Genetics articles within Nature Communications

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  • Article
    | Open Access

    A small percentage of cardiomyocytes (CM) are of neural crest origin but the function of such cells in the adult zebrafish is unclear. Here, the authors identify this CM subpopulation as expressing the Notch ligand jag2b and if deleted in the embryo, cause severe hypertrophic cardiomyopathy in adulthood.

    • Sarah Abdul-Wajid
    • , Bradley L. Demarest
    •  & H. Joseph Yost

  • Article
    | Open Access

    Giant cell lesions of the jaw (GCLJ) are debilitating benign tumors of unclear origin. The authors identify driver recurrent somatic mutations in TRPV4, KRAS and FGFR1 and show they converge on aberrant activation of the MAPK pathway. Their findings extend the spectrum of TRPV4 channelopathies and provide rationale for targeted therapies at the bedside in GCLJ.

    • Carolina Cavalieri Gomes
    • , Tenzin Gayden
    •  & Nada Jabado

  • Article
    | Open Access

    DNA methylation and H3K9 dimethylation are two linked epigenetic marks of silenced chromatin in plants that depend on the activity of CMT3/2 and SUVH4/5/6. Here the authors identify AGDP1 as an H3K9me2-binding protein required for heterochromatic non-CG DNA methylation, H3K9 dimethylation, and transcriptional silencing.

    • Cuijun Zhang
    • , Xuan Du
    •  & Jian-Kang Zhu

  • Article
    | Open Access

    For various organisms, mRNA and protein copy numbers scale with cell volume. Here, the authors show that this result emerges naturally when ribosomes and RNAPs limit expression. Furthermore, the authors show that within their model this result breaks down for a sufficiently high volume/DNA ratio.

    • Jie Lin
    •  & Ariel Amir

  • Article
    | Open Access

    Divergent transcription from promoters and enhancers occurs in many species, but it is unclear if it is a general feature of all eukaryotic cis regulatory elements. Here the authors define cis regulatory elements in worms, flies, and human; and identify several differences in regulatory architecture among metazoans.

    • Mahmoud M. Ibrahim
    • , Aslihan Karabacak
    •  & Uwe Ohler

  • Article
    | Open Access

    Thyroid dysfunction is a common public health problem and associated with cardiovascular co-morbidities. Here, the authors carry out genome-wide meta-analysis for thyroid hormone (TH) levels, hyper- and hypothyroidism and identify SLC17A4 as a TH transporter and AADAT as a TH metabolizing enzyme.

    • Alexander Teumer
    • , Layal Chaker
    •  & Marco Medici

  • Article
    | Open Access

    Nonalcoholic steatohepatitis (NASH) and dietary cholesterol are risk factors for hepatocellular carcinoma (HCC). Here, the authors utilise mouse models to show that dietary cholesterol induces NASH by deregulating genes involved in metabolism, inflammation and calcium signaling to induce NASH-HCC.

    • Jessie Qiaoyi Liang
    • , Narcissus Teoh
    •  & Jun Yu

  • Article
    | Open Access

    Mutations in genes encoding NAPDH oxidase subunits are known to be causative for the primary immunodeficiency chronic granulomatous disease (CGD). Here, the authors identify CYBC1 mutations in patients with CGD and show that CYBC1 is important for formation of the NADPH complex and respiratory burst.

    • Gudny A. Arnadottir
    • , Gudmundur L. Norddahl
    •  & Kari Stefansson

  • Article
    | Open Access

    Whether plant epigenetic variation is subject to selection and contributes to adaptation is under debate. Here, the authors compare DNA methylation and phenotypes of Arabidopsis lines subject to simulated selection and their nearly isogenic ancestors and provide evidence that epigenetic variation contributes to adaptive responses.

    • Marc W. Schmid
    • , Christian Heichinger
    •  & Ueli Grossniklaus

  • Article
    | Open Access

    Diffuse Gastric Cancer (DGC) is increasingly being considered separate to intestinal type gastric cancer; several fusions events have been reported as drivers of the disease but few of those have been subsequently validated. Here the authors perform RNA-seq on early-onset DGC patients who had not been treated with chemotherapy or radiation and identify a previously unknown fusion.

