Genetics articles within Nature Communications

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  • Article
    | Open Access

    Bacteria have evolved numerous innate and adaptive defence mechanisms. Here, Beavogui et al characterise the impact of biogeography, genetic mobility, and clustering in defense islands, on the defence systems of soil, marine, and human gut bacterial populations genomes.

    • Angelina Beavogui
    • , Auriane Lacroix
    •  & Pedro H. Oliveira

  • Article
    | Open Access

    Thierer and colleagues identify PLA2G12B as a key gene driving triglyceride incorporation into lipoproteins and show that disruption of this activity provides protection from atherosclerosis.

    • James H. Thierer
    • , Ombretta Foresti
    •  & Steven A. Farber

  • Article
    | Open Access

    Compared to traditional Cas9 nucleases prime editors (PEs) are less active. Here the authors use OrthoRep, a yeast-based platform for directed protein evolution to enhance the editing efficiency of PEs: they identify mutations that have a positive effect on kinetics and use this knowledge to generate an efficient in vivo PE.

    • Yanik Weber
    • , Desirée Böck
    •  & Gerald Schwank

  • Article
    | Open Access

    Bacterial capsules provide protection against the environment, including host immune systems. Authors swap capsule loci in Klebsiella pneumoniae to reveal the role of these sugar coats against plasmid conjugation and phage infection, showing that the serotype is a key player in regulating conjugation rates, and phage susceptibility.

    • Matthieu Haudiquet
    • , Julie Le Bris
    •  & Olaya Rendueles

  • Article
    | Open Access

    Rajderkar et al. provide a genome-wide compendium of transcriptional enhancers active in human craniofacial development, along with single-cell resources for studies of mammalian craniofacial morphogenesis.

    • Sudha Sunil Rajderkar
    • , Kitt Paraiso
    •  & Axel Visel

  • Article
    | Open Access

    The authors find that small circular DNA nanostructures which partially match gRNA sequences only minimally activate Cas12a. They report AutoCAR (Autocatalytic Cas12a Circular DNA Amplification Reaction) which allows a single nucleic acid target to activate multiple ribonucleoproteins, and increases reporter cleavage rates.

    • Fei Deng
    • , Yi Li
    •  & Ewa M. Goldys

  • Article
    | Open Access

    DNA methylation plays a major role in establishing cell identity, but the dynamics of DNA methylation patterns are highly variable across species. Here, the authors discover extensive DNA methylation reprogramming during embryonic development of the sea lamprey, a jawless fish with a distinctive, highly disordered methylome.

    • Allegra Angeloni
    • , Skye Fissette
    •  & Ozren Bogdanovic

  • Article
    | Open Access

    The structural connectome is the complete set of anatomical connections between brain cells. Here, the authors perform a genome-wide association study of white-matter structural connectivity in the human brain, finding 30 variants influencing the density of myelinated connections between brain regions.

    • Michael Wainberg
    • , Natalie J. Forde
    •  & Shreejoy J. Tripathy

  • Article
    | Open Access

    All natural AAV serotypes transduce murine hepatocytes more efficiently than their human counterparts in human liver chimeric mouse models. Here the authors developed a novel humanized mouse were human transduction of AAV can be studied.

    • Mercedes Barzi
    • , Tong Chen
    •  & Karl-Dimiter Bissig

  • Article
    | Open Access

    Gut ecosystem colonization impacts lifelong health. Here, authors track mother-infant gut viruses over time, reveal feeding’s influence on early viral colonization, and demonstrate the co-transmission of bacteriophages and bacteria from mothers to infants.

    • Sanzhima Garmaeva
    • , Trishla Sinha
    •  & Alexandra Zhernakova

  • Article
    | Open Access

    Extraocular muscles remain unaffected in muscular dystrophies. Here, the authors show that the gene fhl2b has a protective role in extraocular muscle and that its protective function can be applied to rescue other muscles in a zebrafish model of muscular dystrophy.

    • Nils Dennhag
    • , Abraha Kahsay
    •  & Fatima Pedrosa Domellöf

  • Article
    | Open Access

    Some cyanobacteria excrete nitrite when the supply of inorganic carbon is limiting, but the underlying mechanisms are unclear. Here, Kraus et al. identify a conserved protein that interacts with nitrite reductase, thus regulating nitrogen metabolism and promoting nitrite excretion.

    • Alexander Kraus
    • , Philipp Spät
    •  & Wolfgang R. Hess

  • Article
    | Open Access

    Winged bean is a tropical legume that can produce similar level of seed protein to soybean. Here, the authors report the genome assembly, population genetics, QTL mapping of the plant architecture, protein content and phytonutrients for this species.

    • Wai Kuan Ho
    • , Alberto Stefano Tanzi
    •  & Sean Mayes

  • Article
    | Open Access

    Pathogenic germline variants associated with childhood cancer risk could be subject to evolutionary constraints. Here, the authors analyse publicly available germline data in large cohorts and observe that paediatric cancer predisposition syndrome genes are highly constrained in the general population.

    • Ulrik Kristoffer Stoltze
    • , Jon Foss-Skiftesvik
    •  & Kjeld Schmiegelow

  • Article
    | Open Access

    Studying individuals with autism only, this study investigated the genomic architecture of autism-related phenotypes using a multivariate modelling framework. This work identified distinct genomic factors linked to language performance, behaviour and developmental motor delay.

    • Lucía de Hoyos
    • , Maria T. Barendse
    •  & Beate St Pourcain

  • Article
    | Open Access

    Despite many common genetic variants being linked to depression, the impact of rare coding variants on depression remains largely unknown. Here, the authors perform a whole-exome sequencing study of depression, providing insights into the rare genetic architecture of depression.

