Genetics articles within Nature Communications

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  • Article
    | Open Access

    Transient aneuploidy enables cells to survive sudden environmental changes before longterm cellular adaptations are established. Here, the authors show that yeast cells respond to the acute loss of Ulp2 SUMO protease by rapid induction of aneuploidy, and reveal predictable long-term adaptation mechanisms that restore euploidy.

    • Hong-Yeoul Ryu
    • , Francesc López-Giráldez
    •  & Mark Hochstrasser

  • Article
    | Open Access

    Male pattern baldness (MPB) is a polygenic trait that affects the majority of European men. Here, Yap et al. estimate heritability, partitioned by autosomes and the X-chromosome, of MPB in the UK Biobank cohort, perform GWAS for MPB and find genetic correlation with other sex-specific traits.

    • Chloe X. Yap
    • , Julia Sidorenko
    •  & Peter M. Visscher

  • Article
    | Open Access

    Latin Americans trace their ancestry to the admixture of Native Americans, Europeans and Sub-Saharan Africans. Here, the authors develop a novel haplotype-based approach and analyse over 6,500 Latin Americans to infer the geographically-detailed genetic structure of this population.

    • Juan-Camilo Chacón-Duque
    • , Kaustubh Adhikari
    •  & Andrés Ruiz-Linares

  • Article
    | Open Access

    Candida auris is an emergent fungal pathogen that is resistant to multiple antifungals. Here, Muñoz et al. analyse genomic sequences for isolates from each of the four major C. auris clades and for three related species, and identify genetic features associated with virulence, antifungal resistance and mating.

    • José F. Muñoz
    • , Lalitha Gade
    •  & Christina A. Cuomo

  • Article
    | Open Access

    ATR kinase is a key regulator of chromosome integrity. Here the authors by analysing the phenotype of a mouse model expressing a kinase-dead ATR, reveal the effect of ATR inhibition compared to ATR loss and its consequences for meiosis, DNA replication, checkpoint activation and genome instability .

    • Demis Menolfi
    • , Wenxia Jiang
    •  & Shan Zha

  • Article
    | Open Access

    Biogenesis and function of miRNAs in somatic cells is well characterized, but their role in the germline has not been established. Here the authors identify and characterize Drosha independent and dependent miRNAs during C. elegans oogenesis, revealing their roles in meiotic progression and oocyte development.

    • Amanda L. Minogue
    • , Michael R. Tackett
    •  & Swathi Arur

  • Article
    | Open Access

    SRY and its target SOX9 are known key determinants in testis development. Here the authors by studying duplications and deletions upstream of SOX9 from patient samples with disorders of sex development (DSD) reveal enhancers for SOX9 critical for human sex development and DSD.

    • Brittany Croft
    • , Thomas Ohnesorg
    •  & Andrew Sinclair

  • Article
    | Open Access

    Viruses are potential vectors for horizontal gene transfer. Here, studying viral infection of sugar beet plants, the authors report the generation of virus-host circular DNA hybrids and provide a picture of the initial steps in virus-mediated horizontal transfer of chromosomal DNA between plant species.

    • Marco Catoni
    • , Emanuela Noris
    •  & Gian Paolo Accotto

  • Article
    | Open Access

    Acne vulgaris is a chronic inflammation of the skin, the genetic basis of which is incompletely understood. Here, Petridis et al. perform GWAS and meta-analysis for acne in 26,722 individuals and identify 12 novel risk loci that implicate structure and maintenance of the skin in severe acne risk.

    • Christos Petridis
    • , Alexander A. Navarini
    •  & Michael A. Simpson

  • Article
    | Open Access

    Increasing insecticide resistance of mosquitoes represents a public health threat, and underlying mechanisms are poorly understood. Here, Ingham et al. identify putative insecticide resistance genes in Anopheles gambiae populations across Africa and develop a web-based application that maps their expression.

    • V. A. Ingham
    • , S. Wagstaff
    •  & H. Ranson

  • Article
    | Open Access

    Natural hair colour in Europeans is a complex genetic trait. Here, the authors carry out a genome-wide association study using UK BioBank data, suggesting that in combination with pigmentation genes, variants with roles in hair texture and growth can affect hair colouration or our perception of it.

    • Michael D. Morgan
    • , Erola Pairo-Castineira
    •  & Ian J. Jackson

  • Article
    | Open Access

    Studying the genetic underpinnings of physical activity and sleep duration can be confounded by self-reporting. Here, Doherty et al. use data from 91,105 UK Biobank participants, whose activity had been monitored for a week by a wearable device, for genome-wide association analysis and identify 14 loci.

    • Aiden Doherty
    • , Karl Smith-Byrne
    •  & Cecilia M. Lindgren

  • Article
    | Open Access

    Epilepsies are common brain disorders and are classified based on clinical phenotyping, imaging and genetics. Here, the authors perform genome-wide association studies for 3 broad and 7 subtypes of epilepsy and identify 16 loci - 11 novel - that are further annotated by eQTL and partitioned heritability analyses.

    • Bassel Abou-Khalil
    • , Pauls Auce
    •  & Fritz Zimprich

  • Article
    | Open Access

    Northern tree populations may not benefit under climate change, with implications for assisted migration and range expansion. Here, Isaac-Renton et al. show that leading-edge lodgepole pine populations have fewer characteristics of drought-tolerance, so may not adapt to tolerate drier conditions.

    • Miriam Isaac-Renton
    • , David Montwé
    •  & Kerstin Treydte

  • Article
    | Open Access

    miRNAs have emerged as regulators of diverse biological processes including cancer. Here the authors present an extended pan-cancer analysis of the miRNAs in 15 epithelial cancers; integrating methylation, transcriptomic and mutation data they reveal alternative mechanisms of tumour suppressors’ regulation in absence of mutation, methylation or copy number alterations.

    • Andrew Dhawan
    • , Jacob G. Scott
    •  & Francesca M. Buffa

  • 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

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