    • Hanna Yang
    • , Dongwan Hong
    •  & Hark Kyun Kim

  • Article
    | Open Access

    The response to respiratory virus exposure can currently not be predicted by pre- or early post-exposure molecular signatures. Here, the authors conduct a community-based analysis of blood gene expression from healthy individuals exposed to respiratory viruses and provide predictive models and biological insight into the physiological response.

    • Slim Fourati
    • , Aarthi Talla
    •  & Solveig K. Sieberts

  • 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

    The transcription factor DAF-16/FOXO is a downstream effector of insulin/insulin-like growth factor signaling and plays an important role in stress resistance and longevity. Here, the authors show that DAF-16/FOXO can form a complex with HLH-30/TFEB to synergistically regulate transcription of target genes in response to certain stress stimuli.

    • Xin-Xuan Lin
    • , Ilke Sen
    •  & Christian G. Riedel

  • Article
    | Open Access

    The halictid bee Lasioglossum albipes has both solitary and eusocial individuals, making it a model for social evolution. Here, Kocher et al. identify a genetic variation associated with this social polymorphism, including a variant that can regulate the expression of an autism-associated gene, syntaxin 1a.

    • Sarah D. Kocher
    • , Ricardo Mallarino
    •  & Naomi E. Pierce

  • Article
    | Open Access

    Common genetic variants in structural proteins contribute to risk of atrial fibrillation (AF). Here, using whole-exome sequencing, the authors identify rare truncating variants in TTN that associate with familial and early-onset AF and show defects in cardiac sarcomere assembly in ttn.2-mutant zebrafish.

    • Gustav Ahlberg
    • , Lena Refsgaard
    •  & Morten S. Olesen

  • Article
    | Open Access

    PWWP2A is a chromatin-binding transcriptional regulator that mediates mitosis-progression. Here, the authors provide evidence that PWWP2A directly interacts with H2A.Z nucleosomes, DNA and H3K36me3, binds to an MTA1-specific subcomplex of the NuRD complex (M1HR) and promotes changes to histone acetylation.

    • Stephanie Link
    • , Ramona M. M. Spitzer
    •  & Sandra B. Hake

  • Article
    | Open Access

    Primordial Germ Cell-Like Cells (PGCLCs) are an in vitro model for primordial germ cell development. Here, the authors couple a novel compound reporter with CRISPR screening to identify key genes for exit from pluripotency and acquisition of PGCLC fate; specifically identifying Nr5a2 and Zfp296.

    • Jamie A. Hackett
    • , Yun Huang
    •  & M. Azim Surani

  • Article
    | Open Access

    Research on racial and ethnic influence on breast cancer mortality is stymied by a lack of genomic studies in diverse populations. Here, the authors genomically interrogate 194 Nigerian breast cancers, unveiling molecular features that could explain the high mortality rate from breast cancer in an indigenous African population.

    • Jason J. Pitt
    • , Markus Riester
    •  & Jordi Barretina

  • Article
    | Open Access

    Genetic loci linked to susceptibility for the common skin cancer cutaneous squamous cell carcinoma (cSCC) have been identified by genome wide association studies (GWAS). Here, the authors impute gene expression levels from GWAS data to perform a transcriptome wide association study (TWAS), identifying five novel genetic loci linked to cSCC susceptibility.

    • Nilah M. Ioannidis
    • , Wei Wang
    •  & Alice S. Whittemore

  • Article
    | Open Access

    Similar to cancers, somatic mutations might lead to neurodegenerative diseases. Here, the authors perform ultra-deep sequencing of 102 genes in 173 adult human brains, detect somatic mutations in 54 brains, and develop a mathematical model to estimate the frequency of mutated foci in human brains.

    • Michael J. Keogh
    • , Wei Wei
    •  & Patrick F. Chinnery

  • Article
    | Open Access

    Barrett’s oesophagus is associated with an increased risk of oseophageal cancer, but its cell of origin is unclear. Here the authors show, using single-cell RNA sequencing of biopsies from six patients and two unaffected subjects, that cells in Barrett’s oesophagus show a transcriptional profile that is similar to that of cells in oesophageal submucosal glands.

