Featured
-
-
Article
| Open AccessDependency on host vitamin B12 has shaped Mycobacterium tuberculosis Complex evolution
Campos-Pardos et al show that the virulence of Mycobacterium tuberculosis is dependent on sufficient uptake of exogenous vitamin B12 from host serum and this phenotype is not conserved in environmental, opportunistic and ancestral lineages.
- Elena Campos-Pardos
- , Santiago Uranga
- & Jesús Gonzalo-Asensio
-
Article
| Open AccessInterrogations of single-cell RNA splicing landscapes with SCASL define new cell identities with physiological relevance
RNA splicing serves as a critical layer of gene expression regulation. Here, authors introduce SCASL for investigating the heterogeneity of RNA splicing landscapes at single-cell resolution, offering a novel scheme for classifying cell identities with physiological relevance.
- Xianke Xiang
- , Yao He
- & Xuerui Yang
-
Article
| Open AccessThe defensome of complex bacterial communities
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 AccessN-Acetyltransferase 10 represses Uqcr11 and Uqcrb independently of ac4C modification to promote heart regeneration
Here, Ma et al. investigate the translational profile of cardiac regeneration, pointing to Nat10 as a key regulator of cardiomyocyte proliferative potential, and describing how it regulates cardiac gene expression.
- Wenya Ma
- , Yanan Tian
- & Benzhi Cai
-
Article
| Open AccessNatural variation in BnaA9.NF-YA7 contributes to drought tolerance in Brassica napus L
Rapeseed production is often threatened by drought stress. Here, the authors report transcription factor BnaA9.NFYA7 negatively regulates rapeseed drought tolerance through ABA signal transduction pathway via feedback inhibition of the expression of BnaABF3/4s-related genes.
- Jia Wang
- , Lin Mao
- & Liezhao Liu
-
Article
| Open AccessPla2g12b drives expansion of triglyceride-rich lipoproteins
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 AccessEnhancing prime editor activity by directed protein evolution in yeast
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 AccessProTInSeq: transposon insertion tracking by ultra-deep DNA sequencing to identify translated large and small ORFs
Identifying small proteins is challenging. ProTInSeq uses modified transposons to express markers inserted in-frame to protein-coding genes. This method identifies 153 unannotated small proteins in M. pneumoniae and additional proteomic information.
- Samuel Miravet-Verde
- , Rocco Mazzolini
- & Luis Serrano
-
Article
| Open AccessNatural variation of STKc_GSK3 kinase TaSG-D1 contributes to heat stress tolerance in Indian dwarf wheat
Indian dwarf wheat (Triticum sphaerococcum) is thermotolerant, but the underlying mechanism is unclear. Here, the authors report the cloning of the heat tolerance gene encoding a STKc_GSK3 kinase and its variation affects phosphorylation level of downstream TaPIF4 in determining thermotolerance.
- Jie Cao
- , Zhen Qin
- & Mingming Xin
-
Article
| Open AccessA SWI/SNF-dependent transcriptional regulation mediated by POU2AF2/C11orf53 at enhancer
POU2AF2 is a co-activator of POU2F3 in normal and neoplastic tuft cells, such as small cell lung cancer. Here, the authors report that POU2AF2 dictates opposing transcriptional regulation at distal enhance elements.
- Aileen Szczepanski
- , Natsumi Tsuboyama
- & Lu Wang
-
Article
| Open AccessEpigenetic profiling reveals key genes and cis-regulatory networks specific to human parathyroids
Parathyroid glands are crucial for balancing blood calcium levels. Here, the authors generate comprehensive maps of the chromatin landscape of human parathyroids, linking identified regulatory elements to key functions in calcium homeostasis.
- Youngsook Lucy Jung
- , Wenping Zhao
- & Michael Mannstadt
-
Article
| Open AccessCapsules and their traits shape phage susceptibility and plasmid conjugation efficiency
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 AccessDynamic enhancer landscapes in human craniofacial development
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 AccessTopological barrier to Cas12a activation by circular DNA nanostructures facilitates autocatalysis and transforms DNA/RNA sensing
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 AccessQTL mapping of human retina DNA methylation identifies 87 gene-epigenome interactions in age-related macular degeneration
Here, the authors perform genome-wide mapping of DNA methylation and expression quantitative trait loci, revealing associations among genotype, epigenome and transcriptome, uncovering genes and gene-environment interactions contributing to age-related macular degeneration (AMD).
- Jayshree Advani
- , Puja A. Mehta
- & Anand Swaroop
-
Article
| Open AccessExtensive DNA methylome rearrangement during early lamprey embryogenesis
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 AccessGenetic architecture of the structural connectome
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 AccessA humanized mouse model for adeno-associated viral gene therapy
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 AccessTransmission and dynamics of mother-infant gut viruses during pregnancy and early life
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 AccessQuantitative pathogenicity and host adaptation in a fungal plant pathogen revealed by whole-genome sequencing
The understanding of pathogenicity in quantitative plant pathosystems remains limited. This study reveals the genetic architecture of quantitative pathogenicity traits in a significant fungal plant pathogen, shedding light on potential evolutionary mechanisms involved in host adaptation.
- Reda Amezrou
- , Aurélie Ducasse
- & Thierry C. Marcel
-
Article
| Open Accessfhl2b mediates extraocular muscle protection in zebrafish models of muscular dystrophies and its ectopic expression ameliorates affected body muscles
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 AccessProtein NirP1 regulates nitrite reductase and nitrite excretion in cyanobacteria
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 AccessA genomic toolkit for winged bean Psophocarpus tetragonolobus
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 AccessThe evolutionary impact of childhood cancer on the human gene pool
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 AccessStructural models of genome-wide covariance identify multiple common dimensions in autism
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 AccessA distinct class of pan-cancer susceptibility genes revealed by an alternative polyadenylation transcriptome-wide association study
Alternative polyadenylation (APA) can play a key role in cancer initiation and progression. Here, the authors conducted a comprehensive pan-cancer APA TWAS analysis and discovered a distinct class of APA-mediated cancer susceptibility genes across 22 cancer types.
