Genetics articles within Nature Communications

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  • Article
    | Open Access

    Histone lysine demethylases (KDMs) can mediate transcriptional reprogramming in disease states. Here the authors show that KDM3A promotes left ventricular hypertrophy and cardiac fibrosis by activating the transcription of Timp1, and that pharmacological inhibition of KDM3A attenuates cardiac remodeling induced by pressure overload.

    • Qing-Jun Zhang
    • , Tram Anh T. Tran
    •  & Zhi-Ping Liu

  • Article
    | Open Access

    Drought is a major factor limiting crop productivity. Here, via eQTL analysis and comparative genomics, the authors show compensatory evolution between trans-regulatory loci and transcription factor binding sites that shape the drought response networks in the model C4 grass Panicum hallii.

    • John T. Lovell
    • , Jerry Jenkins
    •  & Thomas E. Juenger

  • Article
    | Open Access

    Zelda is a pioneer factor that regulates transcription in Drosophila embryos. Here, the authors use quantitative live imaging and mathematical modeling to measure the effect of Zelda on transcriptional dynamics and memory, observing temporal control of gene expression by Zelda through transient interactions in hubs.

    • Jeremy Dufourt
    • , Antonio Trullo
    •  & Mounia Lagha

  • Article
    | Open Access

    Multimorbidities of common diseases often have shared underlying predisposing factors. Here Fadason et al. study the pleiotropy of SNPs and their effects on target genes by integrating chromatin interaction and expression quantitative trait loci data to identify target genes shared between phenotypes.

    • Tayaza Fadason
    • , William Schierding
    •  & Justin M. O’Sullivan

  • Article
    | Open Access

    Multigenerational outbred populations from an advanced intercross line (AIL) of mice represent useful resources for genome wide association analysis. Here, the authors analyze 1,063 LG x SM AIL mice to identify significant associations for 50 traits relevant to human health and disease.

    • Natalia M. Gonzales
    • , Jungkyun Seo
    •  & Abraham A. Palmer

  • Article
    | Open Access

    Royal jelly is the queen-maker for the honey bee that also has effects on longevity, fertility, and regeneration in mammals. Here the authors provide evidence that its major protein component Royalactin, and the mammalian structural analog Regina, maintain pluripotency in mouse ESCs by activating a ground-state pluripotency-like gene network.

    • Derrick C. Wan
    • , Stefanie L. Morgan
    •  & Kevin C. Wang

  • Article
    | Open Access

    Cross-cell heterogeneity of genotypes can be revealed by analyzing single-cell sequencing data. Here the authors develop a tool for single-cell variant calling via phylogenetic inference, and use it to analyze cancer genomics datasets.

    • Jochen Singer
    • , Jack Kuipers
    •  & Niko Beerenwinkel

  • Article
    | Open Access

    Carotid intima-media thickness (cIMT) and plaque are associated with subclinical atherosclerosis and coronary heart disease (CHD). Here, the authors identify and prioritize genetic loci for cIMT and plaque by GWAS and colocalization approaches and further demonstrate genetic correlation with CHD and stroke.

    • Nora Franceschini
    • , Claudia Giambartolomei
    •  & Christopher J. O’Donnell

  • Article
    | Open Access

    The BAF complex is a multi-subunit chromatin remodeling complex that plays important roles in transcription regulation. Here the authors provide evidence that BRD9 and GLTSCR1/BICRA or its paralog GLTSCR1-like/BICRAL define a non-canonical BAF complex that regulates naive pluripotency in mouse embryonic stem cells.

    • Jovylyn Gatchalian
    • , Shivani Malik
    •  & Diana C. Hargreaves

  • Article
    | Open Access

    Genome-wide association studies have so far identified eight risk loci for gallstone disease. Here, the authors perform meta-analysis in cohorts from Iceland and the UK which reveals further 21 common and low-frequency risk variants that highlight the role of bile acid homeostasis in gallstone disease.