    • Richard Peter Owen
    • , Michael Joseph White
    •  & Xin Lu

  • Article
    | Open Access

    Genetic variants in ACTB and ACTG1 have been associated with Baraitser-Winter Cerebrofrontofacial syndrome. Here, the authors report of a syndromic thrombocytopenia caused by variants in ACTB exons 5 or 6 that compromise the organization and coupling of the cytoskeleton, leading to impaired platelet maturation.

    • Sharissa L. Latham
    • , Nadja Ehmke
    •  & Nataliya Di Donato

  • Article
    | Open Access

    Meiotic drive elements are selfish genetic elements that mediate a skew in their sexual transmission from parent to offspring. Here, the authors sequence and analyze large and complex genomic regions associated with meiotic drive elements in the fungus Neurospora intermedia.

    • Jesper Svedberg
    • , Sara Hosseini
    •  & Hanna Johannesson

  • Article
    | Open Access

    Elevated serum urate levels are a risk factor for gout. Here, Tin et al. perform whole-exome sequencing in 19,517 individuals and detect low-frequency genetic variants in urate transporter genes, SLC22A12 and SLC2A9, associated with serum urate levels and confirm their damaging nature in vitro and in silico.

    • Adrienne Tin
    • , Yong Li
    •  & Anna Köttgen

  • Article
    | Open Access

    miR-34 is known to regulate age-related gene expression in the Drosophila brain, and miR-34 overexpression can attenuate neurodegeneration induced by polyQ-expanded proteins. Here, Kennerdell and colleagues show that miR-34 confers longevity and neuroprotection via an epigenetic regulator Polycomb Repressive Complex 2 and molecular chaperone expression.

    • Jason R. Kennerdell
    • , Nan Liu
    •  & Nancy M. Bonini

  • Article
    | Open Access

    Waldenström macroglobulinemia (WM)/lymphoplasmacytic lymphoma (LPL) is a non-Hodgkin-type B cell lymphoma. Here, the authors identify two risk loci for WM/LPL in a two-stage GWAS involving a family-oversampling approach and provide evidence for a functional role of the non-coding SNP rs116446171.

    • Mary L. McMaster
    • , Sonja I. Berndt
    •  & Neil E. Caporaso

  • Article
    | Open Access

    The majority of scoliosis is considered idiopathic with onset in adolescence (AIS) and has a genetic contribution. Here, the authors perform an exome wide association study of data from 457 severe AIS cases and 987 controls, and find a missense variant in SLC39A8 is associated with AIS.

    • Gabe Haller
    • , Kevin McCall
    •  & Christina A. Gurnett

  • Article
    | Open Access

    Approximately 30% of psoriasis patients develop psoriatic arthritis (PsA) and early diagnosis is crucial for the management of PsA. Here, Patrick et al. develop a computational pipeline involving statistical and machine-learning methods that can assess the risk of progression to PsA based on genetic markers.

    • Matthew T. Patrick
    • , Philip E. Stuart
    •  & Lam C. Tsoi

  • Article
    | Open Access

    Vector alteration strategies are emerging as attractive tools for malaria transmission control. Here, Shane et al. engineer a bacterial strain, isolated from mosquitoes, to produce an antiplasmodial protein in the presence of blood meal, causing the mosquitoes to become refractory to Plasmodium infection.

    • Jackie L. Shane
    • , Christina L. Grogan
    •  & David J. Lampe

  • Article
    | Open Access

    Spatial mapping of genomic programs in tissue cells is an important step in the understanding of organ function and disease. Here, the authors provide a spatially resolved epigenomic and transcriptomic map of human liver and show porto-central gradients in metabolic and morphogen networks and transcription factor binding sites as a basis to better understand liver regeneration and function.

    • Mario Brosch
    • , Kathrin Kattler
    •  & Jochen Hampe

  • Article
    | Open Access

    Epigenetic regulation is critical for the maintenance of germ cell identity. Here the authors show that H3K9me3-mediated gene silencing is critical for repression of testis-specific transcription in Drosophila female germ cells, indicating H3K9me3 maintains female germ cell sexual identity.

