Genetics articles within Nature Communications

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  • Article
    | Open Access

    Here, Libertini and colleagues devise a computation tool that can analyze whole-genome bisulfite sequencing (WGBS) data to recover of ∼30% of the lost differential methylation position information. They use COMETgazer and COMETvintage to analyze 13 diffferent methylome data to demonstrate their performance.

    • Emanuele Libertini
    • , Simon C. Heath
    •  & Stephan Beck

  • Article
    | Open Access

    Chronic lymphocytic leukemia (CLL) is characterized by substantial clinical heterogeneity. Here, the authors report the genome-wide chromatin accessibility maps for 88 CLL samples from 55 patients using ATAC-seq, and 10 matched RNA-seq datasets, providing a resource for studying epigenome deregulation in CLL.

    • André F. Rendeiro
    • , Christian Schmidl
    •  & Christoph Bock

  • Article
    | Open Access

    The genetic factors that predispose individuals to familial colorectal cancer are poorly understood. In this study, the authors use whole exome sequencing of 1,006 patients and 1,609 healthy controls and show it is unlikely that further major high-penetrance susceptibility genes exist.

    • Daniel Chubb
    • , Peter Broderick
    •  & Richard S. Houlston

  • Article
    | Open Access

    Transcription factors Distal-less(Dll) and spalt were co-opted during the evolution of butterfly eyespots. Here, Zhang and Reed use CRISPR/Cas9 genome editing to show that while spalt is a positive regulator of eyespots as predicted, Dll knockouts have positive effects on both eyespot size and number, thus suggesting that Dllis an eyespot repressor, not an activator as previously thought.

    • Linlin Zhang
    •  & Robert D. Reed

  • Article
    | Open Access

    APC is a well-known tumour suppressor that is frequently inactivated in colorectal cancer. Here, the authors sequence more than 1000 cancer genes in 468 colorectal cancers and show that mutation signatures can be used to classify the tumours and that multiple mutations in APCare associated with a poor prognosis.

    • Michael J. Schell
    • , Mingli Yang
    •  & Timothy J. Yeatman

  • Article
    | Open Access

    It has been increasingly recognised that tumours are not made up of a homogeneous population of cells. Here, the authors show heterogeneous expression of five protein markers in renal cell cancer and demonstrate that the progression of the tumour does not influence the degree of heterogeneity in the tumour.

    • Rouven Hoefflin
    • , Bernd Lahrmann
    •  & Stefan Duensing

  • Article
    | Open Access

    CRISPR/Cas9-mediated forward genetic screens and gene-trap mutagenesis screens in haploid cells are both powerful techniques to examine gene function. Here, the authors show the two approaches have high concordance and identify an uncharacterized gene, TXNDC11, which is involved in endoplasmic reticulum-associated degradation.

    • Richard T. Timms
    • , Sam A. Menzies
    •  & Paul J. Lehner

  • Article
    | Open Access

    While the CRISPR-Cas9 system has revolutionised molecular biology, it is still a mystery why not every guide RNA elicits target DNA cleavage. Here the authors show that genomic context and internal gRNA interactions can inhibit cleavage.

    • Summer B. Thyme
    • , Laila Akhmetova
    •  & Alexander F. Schier

  • Article
    | Open Access

    Clinical RNA-seq datasets can predict clinical outcomes. Here, Shen et al. report a statistical method for survival analysis of mRNA isoform variation using clinical RNA-seq datasets, and the identified isoform based survival predictors outperform gene expression based survival predictors using TCGA data on six cancer types.

    • Shihao Shen
    • , Yuanyuan Wang
    •  & Yi Xing

  • Article
    | Open Access

    The T300A substitution in ATG16L is associated with Crohn’s disease risk and disrupts clearance of intracellular pathogens by autophagy. Here the authors show that the mutation impairs interaction of ATG16L with TMEM59 and disrupts unconventional TMEM-induced autophagy, an aspect of innate immunity.

    • Emilio Boada-Romero
    • , Inmaculada Serramito-Gómez
    •  & Felipe X. Pimentel-Muiños

  • Article
    | Open Access

    The t(8;21) translocation is often found in acute myeloid leukaemia but is not sufficient for development of the disease. In this study, the authors identify frequent mutations in the transcriptional repressor, ZBTB7A, in these patients and show that the mutations reduce DNA binding activity.

    • Luise Hartmann
    • , Sayantanee Dutta
    •  & Philipp A. Greif

  • Article
    | Open Access

    Bacteria of the genus Streptomyces produce a great variety of natural products, the biosynthesis of which is subject to complex regulatory networks. Here the authors present a high-resolution, genome-wide analysis of the transcriptome and translatome of Streptomyces coelicolorunder various growth conditions.