- Hui Chen
- , Zeyang Wang
- & Lei Li
-
Article
| Open AccessWhole-exome sequencing in UK Biobank reveals rare genetic architecture for depression
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 AccessImplications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen
The spatial organization of eukaryotic genomes is linked to their biological functions. Here, the authors study the 3D genome organization of the phytopathogenic fungus Verticillium dahliae, revealing links to evolutionary features conserved throughout the Verticillium genus.
- David E. Torres
- , H. Martin Kramer
- & Bart P. H. J. Thomma
-
Article
| Open AccessEvolution and expression patterns of the neo-sex chromosomes of the crested ibis
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 AccessComplex regulatory networks influence pluripotent cell state transitions in human iPSCs
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 AccessGenomic evidence for rediploidization and adaptive evolution following the whole-genome triplication
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 AccessTREX tetramer disruption alters RNA processing necessary for corticogenesis in THOC6 Intellectual Disability Syndrome
THOC6 is required for TREX tetramer formation. Analysis of pathogenic THOC6 variants differentiate the conserved mRNA export functions of TREX dimers and RNA processing functions of TREX tetramers underlying THOC6 Intellectual Disability Syndrome.
- Elizabeth A. Werren
- , Geneva R. LaForce
- & Ashleigh E. Schaffer
-
Article
| Open AccessPorous borders at the wild-crop interface promote weed adaptation in Southeast Asia
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 AccessMulti-omics analysis in human retina uncovers ultraconserved cis-regulatory elements at rare eye disease loci
Ultraconserved non-coding elements (UCNEs) can regulate developmental gene expression. Retinal multi-omics data integration revealed UCNEs to be candidate cis-regulatory elements during retinal development, which may be implicated in rare eye diseases.
- Victor Lopez Soriano
- , Alfredo Dueñas Rey
- & Elfride De Baere
-
Article
| Open AccessOrthogonal inducible control of Cas13 circuits enables programmable RNA regulation in mammalian cells
The lack of control over Cas13 activity has limited its utility. Here the authors report Control of RNA with Inducible SpliT CAs13 Orthologs and Exogenous Ligands (CRISTAL), controlled by orthogonal split inducible Cas13 effectors that can be turned ON or OFF, providing precise temporal control.
- Yage Ding
- , Cristina Tous
- & Wilson W. Wong
-
Article
| Open AccessConverging and evolving immuno-genomic routes toward immune escape in breast cancer
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 AccessCases of trisomy 21 and trisomy 18 among historic and prehistoric individuals discovered from ancient DNA
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 AccessCepharanthine analogs mining and genomes of Stephania accelerate anti-coronavirus drug discovery
Cepharanthine is a secondary metabolite isolated from Stephania with a variety of medicinal properties. Here, the authors assembled three Stephania genomes, propose cepharanthine biosynthetic pathway, and assess the antiviral potential of cepharanthine-related metabolites.
- Liang Leng
- , Zhichao Xu
- & Shilin Chen
-
Article
| Open AccessA mutational atlas for Parkin proteostasis
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 AccessRecurrent evolutionary switches of mitochondrial cytochrome c maturation systems in Archaeplastida
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 AccessGenetic influences on circulating retinol and its relationship to human health
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 AccessGenetic control of thermomorphogenesis in tomato inflorescences
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 AccessDomain-inlaid Nme2Cas9 adenine base editors with improved activity and targeting scope
Nme2Cas9 has been well established as a genome editing platform. Here the authors engineer Nme2Cas9 to further increase the activity and targeting scope of compact Nme2Cas9 base editors and validate domain-inlaid Nme2-ABEs for single-AAV delivery in vivo.
- Nathan Bamidele
- , Han Zhang
- & Erik J. Sontheimer
-
Article
| Open AccessDuplicated antibiotic resistance genes reveal ongoing selection and horizontal gene transfer in bacteria
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 AccessA landscape of gene expression regulation for synovium in arthritis
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 AccessExperimental evidence for cancer resistance in a bat species
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 AccessDiversity and evolution of the vertebrate chemoreceptor gene repertoire
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 AccessCompact zinc finger architecture utilizing toxin-derived cytidine deaminases for highly efficient base editing in human cells
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
-
Article
| Open AccessEpiallelic variation of non-coding RNA genes and their phenotypic consequences
This study uncovers abundant DNA methylation variations of non-coding RNA genes in the natural Arabidopsis population and shows the importance of epigenetic variations in plant phenotypic plasticity and diversity.
- Jie Liu
- & Xuehua Zhong
Browse broader subjects
Browse narrower subjects
- Agricultural genetics
- Animal breeding
- Behavioural genetics
- Cancer genetics
- Cancer genomics
- Clinical genetics
- Consanguinity
- CRISPR-Cas systems
- Cytogenetics
- Development
- Epigenetics
- Epigenomics
- Eukaryote
- Evolutionary biology
- Functional genomics
- Gene expression
- Gene regulation
- Genetic association study
- Genetic hybridization
- Genetic interaction
- Genetic linkage study
- Genetic markers
- Genome
- Genomic instability
- Genomics
- Genotype
- Haplotypes
- Heritable quantitative trait
- Immunogenetics
- Inbreeding
- Medical genetics
- Microbial genetics
- Mutation
- Neurodevelopmental disorders
- Plant breeding
- Plant genetics
- Polyploidy
- Population genetics
- Prokaryote
- Quantitative trait
- RNA splicing
- RNAi
- Sequencing