    • Egil Ferkingstad
    • , Asmundur Oddsson
    •  & Kari Stefansson

  • Article
    | Open Access

    The methylation status of circulating cell-free DNA (cfDNA) can be informative about recent cell death events. Here the authors present an approach to determine the tissue origins of cfDNA, using a reference methylation atlas of 25 human tissues and cell types, and find that cfDNA from patients reveals tissue contributions that agree with clinical findings.

    • Joshua Moss
    • , Judith Magenheim
    •  & Yuval Dor

  • Article
    | Open Access

    A small RNA-based signaling cascade prevents the induction of plant resistance genes (R-genes) in the absence of pathogen challenge. Here Cai et al. show that nuclear accumulation of the R protein SNC1 can activate immunity by suppressing small RNA production and releasing R-gene repression.

    • Qiang Cai
    • , Chao Liang
    •  & Xuemei Chen

  • Article
    | Open Access

    Little is known about how sex is determined in diatoms. Here, Russo et al. show that in the diatom Pseudo-nitzschia multistriata, the gene MRP3 regulates mating type and the expression of four other mating-type biased genes.

    • Monia T. Russo
    • , Laura Vitale
    •  & Maria I. Ferrante

  • Article
    | Open Access

    Staphylococcus epidermidis is carried asymptomatically by virtually all humans but is also a major cause of nosocomial infection. Here, the authors study 141 isolates from healthy carriage and 274 isolates from clinical infections, and identify genes and genetic elements associated with pathogenicity.

    • Guillaume Méric
    • , Leonardos Mageiros
    •  & Samuel K. Sheppard

  • Article
    | Open Access

    Blood pressure (BP) is a major risk factor for cardiovascular disease and more than 200 genetic loci associated with BP are known. Here, the authors perform discovery GWAS for BP in East Asians and meta-analysis in East Asians and Europeans and report ancestry-specific BP SNPs and selection signals.

    • Fumihiko Takeuchi
    • , Masato Akiyama
    •  & Norihiro Kato

  • Article
    | Open Access

    Myoblast fusion in skeletal muscle is a complex process but how this is regulated is unclear. Here, the authors identify Ash1L, a histone methyltransferase, as modulating myoblast fusion via activation of the myogenesis gene Cdon, and observe decreased Ash1L expression in Duchenne muscular dystrophy.

    • Ilaria Castiglioni
    • , Roberta Caccia
    •  & Davide Gabellini

  • Article
    | Open Access

    Populations from North-eastern Europe, in particular those speaking Uralic languages, carry additional ancestry in similarity with modern East Asian populations. Here, the authors analyse ancient genomic data from 11 individuals from Finland and Northwest Russia, and identify genomic signals of migrations from Siberia that began at least 3500 years ago.

    • Thiseas C. Lamnidis
    • , Kerttu Majander
    •  & Stephan Schiffels

  • Article
    | Open Access

    The mammalian inactive X-chromosome (Xi) is organized into megadomains and superloops directed by the noncoding loci, Dxz4 and Firre. Here the authors provide evidence that megadomains do not precede Xist expression or Xi gene silencing, and suggest that Dxz4, Firre, and megadomains are dispensable for Xi silencing and escape from X-inactivation.

    • John E. Froberg
    • , Stefan F. Pinter
    •  & Jeannie T. Lee

  • Article
    | Open Access

    Germline mono-allelic loss of the tumour suppressor NF1 predisposes patients to the development of benign lesions but rarely further progression into cancer development. Here the authors use mouse models to show that an NF1 heterozygous microenvironment accelerates the formation of benign tumours but impairs progression to malignancy.

    • Jean-Philippe Brosseau
    • , Chung-Ping Liao
    •  & Lu Q. Le

  • Article
    | Open Access

    During early embryogenesis, critical cardiac specification events occur. Here the authors isolate cardiac progenitor cells from early zebrafish embryos and characterize accessible chromatin regions specific to this cell population, finding that many of these regions overlap with conserved non-coding elements that are ortholgous to accessible chromatin regions in human.

