Genetics articles within Nature Communications

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  • 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

  • Article
    | Open Access

    DNA methylation is an epigenetic mark involved in gene regulation. Here the authors investigate the extent to which genetics, sex and pregnancy influence genomic DNA methylation in mice, providing evidence of the stability of CpG methylation across generation and suggest that CpG methylation may serve as an epigenetic record of life events in somatic tissues at loci whose expression is linked to the relevant biology.

    • Sara A. Grimm
    • , Takashi Shimbo
    •  & Paul A. Wade

  • 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

    Population structure can bias the results of genetic and epidemiological analysis. Here, Haworth et al. report that fine-scale structure is detectable in apparently homogeneous samples such as ALSPAC when measured very precisely, and remains detectable in UK Biobank despite conventional approaches to account for it.

    • Simon Haworth
    • , Ruth Mitchell
    •  & Nicholas J. Timpson

  • Article
    | Open Access

    There are distinct hypermethylation patterns in gene promoters in hepatocellular carcinomas (HCCs). Here, the authors show that the enhancer of C/EBPβ is recurrently hypomethylated in human HCCs, recapitulating this in a transgenic murine model and linking aberrant enhancer hypomethylation to hepatocarcinogenesis.

    • Lei Xiong
    • , Feng Wu
    •  & Ka-Fai To

  • Article
    | Open Access

    Gain of function methods based on gene overexpression are not easily applied to high-throughput screening across different experimental conditions. Here, the authors present Dub-seq, which separates overexpression library characterization from functional screening and uses random DNA barcodes to increase the experimental throughput.

    • Vivek K. Mutalik
    • , Pavel S. Novichkov
    •  & Adam P. Arkin

  • Article
    | Open Access

    Glucocorticoids (GCs) are widely used anti-inflammatory drugs; however, long-term treatment causes metabolic side effects. Here, the authors show that E47 is a modulator of glucocorticoid receptor activity for a subset of target genes in mouse liver, and that loss of E47 protects mice from hyperglycemia and hepatic steatosis in response to GCs.

    • M. Charlotte Hemmer
    • , Michael Wierer
    •  & N. Henriette Uhlenhaut

  • Article
    | Open Access

    Introgression of Neanderthals and Denisovans left genomic signals in anatomically modern human after Out-of-Africa event. Here, the authors identify a third archaic introgression common to all Asian and Oceanian human populations by applying an approximate Bayesian computation with a Deep Learning framework.

    • Mayukh Mondal
    • , Jaume Bertranpetit
    •  & Oscar Lao

  • Article
    | Open Access

    In fission yeast, Erh1, ortholog of human ERH, interacts with the YTH family RNA binding protein Mmi1 to form the Erh1-Mmi1 complex (EMC), which has been implicated in gene silencing. Here, the authors present the cocrystal structure of Erh1 homodimers interacting with Mmi1 and further characterise the role of EMC in facultative heterochromatin assembly and gene silencing.

    • Guodong Xie
    • , Tommy V. Vo
    •  & Shiv I. S. Grewal

  • Article
    | Open Access

    Stocking of hatchery produced fish is widely used to supplement wild fish populations. Here, the authors show that supplementary stocking can unintentionally favour introgressed individuals with domestic genotypes and compromise the fitness of a wild population of Atlantic salmon.

    • Ingerid J. Hagen
    • , Arne J. Jensen
    •  & Sten Karlsson

  • Article
    | Open Access

    Animal studies have shown that the nutritional status of parents can predispose the offspring to obesity and obesity-related diseases. Here the authors show that cardiac dysfunction induced by a high-fat diet persists for two generations in Drosophila, and that targeted expression of ATGL/bmm in the offspring, as well as inhibition of H3K27 trimethylation, is cardioprotective.

    • Maria Clara Guida
    • , Ryan Tyge Birse
    •  & Rolf Bodmer

  • Article
    | Open Access

    Meningitis is a severe form of invasive pneumococcal disease (IPD). To study the contribution of bacterial genomic variation, here Li et al. perform whole genome sequencing of pneumococcal isolates from IPD patients and identify an association for higher risk of meningitis with a pbp1bA641C variant

    • Yuan Li
    • , Benjamin J. Metcalf
    •  & Bernard W. Beall

  • Article
    | Open Access

    Turnovers in sex determination systems occur quite frequently, yet the evolutionary drivers of these turnovers are not well understood. Here, the authors study the sex determination systems in sticklebacks and propose chromosomal inversions as a possible driver of the evolution of sex determination.

