, Catherine Schaefer et al. doi:10.1038/ng.3715 Thomas Hoffmann, Neil Risch and colleagues use longitudinal electronic health records from almost 100,000 individuals to conduct genome-wide association studies for blood pressure measurements. They find new significant loci that replicate in independent cohorts and can double the variance explained by using multiple blood pressure data points. Pan-cancer analysis of somatic copy-number alterations implicates IRS4 and IGF2 in enhancer hijacking   pp65 - 74 Joachim Weischenfeldt, Taronish Dubash, Alexandros P Drainas, Balca R Mardin, Yuanyuan Chen et al. doi:10.1038/ng.3722 Hanno Glimm, Jan Korbel and colleagues present a computational framework called cis expression structural alteration mapping (CESAM), which they use to identify somatic copy-number alterations affecting cis-regulatory elements in cancer. They find that enhancer hijacking leads to overexpression of IRS4 and IGF2 in cancer. See also: News and Views by Beroukhim et al. Qki deficiency maintains stemness of glioma stem cells in suboptimal environment by downregulating endolysosomal degradation   pp75 - 86 Takashi Shingu, Allen L Ho, Liang Yuan, Xin Zhou, Congxin Dai et al. doi:10.1038/ng.3711 Jian Hu and colleagues use mouse models to show that Qki deficiency promotes gliomagenesis by allowing neural stem cells to maintain their stemness outside the subventricular zone. Mechanistically, they show that Qki deficiency decreases endolysosome-mediated degradation of receptors that are essential for maintaining self-renewal, allowing cells to cope with low ligand levels outside of their niche. Inactivation of Capicua drives cancer metastasis   pp87 - 96 Ross A Okimoto, Frank Breitenbuecher, Victor R Olivas, Wei Wu, Beatrice Gini et al. doi:10.1038/ng.3728 Trever Bivona and colleagues use an in vivo lung cancer metastasis model to show that the transcriptional repressor Capicua (CIC) suppresses invasion and metastasis. CIC inactivation leads to upregulation of ETV4 and MMP24, which is necessary and sufficient for metastasis. An iPSC-derived vascular model of Marfan syndrome identifies key mediators of smooth muscle cell death   pp97 - 109 Alessandra Granata, Felipe Serrano, William George Bernard, Madeline McNamara, Lucinda Low et al. doi:10.1038/ng.3723 Sanjay Sinha and colleagues use a vascular model derived from human induced pluripotent stem cells from patients with Marfan syndrome with fibrillin-1 alterations to study aortic aneurysms. They find defects that mimic Marfan pathology as well as novel targets for treatment and can rescue the phenotype by correcting the mutation through genome editing. Transient transcription in the early embryo sets an epigenetic state that programs postnatal growth   pp110 - 118 Maxim V C Greenberg, Juliane Glaser, Máté Borsos, Fatima El Marjou, Marius Walter et al. doi:10.1038/ng.3718 Deborah Bourc'his and colleagues report that mouse embryos deficient for Liz (long isoform of Zdbf2) develop normally but fail to activate Zdbf2 in the postnatal brain and show growth reduction. These data suggest that transcription during an early embryonic stage may program a stable epigenetic state with later physiological consequences. Letters Top The genome and transcriptome of Japanese flounder provide insights into flatfish asymmetry OPEN   pp119 - 124 Changwei Shao, Baolong Bao, Zhiyuan Xie, Xinye Chen, Bo Li et al. doi:10.1038/ng.3732 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. Multiethnic genome-wide meta-analysis of ectopic fat depots identifies loci associated with adipocyte development and differentiation   pp125 - 130 Audrey Y Chu, Xuan Deng, Virginia A Fisher, Alexander Drong, Yang Zhang et al. doi:10.1038/ng.3738 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. Disease variants alter transcription factor levels and methylation of their binding sites   pp131 - 138 Marc Jan Bonder, René Luijk, Daria V Zhernakova, Matthijs Moed, Patrick Deelen et al. doi:10.1038/ng.3721 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. Identification of context-dependent expression quantitative trait loci in whole blood   pp139 - 145 Daria V Zhernakova, Patrick Deelen, Martijn Vermaat, Maarten van Iterson, Michiel van Galen et al. doi:10.1038/ng.3737 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. ADARB1 catalyzes circadian A-to-I editing and regulates RNA rhythm   pp146 - 151 Hideki Terajima, Hikari Yoshitane, Haruka Ozaki, Yutaka Suzuki, Shigeki Shimba et al. doi:10.1038/ng.3731 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. Genome-wide analyses for personality traits identify six genomic loci and show correlations with psychiatric disorders   pp152 - 156 Min-Tzu Lo, David A Hinds, Joyce Y Tung, Carol Franz, Chun-Chieh Fan et al. doi:10.1038/ng.3736 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. VRS2 regulates hormone-mediated inflorescence patterning in barley   pp157 - 161 Helmy M Youssef, Kai Eggert, Ravi Koppolu, Ahmad M Alqudah, Naser Poursarebani et al. doi:10.1038/ng.3717 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. See also: News and Views by Boden Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato   pp162 - 168 Sebastian Soyk, Niels A Müller, Soon Ju Park, Inga Schmalenbach, Ke Jiang et al. doi:10.1038/ng.3733 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. Top Natureevents is a fully searchable, multi-disciplinary database designed to maximise exposure for events organisers. The contents of the Natureevents Directory are now live. The digital version is available here. Find the latest scientific conferences, courses, meetings and symposia on natureevents.com. 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