Genetics articles within Nature Communications

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  • Article
    | Open Access

    GWAS have identified over 41 susceptibility loci for Parkinson’s disease (PD). Here, the authors integrate PD GWAS summary statistics with transcriptome data from monocytes and DLFPC tissue in a TWAS approach and find 66 significant associations with PD risk highlighting lysosomal and innate immune functions.

    • Yang I. Li
    • , Garrett Wong
    •  & Towfique Raj

  • Article
    | Open Access

    An essential gene may become non-essential when another gene is mutated. Here, the authors investigate this type of digenic interaction, termed ‘bypass of essentiality’, in the fission yeast Schizosaccharomyces pombe, and show that bypassable essential genes are common and share certain features.

    • Jun Li
    • , Hai-Tao Wang
    •  & Li-Lin Du

  • Article
    | Open Access

    LncRNA TERRA forms RNA-DNA hybrids at telomere sites leading to telomere instability. Here the authors identify the RNA interacting factors NONO and SFPQ as proteins that interact with TERRA and telomere chromatin and reveal putative roles for these factors in telomere integry maintenance by interfering with RNA:DNA hybrid formation.

    • Eleonora Petti
    • , Valentina Buemi
    •  & Stefan Schoeftner

  • Article
    | Open Access

    Hybridization can contribute to diversity from the genomic to the species level. Here, Eberlein, Hénault et al. investigate genomic, transcriptomic and phenotypic variation among wild lineages of the yeast Saccharomyces paradoxus and suggest that an incipient species has formed by recurrent hybridization.

    • Chris Eberlein
    • , Mathieu Hénault
    •  & Christian R. Landry

  • Article
    | Open Access

    The burden of asthma varies between ancestries, but GWAS have so far focused on mainly European ancestry populations. Here, Daya et al. perform GWAS for asthma in 14,654 individuals of African ancestry and, besides confirming previously known loci, identify two potentially African ancestry-specific loci.

    • Michelle Daya
    • , Nicholas Rafaels
    •  & Maria Yazdanbakhsh

  • Article
    | Open Access

    Autophagic activity decreases with age via unknown mechanisms. Here the authors show that expression of the negative autophagy regulator Rubicon increases with age, that its genetic ablation improves lifespan and ameliorates a number of age-associated phenotypes in invertebrates and in mouse models.

    • Shuhei Nakamura
    • , Masaki Oba
    •  & Tamotsu Yoshimori

  • Article
    | Open Access

    Negative selection removes deleterious genetic variation, and can influence genetic architectures and evolution of complex traits. Here, the authors analyze data from 25 UK Biobank diseases and complex traits, and quantify frequency-dependent genetic architectures which suggests actions of negative selection.

    • Armin P. Schoech
    • , Daniel M. Jordan
    •  & Alkes L. Price

  • Article
    | Open Access

    Whether the Wnt enhanceosome’ components BCL9/9l can affect intestinal homeostasis and tumorigenesis is still unclear. Using conditional Bcl9/9l KO mice, the authors of this study show that the BCL9/9l complex is required for intestinal stem cells to drive tissue regeneration and that loss of BCL9/9l suppresses Wnt-driven transformation.

    • David M. Gay
    • , Rachel A. Ridgway
    •  & Owen J. Sansom

  • Article
    | Open Access

    BCL9 and Pygo are components of Wnt enhanceosome, which facilitates β-catenin-dependent transcription. Here, the authors show that deletion of Bcl9 and Pygo suppresses tumorigenesis and extends disease free survival in two different colorectal cancer models, suggesting a strategy for drugging β-catenin signalling in this cancer.

    • Juliusz Mieszczanek
    • , Laurens M. van Tienen
    •  & Mariann Bienz

  • Article
    | Open Access

    Valyl-tRNA synthetase (VARS) charges valyl-tRNA with the amino acid valine, required for translation. Here, the authors describe a progressive epileptic encephalopathy in individuals from five families carrying biallelic mutations in the VARS gene that leave the enzyme activity partially intact.

