| |  | | | News & Views | |  | | | Letters | | |  | | | Association analysis in over 329,000 individuals identifies 116 independent variants influencing neuroticism pp6 - 11
Michelle Luciano, Saskia P. Hagenaars, Gail Davies, W. David Hill, Toni-Kim Clarke et al.
doi:10.1038/s41588-017-0013-8
Analysis of 329,000 individuals in the UK Biobank identifies 116 loci associated with neuroticism. Genes implicated are enriched in neuronal differentiation pathways, and genetic correlations between neuroticism and other mental health traits are elucidated. | | | | | Single-cell DNA methylome sequencing of human preimplantation embryos pp12 - 19
Ping Zhu, Hongshan Guo, Yixin Ren, Yu Hou, Ji Dong et al.
doi:10.1038/s41588-017-0007-6
An analysis of single-cell DNA methylome sequencing data from human preimplantation embryos finds evidence for de novo methylation. Methylation reprogramming at this stage is a balance between global demethylation, which is faster in the paternal genome, and focused remethylation. | | | | | Hidden genetic variation shapes the structure of functional elements in Drosophila pp20 - 25
Mahul Chakraborty, Nicholas W. VanKuren, Roy Zhao, Xinwen Zhang, Shannon Kalsow et al.
doi:10.1038/s41588-017-0010-y
A reference-quality genome assembly of a Drosophila melanogaster strain allows for accurate mapping of structural variants through comparative analysis with the existing Drosophila genome. Previously hidden structural variation alters a larger fraction of the genome than SNPs and often affects candidate genes underlying complex traits. | | | Advertisement | | npj Molecular Phenomics is an online-only, open access journal that provides a forum for cutting-edge scientific advances in the emerging field of phenomics, the study of the physical and chemical characteristics of an individual in quantitative terms. Part of the Nature Partner Journals series, npj Molecular Phenomics is published in partnership with Fudan University. The journal is now open for submissions. |  | | | | | | Articles | | | | | | Protein-altering variants associated with body mass index implicate pathways that control energy intake and expenditure in obesity pp26 - 41
Valérie Turcot, Yingchang Lu, Heather M. Highland, Claudia Schurmann, Anne E. Justice et al.
doi:10.1038/s41588-017-0011-x
Exome-wide analysis identifies rare and low-frequency coding variants associated with body mass index. Gene-based meta-analysis and functional studies implicate 13 genes, eight of which are novel, and neuronal pathways as factors in human obesity. | | | | | Multiancestry association study identifies new asthma risk loci that colocalize with immune-cell enhancer marks pp42 - 53
Florence Demenais, Patricia Margaritte-Jeannin, Kathleen C. Barnes, William O. C. Cookson, Janine Altmüller et al.
doi:10.1038/s41588-017-0014-7
The authors perform meta-analysis of GWAS studies for asthma from multiancestral cohorts. They identify five new loci and find that the asthma-associated loci are enriched near enhancer marks in immune cells. | | | | | Molecular and functional variation in iPSC-derived sensory neurons pp54 - 61
Jeremy Schwartzentruber, Stefanie Foskolou, Helena Kilpinen, Julia Rodrigues, Kaur Alasoo et al.
doi:10.1038/s41588-017-0005-8
This study identifies regulatory variants in sensory neurons derived from induced pluripotent stem cells. Despite differentiation-induced variability, an allele-specific method allowed detection of loci influencing gene expression, chromatin accessibility and RNA splicing. | | | | | Mutant-IDH1-dependent chromatin state reprogramming, reversibility, and persistence pp62 - 72
Sevin Turcan, Vladimir Makarov, Julian Taranda, Yuxiang Wang, Armida W. M. Fabius et al.
doi:10.1038/s41588-017-0001-z
This study uses human astrocytes and glioma tumorspheres to generate an atlas of mutant-IDH1-induced epigenomic reprogramming. The findings have implications for understanding mutant IDH function and for optimizing approaches to target IDH-mutant tumors. | | | | | Identification of H3K4me1-associated proteins at mammalian enhancers pp73 - 82
Andrea Local, Hui Huang, Claudio P. Albuquerque, Namit Singh, Ah Young Lee et al.
