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TABLE OF CONTENTS

June 2018 Volume 50, Issue 6

Editorial
News & Views
Letters
Articles
 
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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
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Genomics Project Leaders
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Faculty Positions in Statistical Genetics and Computational Genomics
Genome Institute of Singapore (GIS)
Principal Scientist - Human Genetics, Early Target Discovery
Takeda
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The Genetics of Neuropathic Pain and its Comorbidities
09.09.18
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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.

 

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