    • Heini M. Natri
    • , Juha Merilä
    •  & Takahito Shikano

  • Article
    | Open Access

    It is unclear how some Drosophila neurons develop sex-specific neurites that contribute to dimorphic circuitries required for gendered behavior. The authors show that sex-specific cleavage by the E3 ubiquitin ligase Cullin1 and 26S proteasome of the pleiotropic BTB-ZF transcription factor Lola confers its sexual fate-inducing ability in these neurons.

    • Kosei Sato
    • , Hiroki Ito
    •  & Daisuke Yamamoto

  • Article
    | Open Access

    Examples of overdominance are usually explained by deleterious effects in homozygotes. Here, Kellenberger et al. describe a case of overdominance in the floral color of the Alpine orchid Gymnadenia rhellicani apparently maintained by pollinator preferences without deleterious effects in homozygotes.

    • Roman T. Kellenberger
    • , Kelsey J. R. P. Byers
    •  & Philipp M. Schlüter

  • Article
    | Open Access

    Mutations in the ATM tumor suppressor gene confer hypersensitivity to DNA-damaging chemotherapeutic agents. Here, the authors provide evidence that these hypersensitivities reflect a crucial role for ATM at damaged replication forks being to prevent toxic DNA end-joining leading to chromosome fusions and cell death.

    • Gabriel Balmus
    • , Domenic Pilger
    •  & Stephen P. Jackson

  • Article
    | Open Access

    Adenine base editors are an important contribution to the genome editing toolbox. Here the authors present EndoV-seq, an endonuclease-based assay for evaluating genomewide off-target effects of base editing.

    • Puping Liang
    • , Xiaowei Xie
    •  & Zhou Songyang

  • Article
    | Open Access

    While human lifespan is only moderately heritable, “getting old” runs in families. Here, van den Berg et al. study mortality data from three-generation cohorts to define a threshold for longevity and find that individuals have an increasing survival advantage with each additional relative in the top 10% survivors of their birth cohort.

    • Niels van den Berg
    • , Mar Rodríguez-Girondo
    •  & P. Eline Slagboom

  • 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

    A current challenge in genome editing is delivering Cas9 and sgRNA into target cells. Here the authors engineer a delivery system based on murine leukemia virus-like particles loaded with Cas9-sgRNA ribonucleoproteins to induce efficient genome editing in both cell culture and in vivo in mouse.

    • Philippe E. Mangeot
    • , Valérie Risson
    •  & Emiliano P. Ricci

  • Article
    | Open Access

    The inactive X chromosome (Xi) has an atypical structure, with global loss of TADs, A/B compartments and formation of mega-domains. Here the authors show that the non-canonical SMC family protein, SmcHD1, important for developmental gene silencing on Xi, antagonises TAD formation and compartmentalization on the Xi in a transcription independent way.

    • Michal R. Gdula
    • , Tatyana B. Nesterova
    •  & Neil Brockdorff

  • Article
    | Open Access

    Due to various structural and sequence complexities, the human Y chromosome is challenging to sequence and characterize. Here, the authors develop a strategy to sequence native, unamplified flow sorted Y chromosomes with a nanopore sequencing platform, and report the first assembly of a human Y chromosome of African origin.

    • Lukas F. K. Kuderna
    • , Esther Lizano
    •  & Tomas Marques-Bonet

  • Article
    | Open Access

    Ezh2 is an histone methyltransferase that catalyzes H3K27me3. Here the authors show that Ezh2 promotes T follicular helper (TFH) differentiation and helper activity, by cooperating with Tcf1 to activate Bcl6 transcription and epigenetically repressing p19Arf, an antagonist of Bcl6 function and TFH cell survival.

    • Fengyin Li
    • , Zhouhao Zeng
    •  & Hai-Hui Xue

  • Article
    | Open Access

    The origin of Tibetan barley (qingke) has been a controversial issue for many years. Here, the authors conduct population genomics study to support that qingke is derived from eastern domesticated barley instead of Tibetan wild barley and suggest southern Tibetan Plateau as its introduction route.

    • Xingquan Zeng
    • , Yu Guo
    •  & Nyima Tashi

  • 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

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