doi:10.1038/s41588-017-0015-6
The authors conduct mass spectrometry experiments identifying H3K4me1-associated proteins, including members of the BAF chromatin-remodeling complex. They show that H3K4me1 augments association of the BAF complex with enhancers in vivo and that H3K4me1-marked nucleosomes are more efficiently remodeled by the BAF complex in vitro. | | | | | TET proteins safeguard bivalent promoters from de novo methylation in human embryonic stem cells pp83 - 95
Nipun Verma, Heng Pan, Louis C. Doré, Abhijit Shukla, Qing V. Li et al.
doi:10.1038/s41588-017-0002-y
TET1, TET2 and TET3 triple-knockout (TKO) human embryonic stem cells (hESCs) exhibit bivalent promoter hypermethylation without a corresponding decrease in gene expression in the undifferentiated state. However, PAX6 promoter hypermethylation in TKO hESCs impairs neural differentiation. | | | | | Dynamic epigenomic landscapes during early lineage specification in mouse embryos pp96 - 105
Yu Zhang, Yunlong Xiang, Qiangzong Yin, Zhenhai Du, Xu Peng et al.
doi:10.1038/s41588-017-0003-x
Transcriptome, DNA methylome and Hi-C profiling of peri- and post-implantation mouse cell lineages identified allele- and lineage-specific methylation patterns. Global demethylation and remethylation correlate with megabase chromatin compartments. | | | | | A molecular roadmap for the emergence of early-embryonic-like cells in culture pp106 - 119
Diego Rodriguez-Terrones, Xavier Gaume, Takashi Ishiuchi, Amélie Weiss, Arnaud Kopp et al.
doi:10.1038/s41588-017-0016-5
Rare cells resembling the 2-cell-stage embryo (2 C) arise in embryonic stem cell cultures. By performing single-cell analyses and an siRNA screen, the authors identify the intermediate cellular states and epigenetic regulators that underpin the transition to a 2C-like state. | | | | | Mutations in SELENBP1, encoding a novel human methanethiol oxidase, cause extraoral halitosis pp120 - 129
Arjan Pol, G. Herma Renkema, Albert Tangerman, Edwin G. Winkel, Udo F. Engelke et al.
doi:10.1038/s41588-017-0006-7
Ron Wevers and colleagues report that mutations in the methanethiol oxidase gene SELENBP1 cause chronic extraoral halitosis. They find that enzyme deficiency leads to increased levels of methanethiol and dimethylsulfide in the breath and that knockout mice have similar biochemical phenotypes. | | | | | Sexual-lineage-specific DNA methylation regulates meiosis in Arabidopsis pp130 - 137
James Walker, Hongbo Gao, Jingyi Zhang, Billy Aldridge, Martin Vickers et al.
doi:10.1038/s41588-017-0008-5
RNA-directed DNA methylation (RdDM) in the Arabidopsis thaliana male sexual lineage is shown here to regulate gene expression in meiocytes. Loss of sexual-lineage-specific RdDM causes mis-splicing of the MPS1 gene, thereby disrupting meiosis | | | | | Genomic features of bacterial adaptation to plants pp138 - 150
Asaf Levy, Isai Salas Gonzalez, Maximilian Mittelviefhaus, Scott Clingenpeel, Sur Herrera Paredes et al.
doi:10.1038/s41588-017-0012-9
Comparative genomic analysis of 3,837 bacterial genomes, including new sequences from 484 root-associated isolates, identifies plant-associated gene clusters and plant-mimicking domains. | | | Advertisement | | | | | | | |  | Technical Reports | | | | | | Annotation-free quantification of RNA splicing using LeafCutter pp151 - 158
Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson et al.
doi:10.1038/s41588-017-0004-9
LeafCutter is a new tool that identifies variable intron splicing events from RNA-seq data for analysis of complex alternative splicing. The method does not require transcript annotation and can be used to map splicing quantitative trait loci. | | | Advertisement | | Nature Reviews Disease Primers — Stay updated
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