Nature Genetics Contents: June 2018 Volume 50 Number 6

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Advertisement Harness the Power of Machine Learning to Select Antibodies  BenchSci decodes millions of scientific papers to extract published figures with their antibody usage information. You can view 3,161,807 figures from publications, vendors, and independent organizations. It's free for academic researchers. Sign Up Now! TABLE OF CONTENTS June 2018 Volume 50, Issue 6 Editorial News & Views Letters Articles   Advertisement   Purify Entire Genes with CATCH: Using customized Cas9 nucleases, researchers can purify large genomic targets with the SageHLS from Sage Science. Achieve complete phasing and detect SVs with short-read sequencing. Learn more about this study from Stanford University.   Editorial   A rose on the garden fair    p769 doi:10.1038/s41588-018-0146-4 News & Views   The genomic floral language of rose    pp770 - 771 Qing Xu & Zhong-Jian Liu doi:10.1038/s41588-018-0141-9 Genetics JOBS of the week Postdoctoral Fellow / Genetics, Genomics and Informatics - 18000000JP The University of Tennessee Health Science Center (UTHSC) Genomics Project Leaders AstraZeneca Staff Scientist VA Boston Healthcare System Faculty Positions in Statistical Genetics and Computational Genomics Genome Institute of Singapore (GIS) Principal Scientist - Human Genetics, Early Target Discovery Takeda More Science jobs from Genetics EVENT The Genetics of Neuropathic Pain and its Comorbidities 09.09.18 Bar Harbor, USA More science events from Advertisement Do you have a career question?  The Naturejobs podcast features one-on-one Q&As, panel discussions and other exclusive content to help scientists with their careers. Hosted on the Naturejobs blog, the podcast is also available on iTunes and Soundcloud.  Listen today!   Letters   The Rosa genome provides new insights into the domestication of modern roses    pp772 - 777 Olivier Raymond, Jérôme Gouzy, Jérémy Just, Hélène Badouin, Marion Verdenaud et al. doi:10.1038/s41588-018-0110-3 High-quality genome assembly of diploid Rosa chinensis and resequencing of major genotypes highlights the origin of modern rose cultivars and provides insights into color biosynthesis and scent pathways.   Genome-wide analyses identify 68 new loci associated with intraocular pressure and improve risk prediction for primary open-angle glaucoma    pp778 - 782 Anthony P. Khawaja, Jessica N. Cooke Bailey, Nicholas J. Wareham, Robert A. Scott, Mark Simcoe et al. doi:10.1038/s41588-018-0126-8 A meta-analysis of 139,555 Europeans identifies 68 new genomic loci associated with intraocular pressure. Incorporating these new findings into genetic models improves risk prediction for primary open-angle glaucoma.   3′ UTR shortening represses tumor-suppressor genes in trans by disrupting ceRNA crosstalk    pp783 - 789 Hyun Jung Park, Ping Ji, Soyeon Kim, Zheng Xia, Benjamin Rodriguez et al. doi:10.1038/s41588-018-0118-8 Shortening of mRNA 3′ UTRs is often observed in cancer. A combination of model-based analysis and experiments suggests that 3′ UTR shortening disrupts competing endogenous RNA crosstalk, thus influencing tumor-suppressor expression in trans.   The fecal metabolome as a functional readout of the gut microbiome    pp790 - 795 Jonas Zierer, Matthew A. Jackson, Gabi Kastenmüller, Massimo Mangino, Tao Long et al. doi:10.1038/s41588-018-0135-7 Comprehensive fecal metabolic profiling in 786 individuals from TwinsUK provides insights into the influence of host genetics and gut microbial composition on metabolites that may mediate microbiome-associated phenotypes.   Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits    pp796 - 802 Xiongming Du, Gai Huang, Shoupu He, Zhaoen Yang, Gaofei Sun et al. doi:10.1038/s41588-018-0116-x The authors report an improved genome assembly of G. arboretum and resequencing of 243 diploid cotton accessions. GWAS and QTL-seq identify a number of candidate loci that associate with seed oil content, disease resistance and yield traits in cotton.   Articles   Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield    pp803 - 813 Zhiying Ma, Shoupu He, Xingfen Wang, Junling Sun, Yan Zhang et al. doi:10.1038/s41588-018-0119-7 The authors resequence a core collection of upland cotton (Gossypium hirsutum) comprising 419 accessions. They analyze genomic variation and conduct a genome-wide association study for 13 fiber quality and yield traits in 12 different environments.   Analysis of the androgen receptor–regulated lncRNA landscape identifies a role for ARLNC1 in prostate cancer progression    pp814 - 824 Yajia Zhang, Sethuramasundaram Pitchiaya, Marcin Cieślik, Yashar S. Niknafs, Jean C.