    • Yujin Jeong
    • , Ji-Nu Kim
    •  & Byung-Kwan Cho

  • Article
    | Open Access

    Cryptic genetic variants may not individually show discernible phenotypic effects, but collectively, these polymorphisms can lead to unexpected, genetically complex traits that might be relevant to evolution and disease. Here, the authors use large yeast populations to comprehensively dissect the genetic bases of 17 independent occurrences of a phenotype that arises due to combinations of epistatically interacting cryptic variants.

    • Matthew B. Taylor
    • , Joann Phan
    •  & Ian M. Ehrenreich

  • Article
    | Open Access

    Killer whales have evolved into specialized ecotypes based on hunting strategies and ecological niches. Here, Andrew Foote and colleagues sequenced the whole genome of individual killer whales representing 5 different ecotypes from North Pacific and Antarctic, and show expansion of small founder groups to adapt to specific ecological niches.

    • Andrew D. Foote
    • , Nagarjun Vijay
    •  & Jochen B.W. Wolf

  • Article
    | Open Access

    3D genome structures are plastic and vary from cell to cell even in an isogenic sample. Here, the authors present an approach to identify frequent 3D chromatin clusters across a population of genome structures, either deconvoluted from ensemble-averaged Hi-C data or from a collection of single-cell Hi-C data.

    • Chao Dai
    • , Wenyuan Li
    •  & Xianghong Jasmine Zhou

  • Article
    | Open Access

    Here, Dirk Lefeber and colleagues identify functional mutations in ATP6AP1 encoding Ac45. The authors show that Ac45 is the functional ortholog of yeast V-ATPase assembly factor Voa1 and provide evidence for tissue-specific Ac45 processing, associated with the clinical phenotype of immunodeficiency, hepatopathy, and neurocognitive abnormalities.

    • Eric J. R. Jansen
    • , Sharita Timal
    •  & Dirk J. Lefeber

  • Article
    | Open Access

    The transcription factor Hsf1 and the molecular chaperone Hsp90 modulate the heat shock response in the pathogen Candida albicans. Here, Leach et al. reveal a complex interplay between the two factors that regulates the expression of genes involved in the heat shock response and virulence.

    • Michelle D. Leach
    • , Rhys A. Farrer
    •  & Leah E. Cowen

  • Article
    | Open Access

    Women with germline variants in BRCA genes are predisposed to ovarian cancer. In this study, the authors demonstrate that fimbrial tissue from the ovary, the site of ovarian cancer, in BRCAmutant carriers contains marked DNA methylation changes compared with the proximal region of the ovary.

    • Thomas E. Bartlett
    • , Kantaraja Chindera
    •  & Martin Widschwendter

  • Article
    | Open Access

    A fundamental question in evolutionary biology is how complex innovations requiring multiple genetic changes arise. Here the authors provide lines of evidence that changing environments facilitate the adaptive evolution of complex metabolic innovations via stepwise acquisition of single reactions.

    • Balázs Szappanos
    • , Jonathan Fritzemeier
    •  & Balázs Papp

  • Article
    | Open Access

    Humans show great diversity in facial appearance and this variation is highly heritable. Here, Andres Ruiz-Linares and colleagues examined facial features in admixed Latin Americans and identify genome-wide associations for 14 facial traits, including four gene loci (RUNX2, GLI3, DCHS2 and PAX1) influencing nose morphology.

    • Kaustubh Adhikari
    • , Macarena Fuentes-Guajardo
    •  & Andrés Ruiz-Linares

  • Article
    | Open Access

    Antimalarial chemotherapy relies on combination therapies (ACTs) consisting of an artemisinin derivative and a partner drug. Here, the authors study the effects of globally prevalent mutations in a multidrug resistance transporter (PfMDR1) on the parasite’s susceptibility to ACT drugs.

    • M. Isabel Veiga
    • , Satish K. Dhingra
    •  & David A. Fidock

  • Article
    | Open Access

    Giraffe’s unique anatomy and physiology include its stature and associated cardiovascular adaptation. Here, Douglas Cavener and colleagues provide de novogenome assemblies of giraffe and its closest relative okapi and provide comparative analyses to infer insights into evolution and adaptation.

    • Morris Agaba
    • , Edson Ishengoma
    •  & Douglas R. Cavener

  • Article
    | Open Access

    Analysing multiple tumours from the same patient permits the study of the germline contribution to cancer. Here, the authors sequence multiple renal tumours from VHL patients and find that intra-patient tumours are clonally distinct but share some genetic features, suggesting that patient-specific factors influence tumour formation.

    • Suzanne S. Fei
    • , Asia D. Mitchell
    •  & Paul T. Spellman

  • Article
    | Open Access

    Physiological effects of psychological stress and infection in mothers can increase the incidence of anxiety and psychiatric diseases in offsprings and in subsequent generation. Here, Miklos Toth and colleagues show that intergenerational inheritance of neurological traits is propagated across multiple generations independently by parallel non-genetic mechanisms involving independent segregation of epigenetic specific loci.