    • Jennifer Friedman
    • , Desiree E. Smith
    •  & Joseph G. Gleeson

  • Article
    | Open Access

    tRNAs are linked with their cognate amino acid by aminoacyl tRNA synthetases (ARS). Here, the authors report a developmental encephalopathy associated with biallelic VARS variants (valyl-tRNA synthetase) that lead to loss of function, as determined by several in vitro assays and a vars knockout zebrafish model.

    • Aleksandra Siekierska
    • , Hannah Stamberger
    •  & Peter De Jonghe

  • Article
    | Open Access

    We know a large number of risk SNPs for schizophrenia, but little about how these SNPs contribute to the disorder. Here, the authors use functional genomics to identify risk SNPs that disrupt transcription factor binding and validate the regulatory effects of the transcription factor binding-disrupting SNPs.

    • Yongxia Huo
    • , Shiwu Li
    •  & Xiong-Jian Luo

  • Article
    | Open Access

    Oxytocin is a hormone and neurotransmitter involved in reproductive and social behavior, but the role of oxytocin-related genes in the human brain remains unclear. Here, the authors map oxytocin pathway gene expression and show that it overlaps with brain regions involved in reward and emotional states.

    • Daniel S. Quintana
    • , Jaroslav Rokicki
    •  & Lars T. Westlye

  • Article
    | Open Access

    High-throughput sequencing and analyzes of antibody repertoire provide important information on immune responses, but current methodologies are limited in sequence assembly precision and haplotype inference validity. Here the authors propose a new Bayesian haplotyping method, and attest its broad application with a large, multi-individual dataset.

    • Moriah Gidoni
    • , Omri Snir
    •  & Gur Yaari

  • Article
    | Open Access

    Few tools exist to study molecular diversity during neurodevelopment. Here the authors apply a genetic immortalization method in Drosophila to generate a fate map of olfactory sensory lineages, examine the relationships of this map and the neuroanatomical, molecular and evolutionary properties of the mature circuits, and identify a novel factor controlling lineage development.

    • Phing Chian Chai
    • , Steeve Cruchet
    •  & Richard Benton

  • Article
    | Open Access

    Nuclear envelopathies are a group of diseases caused by genetic mutations in essential nuclear envelope genes. Here, the authors report a nuclear envelopathy with a homozygous nonsense variant in TOR1AIP1 which leads to changes in the nuclear morphology including large nuclear-spanning channels in patients’ fibroblasts.

    • Boris Fichtman
    • , Fadia Zagairy
    •  & Ronen Spiegel

  • Article
    | Open Access

    The Caucasus mountain range has impacted on the culture and genetics of the wider region. Here, the authors generate genome-wide SNP data for 45 Eneolithic and Bronze Age individuals across the Caucasus, and find distinct genetic clusters between mountain and steppe zones as well as occasional gene-flow.

    • Chuan-Chao Wang
    • , Sabine Reinhold
    •  & Wolfgang Haak

  • Article
    | Open Access

    N6-methyladenine is involved in many biological pathways for microbial survival and host interaction. Here the authors train a neural network for improved m6A detection in nanopore sequencing data and validate methylomes for a microbial reference community.

    • Alexa B. R. McIntyre
    • , Noah Alexander
    •  & Christopher E. Mason

  • Article
    | Open Access

    Individuals show large variability in their capacity to lose weight and maintain this weight. Here, the authors perform GWAS in two weight loss intervention cohorts and identify two genetic loci associated with weight loss that are taken forward for Bayesian fine-mapping and functional assessment in flies.

    • Armand Valsesia
    • , Qiao-Ping Wang
    •  & Jörg Hager

  • Article
    | Open Access

    Adeno-associated viral vectors (AAV) are being developed for gene therapy of skeletal muscle, but it is a challenge to achieve robust gene expression. Here, the authors identify muscle-specific cisregulatory elements that lead to a substantial increase in micro-dystrophin and follistatin expression, resulting in a safe and sustainable rescue of the dystrophic phenotype in mouse models.

    • S. Sarcar
    • , W. Tulalamba
    •  & M. K. Chuah

  • Article
    | Open Access

    Mammalian transcription factors (TFs) differ broadly in their DNA binding properties. Here authors quantify mitotic chromosome binding (MCB) of 501 TFs and suggest that MCB can be used as a proxy for non-specific TF-DNA interactions that regulate TF search for specific genomic sites.

    • Mahé Raccaud
    • , Elias T. Friman
    •  & David M. Suter

  • Article
    | Open Access

    GWAS have previously found 24 genomic loci associated with chronotype, an individual’s preference for early or late sleep timing. Here, the authors identify 327 additional loci in a sample of 697,828 individuals and further explore the relationships of chronotype with metabolic and psychiatric diseases.

    • Samuel E. Jones
    • , Jacqueline M. Lane
    •  & Michael N. Weedon

  • Article
    | Open Access

    Most cyanobacteria are oxygenic photoautotrophs, and fermenters under dark anoxic conditions. Here, the authors analyse genomic sequences of related uncultivated bacteria, inferring their metabolic potential, and supporting that their common ancestor was an anaerobe capable of fermentation and H2 metabolism.

    • Paula B. Matheus Carnevali
    • , Frederik Schulz
    •  & Jillian F. Banfield

  • Article
    | Open Access

    The inactive X chromosome (Xi) is a model for establishment and maintenance of repressed chromatin and the function of polycomb repressive complexes. Here the authors show that Xi transiently relocates from the nuclear periphery during replication in a CIZ1-dependent manner, which plays a role in maintaining PRC-mediated repressed chromatin.

    • Emma R. Stewart
    • , Robert M. L. Turner
    •  & Dawn Coverley

  • Article
    | Open Access

    Multiple morphological abnormalities of the sperm flagella (MMAF) is a cause of male infertility. Here the authors identify homozygous nonsense mutations of the glutamine rich 2 (QRICH2) gene in two MMAF patients from 2 consanguineous families and show using QRICH2 knockout mice that the protein is required for sperm flagellar formation and motility.

    • Ying Shen
    • , Feng Zhang
    •  & Wenming Xu

  • Article
    | Open Access

    Similarities in cancers can be studied to interrogate their etiology. Here, the authors use genome-wide association study summary statistics from six cancer types based on 296,215 cases and 301,319 controls of European ancestry, showing that solid tumours arising from different tissues share a degree of common germline genetic basis.

    • Xia Jiang
    • , Hilary K. Finucane
    •  & Sara Lindström

  • Article
    | Open Access

    Broomcorn millet is one of the earliest domesticated plants and has the highest water use efficiency among cereals. Here, the authors report its genome assembly and annotation, which provides a valuable resource for breeders and paves the way for studying plant drought tolerance and C4 photosynthesis.

    • Changsong Zou
    • , Leiting Li
    •  & Heng Zhang

  • Article
    | Open Access

    Broomcorn millet is one of the oldest crops cultivated by human that has strong abiotic stress tolerance. To facilitate genome assisted breeding of this and related species, the authors report its genome assembly and conduct comparative genome structure and evolution analyses with foxtail millet.

    • Junpeng Shi
    • , Xuxu Ma
    •  & Jinsheng Lai

  • Article
    | Open Access

    The connection between DNA replication timing and changes that occur to the epigenome in cancer are still poorly understood. Here, the authors perform Repli-Seq and integrated epigenome analyses and find that genomic regions that undergo long-range epigenetic deregulation in prostate cancer also show concordant differences in replication timing.

    • Qian Du
    • , Saul A. Bert
    •  & Susan J. Clark

  • Article
    | Open Access

    Transcription factors of the AP-1 family can play diverse roles despite recognizing the same DNA sequence. Here the authors investigate the DNA binding activities of AP-1 members in mouse macrophages and apply a machine learning approach to identify motifs predicted to drive factor-specific binding profiles.

    • Gregory J. Fonseca
    • , Jenhan Tao
    •  & Christopher K. Glass

  • Article
    | Open Access

    The consequences of microglial activation in the aging human brain remain unknown. This study quantified microglial morphology and density in the elderly human brain to show that cortical microglial activation strongly associates with AD pathogenesis and may be an upstream contributor to cognitive decline via the accumulation of tau pathology.

    • Daniel Felsky
    • , Tina Roostaei
    •  & Philip L. De Jager

  • Article
    | Open Access

    GWAS have led to the identification of 49 genetic loci associated with vitiligo. Here, the authors observe a bimodal distribution of age-of-onset and find a novel genetic locus specifically associated with early-onset vitiligo, located in a regulatory element in the MHC class II region.

    • Ying Jin
    • , Genevieve H. L. Roberts
    •  & Richard A. Spritz

  • Article
    | Open Access

    Somatic alterations in the exonuclease domain of DNA polymerase ɛ have been linked to the development of highly mutated cancers. Here, the authors report that a major consequence of the most common cancer-associated Polɛ variant is a dramatically increased DNA polymerase activity.

    • Xuanxuan Xing
    • , Daniel P. Kane
    •  & Polina V. Shcherbakova

  • Article
    | Open Access

    The Pacific white shrimp Litopenaeus vannamei is an important aquaculture species and a promising model for crustacean biology. Here, the authors provide a reference genome assembly, and show that gene expansion is involved in the regulation of frequent molting as well as benthic adaptation of the shrimp.

    • Xiaojun Zhang
    • , Jianbo Yuan
    •  & Jianhai Xiang

  • Article
    | Open Access

    Obesity and the distribution of fat within the body are risk factors for cardiometabolic diseases. Here, Rask-Andersen et al. perform GWAS for bio-electrical impedance measurements in UK Biobank participants and identify 29 novel independent loci for fat distribution and a high degree of sex-heterogeneity.

    • Mathias Rask-Andersen
    • , Torgny Karlsson
    •  & Åsa Johansson

  • Article
    | Open Access

    Size and shape of the brain are, among others, influenced by the dimensions of the skull. Here, the authors report genome-wide association studies for head circumference and intracranial volume in children and adults and the identification of nine common or low-frequency variants associated with these traits.

    • Simon Haworth
    • , Chin Yang Shapland
    •  & Beate St Pourcain

  • Article
    | Open Access

    Acinic cell carcinoma (AciCC) is a rare salivary gland carcinoma that is poorly understood. Here the authors perform genomic, transcriptomic and epigenomic profiling of AciCC and find highly recurrent and specific rearrangements [t(4;9)(q13;q31)], which lead to enhancer hijacking that activates oncogenic transcription factor NR4A3.

    • Florian Haller
    • , Matthias Bieg
    •  & Abbas Agaimy

  • Article
    | Open Access

    In Drosophila, the Calypso–ASX complex catalyzes H2A deubiquitination and aids Polycomb in transcriptional silencing. Here the authors show that the orthologous complex, BAP1.com, promotes gene activation by counteracting PRC1-mediated gene silencing.

    • Antoine Campagne
    • , Ming-Kang Lee
    •  & Raphaël Margueron

  • Article
    | Open Access

    Early human embryonic development involves extensive changes in chromatin structure and transcriptional activity. Here the authors present LiCAT-seq, a method enabling simultaneous profiling of chromatin accessibility and gene expression with ultra-low input of cells and map chromatin accessibility and transcriptome landscapes for human pre-implantation embryos.

    • Longqi Liu
    • , Lizhi Leng
    •  & Ge Lin

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