-Y. Tien et al. doi:10.1038/s41588-018-0120-1 ARLNC1 is a newly discovered lncRNA that is induced by androgen receptor (AR) and maintains AR signaling by stabilizing the AR transcript. Knockdown of ARLNC1 suppresses AR expression, AR signaling and prostate cancer growth in vitro and in vivo.   Genetic identification of brain cell types underlying schizophrenia    pp825 - 833 Nathan G. Skene, Julien Bryois, Trygve E. Bakken, Gerome Breen, James J. Crowley et al. doi:10.1038/s41588-018-0129-5 Integration of single-cell RNA sequencing with genome-wide association data implicates specific brain cell types in schizophrenia. Gene sets previously associated with schizophrenia implicate the same cell types, which include pyramidal cells and medium spiny neurons.   Genome-wide association meta-analysis highlights light-induced signaling as a driver for refractive error    pp834 - 848 Milly S. Tedja, Robert Wojciechowski, Pirro G. Hysi, Nicholas Eriksson, Nicholas A. Furlotte et al. doi:10.1038/s41588-018-0127-7 Transancestral GWAS meta-analysis in 160,420 individuals identifies 139 loci associated with refractive error, including myopia. Newly identified genes implicate pathways involved in eye growth and light signaling cascades.   Frequent transmission of the Mycobacterium tuberculosis Beijing lineage and positive selection for the EsxW Beijing variant in Vietnam    pp849 - 856 Kathryn E. Holt, Paul McAdam, Phan Vuong Khac Thai, Nguyen Thuy Thuong Thuong, Dang Thi Minh Ha et al. doi:10.1038/s41588-018-0117-9 Genomic analysis of Mycobacterium tuberculosis (Mtb) isolated from tuberculosis patients identifies the transmission dynamics of Mtb in Vietnam including frequent transmission of Beijing lineage and positive selection for EsxW Beijing variant.   A genome-wide cross-trait analysis from UK Biobank highlights the shared genetic architecture of asthma and allergic diseases    pp857 - 864 Zhaozhong Zhu, Phil H. Lee, Mark D. Chaffin, Wonil Chung, Po-Ru Loh et al. doi:10.1038/s41588-018-0121-0 Genome-wide cross-trait analysis shows a strong genetic correlation between asthma and allergic diseases. Shared susceptibility loci are enriched for genes involved in immune and inflammatory responses and genes expressed in epithelial tissues.   Locus-specific control of the de novo DNA methylation pathway in Arabidopsis by the CLASSY family    pp865 - 873 Ming Zhou, Ana Marie S. Palanca & Julie A. Law doi:10.1038/s41588-018-0115-y CLASSY chromatin remodeling factors (CLSY 1–4) are shown to regulate DNA methylation in Arabidopsis, both globally and in a locus-specific manner. CLSYs and RNA polymerase IV control the production of 24-nucleotide siRNAs, which guide DNA methylation.   Multiplex assessment of protein variant abundance by massively parallel sequencing    pp874 - 882 Kenneth A. Matreyek, Lea M. Starita, Jason J. Stephany, Beth Martin, Melissa A. Chiasson et al. doi:10.1038/s41588-018-0122-z VAMP-seq is a scalable assay that measures the effects of missense variants on intracellular protein abundance. Applying VAMP-seq to thousands of PTEN and TPMT variants helps to classify them as pathogenic or benign.   UTX-mediated enhancer and chromatin remodeling suppresses myeloid leukemogenesis through noncatalytic inverse regulation of ETS and GATA programs    pp883 - 894 Malgorzata Gozdecka, Eshwar Meduri, Milena Mazan, Konstantinos Tzelepis, Monika Dudek et al. doi:10.1038/s41588-018-0114-z This study shows that UTX (KDM6A) suppresses myeloid leukemogenesis through noncatalytic functions. UTX loss leads to alterations in H3K27ac, H3K4me1 and chromatin accessibility, and in gene-regulatory programs mediated by ETS and GATA transcription factors.   Quantification of subclonal selection in cancer from bulk sequencing data    pp895 - 903 Marc J. Williams, Benjamin Werner, Timon Heide, Christina Curtis, Chris P. Barnes et al. doi:10.1038/s41588-018-0128-6 This analysis uses computational modeling of clonal selection to measure evolutionary dynamics in primary human cancers. The method employs high-throughput sequencing data and simultaneously measures the selective advantage and time of appearance of subclones.   Advertisement Adolescence Collection Exploring the science of adolescence and its far-reaching implications for societal challenges  Access the Collection online   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. For event advertising opportunities across the Nature Publishing Group portfolio please contact natureevents@nature.com More Nature Events

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