    • Emma Mitchell
    • , Shifra L. Klein
    •  & Miklos Toth

  • Article
    | Open Access

    MicroRNAs are important small regulatory RNAs produced by sequential Drosha and Dicer cleavage. Here the authors describe 'agotrons', a subclass of small RNAs that bypass the canonical biogenesis machinery.

    • Thomas B. Hansen
    • , Morten T. Venø
    •  & Jørgen Kjems

  • Article
    | Open Access

    The role of wild elk in the spread and persistence of bovine brucellosis in the Great Yellowstone area is unclear. Here, Kamath et al. analyse the genomic sequences of 245 Brucella abortusisolates from elk, bison and cattle, supporting the idea that elk is an important reservoir and source of livestock infections.

    • Pauline L. Kamath
    • , Jeffrey T. Foster
    •  & Paul C. Cross

  • Article
    | Open Access

    Heritability of complex traits can be finely dissected using yeast crosses. Here, Kaspar Märtens and colleagues show that quantitative traits in yeast can be predicted from genotype and phenotype data with an average coefficient of determination of 0.91, providing the most accurate predictions of complex traits to date.

    • Kaspar Märtens
    • , Johan Hallin
    •  & Leopold Parts

  • Article
    | Open Access

    Nucleosome positioning and chromatin accessibility are important contributors to the regulation of gene expression. Here the authors describe a method that allows the simultaneous measurement of nucleosome occupancy and chromatin accessibility in the same assay, revealing new features of chromatin organization linked to gene regulation.

    • Jakub Mieczkowski
    • , April Cook
    •  & Michael Y. Tolstorukov

  • Article
    | Open Access

    Colletotrichum tofieldiae is a beneficial root endophyte, whereas the closely related C. incanumis pathogenic. Here the authors compare the genomes and transcriptomes during host plant interaction and demonstrate that the host plant can respond differently to the beneficial endophyte according to phosphate status.

    • Stéphane Hacquard
    • , Barbara Kracher
    •  & Richard J. O’Connell

  • Article
    | Open Access

    Genome-wide association studies have been performed to identify genetic variants that are associated with susceptibility to colorectal cancer. Here, the authors expand on these studies and identify a variant that regulates the expression of ETV6 and find that over-expression of ETV6 blocks cell proliferation in vitro.

    • Meilin Wang
    • , Dongying Gu
    •  & Jinfei Chen

  • Article
    | Open Access

    Mutational signatures provide evidence of the mechanism of action of a given mutagen and are found in cancer cells. Here, using 560 breast cancer genomes, the authors demonstrate that mutational signatures are frequently associated with genomic architecture including nucleosome positioning and replication timing.

    • Sandro Morganella
    • , Ludmil B. Alexandrov
    •  & Serena Nik-Zainal

  • Article
    | Open Access

    Oestrogen negative breast cancer is associated with a poor prognosis. In this study, the authors perform a meta-analysis of 11 breast cancer genome-wide association studies and identify four new loci associated with oestrogen negative breast cancer risk. These findings may aid in stratifying patients in the clinic.

    • Fergus J. Couch
    • , Karoline B. Kuchenbaecker
    •  & Antonis C. Antoniou

  • Article
    | Open Access

    Extracellular miRNAs are present in a variety of bodily fluids. Here, Freedman et al. analysed plasma-derived RNA by RNA-seq from 40 people followed by targeted RT-qPCR in an additional 2,763 people, and report over 1,000 extracellular RNAs including microRNAs, piwi-interacting RNA and small nucleolar RNAs.

    • Jane E. Freedman
    • , Mark Gerstein
    •  & Kahraman Tanriverdi

  • Article
    | Open Access

    The variability in patient response to radiation treatment is difficult to predict. Here, using more than 500 cell lines the authors measure response to radiation exposure and a large panel of compounds, and show that response can be predicted by genetic alterations of the cells.

    • Brian D. Yard
    • , Drew J. Adams
    •  & Mohamed E. Abazeed

  • Article
    | Open Access

    Use of general linear mixed models (GLMMs) in genetic variance analysis can quantify the relative contribution of additive effects from genetic variation on a given trait. Here, Jonathan Mosley and colleagues apply GLMM in a phenome-wide analysis and show that genetic variations in the HLA region are associated with 44 phenotypes, 5 phenotypes which were not previously reported in GWASes.

    • Jonathan D. Mosley
    • , John S. Witte
    •  & Joshua C. Denny

  • Article
    | Open Access

    Ian Blair and colleagues use genome-wide linkage analysis and whole exome sequencing to identify mutations in the CCNF gene in large cohorts of amyotrophic lateral sclerosis and frontotemporal dementia patients. In addition to validating the mutations in international cohorts, the authors also show that mutant CCNFgene product affects ubiquitination and protein degradation in cultured cells.

    • Kelly L. Williams
    • , Simon Topp
    •  & Ian P. Blair

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