    • Anne E. Smolko
    • , Laura Shapiro-Kulnane
    •  & Helen K. Salz

  • Article
    | Open Access

    Proteoforms arise as protein isoforms or as protein haplotypes, which are the result of genetic variation. Here, the authors develop Haplosaurus, a database that computes protein haplotypes genome-wide from existing genotype data and analyse protein haplotype variability in the 1000 Genomes dataset.

    • William Spooner
    • , William McLaren
    •  & Catherine Chaillan Huntington

  • Article
    | Open Access

    Human APOBEC3H has several haplotypes and splice variants with distinct anti-HIV-1 activities, but the genetics underlying the expression of these variants are unclear. Here, the authors identify an intronic deletion in A3H haplotype II resulting in production of the most active splice variant, which is counteracted by HIV-1 protease.

    • Diako Ebrahimi
    • , Christopher M. Richards
    •  & Reuben S. Harris

  • Article
    | Open Access

    The evolutionary forces that favour transitions in sex chromosomes are not well understood. Here, Jeffries and colleagues show a very high rate of sex chromosome turnover in true frogs, which may be driven by rapid mutation-load accumulation due to the low recombination rate in males.

    • Daniel L. Jeffries
    • , Guillaume Lavanchy
    •  & Nicolas Perrin

  • Article
    | Open Access

    Association between variants in 11 different genes and breast cancer risk has been established and sequencing of these genes is recommended to provide personalized diagnosis, therapy, and surveillance for the high-risk patients and their relatives. Here the authors analyse the frequency of germline pathogenic mutations in these genes specifically in a Japanese population.

    • Yukihide Momozawa
    • , Yusuke Iwasaki
    •  & Michiaki Kubo

  • Article
    | Open Access

    Genome-wide association studies (GWAS) have identified hundreds of genomic risk regions for prostate cancer. Here, the authors perform a transcriptome wide association study (TWAS) by incorporating prostate cancer GWAS with gene expression data to identify potential novel prostate cancer risk loci and possible risk mechanisms.

    • Nicholas Mancuso
    • , Simon Gayther
    •  & Peter Kraft

  • 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

    Genetic risk loci for tuberculosis (TB) have so far been identified in African and Russian populations. Here, the authors perform a three-stage GWAS for TB in Han Chinese populations and find two risk loci near ESRRB and TGM6 and further demonstrate that tgm6 protects mice from Mtb infection.

    • Ruijuan Zheng
    • , Zhiqiang Li
    •  & Baoxue Ge

  • Article
    | Open Access

    Mitochondrial protein synthesis requires charging a mitochondrial tRNA with its amino acid. Here, the authors describe pathogenic variants in the GatCAB protein complex genes required for the generation of glutaminyl-mt-tRNAGln, that impairs mitochondrial translation and presents with cardiomyopathy.

    • Marisa W. Friederich
    • , Sharita Timal
    •  & Johan L. K. Van Hove

  • Article
    | Open Access

    Sharing of whole genome sequencing (WGS) data improves study scale and power, but data from different groups are often incompatible. Here, US genome centers and NIH programs define WGS data processing standards and a flexible validation method, facilitating collaboration in human genetics research.

    • Allison A. Regier
    • , Yossi Farjoun
    •  & Ira M. Hall

  • Article
    | Open Access

    The RNA-binding protein MARF1 is required for post-transcriptional regulation of mRNAs during mouse oogenesis. Here, by analyzing a Drosophila MARF1 mutant, the authors show that MARF1 recruits CCR4-NOT deadenylase to shorten the poly-A tails of target mRNAs such as cyclin A and suppress their translation during Drosophila oogenesis.

    • Li Zhu
    • , Suresh K. Kandasamy
    •  & Ryuya Fukunaga

  • Article
    | Open Access

    Around 10% of high-grade serous ovarian carcinomas (HGSOC) harbor BRCA1 promoter methylation, but it is uncertain how it predicts response to PARP inhibition. Here, the authors show that homozygous BRCA1 methylation predicts response to rucaparib while heterozygous methylation of BRCA1 predicts resistance in HGSOC.

    • Olga Kondrashova
    • , Monique Topp
    •  & Clare L. Scott

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