Thursday, May 31, 2018

Nature Genetics Contents: June 2018 Volume 50 Number 6

If you are unable to see the message below, click here to view.
Nature Genetics

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!

June 2018 Volume 50, Issue 6

News & Views
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.




A rose on the garden fair    p769

News & Views


The genomic floral language of rose    pp770 - 771
Qing Xu & Zhong-Jian Liu

JOBS of the week
Postdoctoral Fellow / Genetics, Genomics and Informatics - 18000000JP
The University of Tennessee Health Science Center (UTHSC)
Genomics Project Leaders
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
More Science jobs from
The Genetics of Neuropathic Pain and its Comorbidities
Bar Harbor, USA
More science events from
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!



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.

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.

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.

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.

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.

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.




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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.


Adolescence Collection

Exploring the science of adolescence and its far-reaching implications for societal challenges 

Access the Collection online
nature events
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 For event advertising opportunities across the Nature Publishing Group portfolio please contact
More Nature Events

You have been sent this Table of Contents Alert because you have opted in to receive it. You can change or discontinue your e-mail alerts at any time, by modifying your preferences on your account at:
(You will need to log in to be recognised as a registrant)

For further technical assistance, please contact our registration department

For print subscription enquiries, please contact our subscription department

For other enquiries, please contact our customer feedback department

Springer Nature | One New York Plaza, Suite 4500 | New York | NY 10004-1562 | USA

Springer Nature's worldwide offices:
London - Paris - Munich - New Delhi - Tokyo - Melbourne
San Diego - San Francisco - Washington - New York - Boston

Macmillan Publishers Limited is a company incorporated in England and Wales under company number 785998 and whose registered office is located at The Campus, 4 Crinan Street, London, N1 9XW.

© 2018 Macmillan Publishers Limited, part of Springer Nature. All Rights Reserved.

Springer Nature

No comments: