Genome articles within Nature Communications

Featured

  • Article
    | Open Access

    Taurine and indicine cattle have different desirable traits making them better adapted to different climates across the world. Here, Low et al. describe a pipeline to produce haplotype-resolved, chromosome-level genomes of Angus and Brahman cattle breeds from a crossbred individual and report on comparisons of the two genomes.

    • Wai Yee Low
    • , Rick Tearle
    •  & John L. Williams

  • Article
    | Open Access

    Many nematode worms, including Caenorhabditis elegans have XX/XO sex determination, while other species have XY. The authors use a new genome assembly of the filarial parasite Brugia malayi and published data to show that nematode sex chromosome evolution is highly plastic.

    • Jeremy M. Foster
    • , Alexandra Grote
    •  & Elodie Ghedin

  • Article
    | Open Access

    Recent evidence has questioned the dogma of strict maternal transmission of mitochondrial DNA (mtDNA) in humans. Wei et al. saw no evidence of paternal transmission of mtDNA in 11,035 human trios, and show that nuclear-mitochondrial segments (NUMTs) can give the impression of paternal mtDNA transmission, but are actually inherited through the nuclear genome.

    • Wei Wei
    • , Alistair T. Pagnamenta
    •  & Patrick F. Chinnery

  • Article
    | Open Access

    Mutations in human pluripotent stem cells (PSC) and whether any form during culture prior to use in a human clinical context are a concern. Here, the authors use hPSCs derived to cGMP standards and show they have low mutation rates after culture, noting this decreases on culturing in low (5%) oxygen conditions.

    • Oliver Thompson
    • , Ferdinand von Meyenn
    •  & Peter W. Andrews

  • Article
    | Open Access

    Horizontal transfer (HT) and evolution of transposable elements (TEs) has rarely been quantified on a large scale. Here, the authors screen 307 vertebrate genomes and infer 975 HT events (93% in ray-finned fishes); all TEs involved in HT evolve within genomes under purifying selection, as do most retrotransposons.

    • Hua-Hao Zhang
    • , Jean Peccoud
    •  & Clément Gilbert

  • Article
    | Open Access

    GWAS analysis currently relies mostly on linear mixed models, which do not account for linkage disequilibrium (LD) between tested variants. Here, Sesia et al. propose KnockoffZoom, a non-parametric statistical method for the simultaneous discovery and fine-mapping of causal variants, assuming only that LD is described by hidden Markov models (HMMs).

    • Matteo Sesia
    • , Eugene Katsevich
    •  & Chiara Sabatti

  • Article
    | Open Access

    Despite tremendous genomic resources in the Arabidopsis community, only a few whole genome de novo assemblies are available. Here, the authors report chromosome-level reference-quality assemblies of seven A. thaliana accessions and reveal hotspots of rearrangements with altered evolutionary dynamics.

    • Wen-Biao Jiao
    •  & Korbinian Schneeberger

  • Article
    | Open Access

    Associations of copy number variations (CNVs) with complex traits are challenging to study because of their low frequency. Here, the authors analyse SNP array and array comparative genomic hybridization data of 100,028 individuals and report their associations with immune-related, cardiometabolic and neuropsychiatric diseases as well as cancer.

    • Yun Rose Li
    • , Joseph T. Glessner
    •  & Hakon Hakonarson

  • Article
    | Open Access

    Whole genome sequencing (WGS) holds promise to solve a subset of Mendelian disease cases for which exome sequencing did not provide a genetic diagnosis. Here, Wells et al. report a supervised machine learning model trained on functional, mutational and structural features for rank-scoring and interpreting variants in non-coding regions from WGS.

    • Alex Wells
    • , David Heckerman
    •  & Julia di Iulio

  • Article
    | Open Access

    During meiotic prophase chromosomes organise into a series of chromatin loops, but the mechanisms of assembly remain unclear. Here the authors use Saccharomyces cerevisiae to elucidate how this elaborate three-dimensional chromosome organisation is linked to genomic sequence, and demonstrate an essential role for cohesin during this process.

    • Stephanie A. Schalbetter
    • , Geoffrey Fudenberg
    •  & Matthew J. Neale

  • Article
    | Open Access

    Estimates of mutation rates differ between species. Here, Lindsay et al. perform side-by-side analyses of germline mutation rates using multi-sibling mouse and human pedigrees and find different mutation rates between species, also stratified by sex and temporal stage of mutation acquisition.

    • Sarah J. Lindsay
    • , Raheleh Rahbari
    •  & Matthew E. Hurles

  • Article
    | Open Access

    Transposable elements (TE) make up a large component of the human genome and have been shown to contribute to human diseases. Here, Hormozdiari et al. estimate the contribution of TEs to the heritability of 41 complex traits and diseases and find enrichment of SINEs in blood traits.

    • Farhad Hormozdiari
    • , Bryce van de Geijn
    •  & Alkes L. Price

  • Article
    | Open Access

    The contribution of transposable elements (TEs) to the creation of heritable mutations is unknown. Here the authors show in Arabidopsis that TEs accumulate exponentially once mobilized and that COPIA retrotransposons preferentially integrate in environmental response genes in a H2A.Z-dependent manner.

    • Leandro Quadrana
    • , Mathilde Etcheverry
    •  & Vincent Colot

  • Article
    | Open Access

    Spatial organization of regulatory elements and its impact on gene expression in plants remain unclear. Here, the authors construct maize chromatin interaction maps using chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) and show their associations with gene expression and agronomic traits.

    • Yong Peng
    • , Dan Xiong
    •  & Xingwang Li

  • Article
    | Open Access

    Chromatin interaction analysis by paired-end tag sequencing (ChIA-PET) can discover specific protein-centered chromatin interactions in high resolution. Here, the authors use ChIA-PET to reveal the complex and dynamic interactions between proximal and distal regulatory regions of genes in maize.

    • En Li
    • , Han Liu
    •  & Jinsheng Lai

  • Article
    | Open Access

    Methodological advances have increased our understanding of chromatin structure through chromosome conformation capture techniques and high resolution imaging, but integration of these datasets is challenging. Here the authors propose GEM-FISH, a method for reconstructing the 3D models of chromosomes through systematically integrating both Hi-C and FISH data with the prior biophysical knowledge of a polymer model.

    • Ahmed Abbas
    • , Xuan He
    •  & Jianyang Zeng

  • Article
    | Open Access

    Curaxins are a recently discovered class of anti-cancer agents that disturbs DNA/histone interactions within. Here the authors provide evidence that curaxins affect the spatial genome organization and compromise enhancer-promoter communication necessary for expression of several oncogenes, including MYC.

    • Omar L. Kantidze
    • , Artem V. Luzhin
    •  & Sergey V. Razin

  • Article
    | Open Access

    Researchers can make use of a variety of computational tools to prioritize genetic variants and predict their pathogenicity. Here, the authors evaluate the performance of six of these tools in three typical biological tasks and find generally low concordance of predictions and experimental confirmation.

    • Li Liu
    • , Maxwell D. Sanderford
    •  & Sudhir Kumar

  • Article
    | Open Access

    Transposable elements (TE) are the dominant constituent of plant genomes. Here the authors develop a tool to analyze TE insertion sites in 3000 rice genomes and provide evidence for recent TE activity during cultivation and that external, rather than genetic, stimuli trigger most activations.

    • Marie-Christine Carpentier
    • , Ernandes Manfroi
    •  & Olivier Panaud

  • 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

    Short-tandem repeats (STR), similar to single nucleotide polymorphisms (SNP), contribute to complex traits, but their ascertainment by next-generation sequencing is costly. Here, Saini et al. provide a SNP+STR haplotype reference panel that allows imputation of STRs from SNP array data.

    • Shubham Saini
    • , Ileena Mitra
    •  & Melissa Gymrek

  • Article
    | Open Access

    Enhancers and promoters are different types of regulatory elements with shared architectural and functional features. Here the authors perform integrated cross-mammalian analyses of DNase hypersensitivity, chromatin modification and transcriptional data, to provide evidence of regulatory repurposing during evolution.

    • Francesco N. Carelli
    • , Angélica Liechti
    •  & Henrik Kaessmann

  • Article
    | Open Access

    The harlequin ladybird beetle, Harmonia axyridis, has remarkable phenotypic diversity, with over 200 colour patterns. Here, Ando et al. show that this patterning is regulated by the transcription factor gene pannier and has diversified by repeated inversions and cis-regulatory modifications of pannier.

    • Toshiya Ando
    • , Takeshi Matsuda
    •  & Teruyuki Niimi

  • Article
    | Open Access

    Common genetic variants associated with plasma lipids have been extensively studied for a better understanding of common diseases. Here, the authors use whole-genome sequencing of 16,324 individuals to analyze rare variant associations and to determine their monogenic and polygenic contribution to lipid traits.

    • Pradeep Natarajan
    • , Gina M. Peloso
    •  & Sebastian Zoellner

  • Article
    | Open Access

    The majority of the human reference genome assembly is represented as a single consensus haplotype. Here, Wong et al. analyze de novo assemblies of 17 diverse, haplotype-resolved genomes to gain insights into the structure of genetic diversity and compile a list of alternative haplotypes across populations.

    • Karen H. Y. Wong
    • , Michal Levy-Sakin
    •  & Pui-Yan Kwok

  • Article
    | Open Access

    Human embryonic stem cell-derived cardiomyocytes (hESC-CM) are a widely used model to study cardiac genomics. Here, Choy et al. perform promoter capture Hi-C to map long-range chromosomal interactions of hESC-CMs and to study overlap of such regions with genetic loci associated with cardiac phenotypes.

    • Mun-Kit Choy
    • , Biola M. Javierre
    •  & Bernard D. Keavney

  • Article
    | Open Access

    Mitochondrial populations in cells may consist of heteroplasmic mixtures of mtDNA types, and their evolution through development, aging and generations is central to genetic diseases. Here the authors dissect these population dynamics using a large mouse-based data set to characterise the dynamics of heteroplasmy mean and variance throughout life and across generations.

    • Joerg P. Burgstaller
    • , Thomas Kolbe
    •  & Iain G. Johnston

  • Article
    | Open Access

    Pulmonary arterial hypertension (PAH) is a rare lung disorder characterised by narrowing and obliteration of small pulmonary arteries ultimately leading to right heart failure. Here, the authors sequence whole genomes of over 1000 PAH patients and identify likely causal variants in GDF2, ATP13A3, AQP1 and SOX17.

    • Stefan Gräf
    • , Matthias Haimel
    •  & Nicholas W. Morrell

  • Article
    | Open Access

    Somatic cells can accumulate structural variations such as deletions. Here, Møller et al. show that normal human cells generate large extrachromosomal circular DNAs (eccDNAs), most likely the products of excised DNA, that can be transcriptionally active and, thus, may have phenotypic consequences.

    • Henrik Devitt Møller
    • , Marghoob Mohiyuddin
    •  & Birgitte Regenberg

  • Article
    | Open Access

    Proteogenomics enables the discovery of protein coding regions and disease-relevant mutations but their verification remains challenging. Here, the authors combine peptide discovery, curation and validation in an integrated proteogenomics workflow, robustly identifying unknown coding regions and mutations.

    • Yafeng Zhu
    • , Lukas M. Orre
    •  & Janne Lehtiö

  • Article
    | Open Access

    Although topologically associating domains (TADs) have been extensively investigated, it is not clear to what extent DNA sequence contributes to their formation. Here the authors develop software to identify high-resolution TAD boundaries and reveal their relationship to underlying DNA motifs.

    • Fidel Ramírez
    • , Vivek Bhardwaj
    •  & Thomas Manke

Browse broader subjects

Browse narrower subjects

Browse Genome across other nature.com journals