    • Xuefei Yuan
    • , Mengyi Song
    •  & Michael D. Wilson

  • Article
    | Open Access

    Numerous microbial symbionts, both commensal and pathogenic, are associated with honey bees. Here, the authors genomically characterize this ‘metagenome’ of the British honey bee, identifying a diversity of commensal microbes as well as known and putative pathogens

    • Tim Regan
    • , Mark W. Barnett
    •  & Tom C. Freeman

  • Article
    | Open Access

    Topoisomerases solve topological problems during DNA metabolism, but their role in RNA metabolism remains unclear. Here the authors provide evidence that in Drosophila, Topoisomerase 3β interacts biochemically and genetically with the RNAi-induced silencing complex (RISC) to promote heterochromatin formation and transcriptional silencing.

    • Seung Kyu Lee
    • , Yutong Xue
    •  & Weidong Wang

  • Article
    | Open Access

    The molecular mechanisms that underlie associations in GWAS, incl. chronic kidney disease (CKD), are largely unknown. Here, the authors perform an integrative analysis of genetic, transcriptomic and epigenomic data from human kidney to pinpoint plausible molecular pathways of CKD genetic associations.

    • Xiaoguang Xu
    • , James M. Eales
    •  & Maciej Tomaszewski

  • Article
    | Open Access

    Standard approaches for heritability and set testing in statistical genetics rely on parametric models that might not hold in reality and give inflated p-values. Here, the authors develop a fast method for permutation-based testing of marker sets and of heritability that does not suffer from model misspecification.

    • Regev Schweiger
    • , Eyal Fisher
    •  & Eran Halperin

  • Article
    | Open Access

    Human induced pluripotent stem cell derived cardiomyocytes are a powerful model for cardiogenesis and disease in vitro. Here the authors comprehensively map cardiac differentiation using multiple modalities, including single-cell RNA seq and CyTOF, in cells with a gain  or loss of function in key cardiac transcription factors.

    • Jared M. Churko
    • , Priyanka Garg
    •  & Joseph C. Wu

  • Article
    | Open Access

    Aerobic ethanol production, a phenomenon referred as Crabtree effect, allows yeast to outcompete other microorganisms in sugar rich environments. Here, the authors show that overexpression of a Gal4-like transcription factor can transform Komagataella phaffii from Crabtree effect negative to positive.

    • Özge Ata
    • , Corinna Rebnegger
    •  & Diethard Mattanovich

  • Article
    | Open Access

    Mutations in genes encoding subunits of the BAF complex can cause Coffin–Siris and Nicolaides–Baraitser syndromes. Here the authors identify overlapping DNA methylation signatures in individuals with subtypes of these two syndromes that suggest a functional link and can be used to diagnose subjects with unclear clinical presentations.

    • Erfan Aref-Eshghi
    • , Eric G. Bend
    •  & Bekim Sadikovic

  • Article
    | Open Access

    Pyrenestes finches have a bill size polymorphism thought to be maintained by disruptive selection. Here, the authors identify a single candidate region, including insulin-like growth factor 1, differentiating small and large bill size morphs and a wider region differentiating the mega-billed morph.

    • Bridgett M. vonHoldt
    • , Rebecca Y. Kartzinel
    •  & Thomas B. Smith

  • Article
    | Open Access

    Assembly of large, repeat-rich eukaryotic genomes remains challenging. Here, the authors use BioNano Genomics DLS optical mapping and single-molecule nanopore sequencing to generate a chromosome-scale assembly of a new Sorghum bicolor accession and identify variation compared to the publicly available S. bicolor genome.

    • Stéphane Deschamps
    • , Yun Zhang
    •  & Haining Lin

  • Article
    | Open Access

    DNA2 encodes a 5′ flap DNA endonuclease involved in replication and DNA double strand break processing. Here the authors by using a conditional degron system together with electron microscopy characterize the role played by Dna2 and Pif1 helicase during unperturbed DNA replication in S. cerevisiae.