    • Ruoyu Tian
    • , Tian Ge
    •  & Chia-Yen Chen

  • Article
    | Open Access

    The evolutionary trajectory of avian sex chromosomes may be more intricate than previously understood. In this study, sequencing and analysis of the neo-sex chromosomes and genome of the Crested Ibis suggests a multidirectional evolution of sex chromosomes in core waterbirds.

    • Lulu Xu
    • , Yandong Ren
    •  & Gang Li

  • Article
    | Open Access

    Stem cells exist in vitro in a spectrum of interconvertible pluripotent states. Here, authors show that pluripotency and self-renewal processes have a high level of regulatory complexity and suggest that genetic factors contribute to cell state transitions in human iPSC lines.

    • Timothy D. Arthur
    • , Jennifer P. Nguyen
    •  & Kelly A. Frazer

  • Article
    | Open Access

    Polyploidization-rediploidization process plays an important role in plant adaptive evolution. Here, the authors assemble the genomes of mangrove species Sonneratia alba and its inland relative Lagerstroemia speciosa, and reveal genomic evidence for rediploidization and adaptive evolution after the whole-genome triplication.

    • Xiao Feng
    • , Qipian Chen
    •  & Ziwen He

  • Article
    | Open Access

    Genome-wide evidence to support that wild rice can contribute to weedy rice evolution by hybridization and adaptive introgression is very limited. Here, the authors sequence the weedy rice genomes and show reproductively compatible wild rice can contribute to weedy rice evolution.

    • Lin-Feng Li
    • , Tonapha Pusadee
    •  & Kenneth M. Olsen

  • Article
    | Open Access

    Immune response during breast cancer progression remains to be explored. Here, the characterisation of sequential and parallel multiregion samples of an index patient and a cohort of metastatic triple-negative breast cancers reveals convergent immune evasion mechanisms and an increase in tumor genomic heterogeneity.

    • Juan Blanco-Heredia
    • , Carla Anjos Souza
    •  & Leticia De Mattos-Arruda

  • Article
    | Open Access

    Information on the occurrence of aneuploidies in prehistory human populations are rare. Here, from a large screen of ancient human genomes and osteological examination, the authors find genetic evidence for six cases of trisomy 21 (Down syndrome) and one case of trisomy 18 (Edwards syndrome) in historic and prehistoric infants.

    • Adam Benjamin Rohrlach
    • , Maïté Rivollat
    •  & Kay Prüfer

  • Article
    | Open Access

    Gene variants can affect folding and stability of the encoded protein. Here, the authors apply deep mutational scanning to provide genotype-phenotype information for 99% of the possible PRKN variants and reveal mechanistic details on how some variants cause loss-of-function and Parkinsons disease.

    • Lene Clausen
    • , Vasileios Voutsinos
    •  & Rasmus Hartmann-Petersen

  • Article
    | Open Access

    Cytochrome c maturation (CCM) is the process of covalent attachment of a heme group to the conserved cysteines to form the holocytochrome. Here, the authors report that the non-adaptive convergent evolution at the pathway level leads to mosaic distribution of CCM systems I and III among Archaeplastida species.

    • Huang Li
    • , Soujanya Akella
    •  & Jeffrey P. Mower

  • Article
    | Open Access

    Retinol, a form of vitamin A, plays an essential role in many biological processes throughout the human lifespan. Here the authors identify genetic variants that influence the level of circulating retinol and use this information to better understand how retinol impacts human health.

    • William R. Reay
    • , Dylan J. Kiltschewskij
    •  & Murray J. Cairns

  • Article
    | Open Access

    Mechanisms underlying changes in inflorescence development in response to high ambient temperature remain unclear. Here, the authors report the cloning of the MIB2, encoding a homology of SPATULA, and its activation of CONSTANS-Like1 for determining tomato inflorescence branching at high ambient temperature.

    • Shuai Sun
    • , Zhiqiang Liu
    •  & Xia Cui

  • Article
    | Open Access

    Mobile genetic elements can promote the duplication of antibiotic resistance genes which may in turn accelerate the evolution of resistance to new drugs. Here, the authors show that duplicated antibiotic resistance genes are enriched in bacterial isolates from environments associated with rampant antibiotic use.

    • Rohan Maddamsetti
    • , Yi Yao
    •  & Lingchong You

  • Article
    | Open Access

    Hundreds of arthritis-associated genetic variants have been identified but in most cases their functions remain unknown. Here the authors develop a resource to reveal the effects of variants on gene expression in human synovium, and identify arthritis-related genes.

    • Feng Jiang
    • , Shou-Ye Hu
    •  & Tie-Lin Yang

  • Article
    | Open Access

    Bats have been suggested to be resistant to cancer due to mechanisms related to their evolved longevity, but the associated molecular drivers are still understudied. Here, the authors examine cancer resistance mechanisms across seven bat species using in vitro and in vivo models, and identify HIF1A, COPS5, and RPS3 as related genes.

    • Rong Hua
    • , Yuan-Shuo Ma
    •  & Zhen Liu

  • Article
    | Open Access

    Chemoreception - the ability to smell and taste - relies on diverse receptor genes. Examining 1,527 vertebrate genomes, this study explores the dynamic evolution, lineage-specific expansions and losses of chemoreceptor genes as well as ecological and morphological factors associated with these.

    • Maxime Policarpo
    • , Maude W. Baldwin
    •  & Walter Salzburger

  • Article
    | Open Access

    The most recent class of base editors utilize DddAtox, a deaminase domain that can act upon double-stranded DNA. Here the authors target DddAtox fragments and a FokI-based nickase to the human CIITA gene by fusing these domains to arrays of engineered zinc fingers; they also identify a variety of DddAtox orthologues.

    • Friedrich Fauser
    • , Bhakti N. Kadam
    •  & Jeffrey C. Miller

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