    • Silvia Emma Rossi
    • , Marco Foiani
    •  & Michele Giannattasio

  • Article
    | Open Access

    It is unclear how metabolic regulation affects development of the skeleton. Here, the authors show that deletion of the glucose transporter Glut1 (Slc2a1) both prior to and following chondrogenesis in the mouse limb impairs chondrocyte proliferation and shortening of the limbs, modulated by BMP signaling.

    • Seung-Yon Lee
    • , E. Dale Abel
    •  & Fanxin Long

  • Article
    | Open Access

    Melanocytic nevus count is associated with melanoma risk. In this study, a meta-analysis of 11 nevus GWAS studies identifies novel SNPs in KITLG and 9q32, and bivariate analysis with melanoma GWAS meta-analysis reveals that most nevus genes affect melanoma risk, while melanoma risk loci do not alter the nevus count.

    • David L. Duffy
    • , Gu Zhu
    •  & Nicholas G. Martin

  • Article
    | Open Access

    Oestrogen receptors α (ERα) are expressed in a subset of mammary epithelial cells. Here, the authors identify cells with low-ERα protein levels and show that distinct cell populations have distinct requirements for the AF1 and AF2 domains of the ERα, and ERα acts in a biphasic manner dependent on developmental stage.

    • Stéphanie Cagnet
    • , Dalya Ataca
    •  & Cathrin Brisken

  • Article
    | Open Access

    Remarkable organ shape morphological diversity exists in fruits, vegetables and seeds. Here, the authors establish a link between OVATE Family Proteins and TONNEAU1 Recruiting Motif family proteins in the development pathway that governs fruit shape of tomato, melon, and cucumber as well as potato tuber shape.

    • Shan Wu
    • , Biyao Zhang
    •  & Esther van der Knaap

  • Article
    | Open Access

    Elderly males are often affected by benign prostatic hyperplasia and associated lower urinary tract symptoms (BPH/LUTS), but their link to prostate cancer risk is not well defined. Here, a genome-wide association study of BPH/LUTS patients from Iceland and the UK found 23 significant variants at 14 loci, and 15 of these variants associate with prostate specific antigen, which is linked to prostate cancer risk.

    • Julius Gudmundsson
    • , Jon K. Sigurdsson
    •  & Kari Stefansson

  • Article
    | Open Access

    Head-on replication-transcription collisions occur within genes encoded on the lagging DNA strand. Here, the authors show that a large number of originally co-oriented (leading strand) genes have inverted to the head-on orientation, increasing both gene-specific mutation rates, and the overall evolvability of several bacterial pathogens.

    • Christopher N. Merrikh
    •  & Houra Merrikh

  • Article
    | Open Access

    Rare genetic variants can contribute to complex traits but this contribution is not well understood. Here, the authors analyse deep whole genome sequencing data across 1457 individuals from an isolated Greek population and find association of rare variant burdens with cardiometabolic traits.

    • Arthur Gilly
    • , Daniel Suveges
    •  & Eleftheria Zeggini

  • Article
    | Open Access

    The treatment of brain metastases is often limited by the ability to diagnose their origins. Here the authors generate DNA methylomes from the three most frequent types of brain metastases, identify epigenetic signatures specific to each type of metastasis and construct a DNA methylation-based classifier (BrainMETH) to advance brain metastasis diagnosis.

    • Javier I. J. Orozco
    • , Theo A. Knijnenburg
    •  & Diego M. Marzese

  • Article
    | Open Access

    Chromodomain Helicase DNA-binding (CHD) proteins have been implicated in neurodevelopmental processes. Here, the authors identify missense variants in CHD3 that disturb its chromatin remodeling activities and cause a neurodevelopmental disorder with macrocephaly and speech and language impairment.

    • Lot Snijders Blok
    • , Justine Rousseau
    •  & Philippe M. Campeau

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