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| Open AccessMutational scanning pinpoints distinct binding sites of key ATGL regulators in lipolysis
ATGL is a key enzyme in intracellular lipolysis. Here, the authors use deep mutational scanning to define the determinants of protein interaction between ATGL and its regulatory partners, gaining insights into lipolysis mechanisms in cells.
- Johanna M. Kohlmayr
- , Gernot F. Grabner
- & Ulrich Stelzl
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Article
| Open AccessGAS41 modulates ferroptosis by anchoring NRF2 on chromatin
GAS41 is recognized as a histone reader and oncogene, but the mechanism by which GAS41 contributes to tumorigenesis is not well understood. Here, the authors discover that GAS41 is a ferroptosis repressor that anchors NRF2 to chromatin, promoting tumor growth.
- Zhe Wang
- , Xin Yang
- & Wei Gu
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Article
| Open AccessSwitching action modes of miR408-5p mediates auxin signaling in rice
miR408-5p typically regulates target IAA30 via translation repression, but switches to cleaving IAA30 mRNA under high auxin conditions. miR393, miR156, miR408-5p and their targets could hierarchically act in auxin pathway and regulate leaf inclination.
- Fuxi Rong
- , Yusong Lv
- & Liang Wu
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Article
| Open AccessAberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma
The downstream molecular mechanisms following the activation of the NF-κB pathway in multiple myeloma (MM) remain to be characterised. Here, it is shown that aberrant non-canonical NF-κB signalling causes epigenomic reprogramming leading to transcriptional changes that favour MM progression.
- Daniel A. Ang
- , Jean-Michel Carter
- & Yinghui Li
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Article
| Open AccessA double-stranded RNA binding protein enhances drought resistance via protein phase separation in rice
Drought is one of the major abiotic stresses affecting rice growth and development. Here, the authors identify a dsRNA-binding protein positively regulates rice drought resistance through promoting stability of OsNCED4 mRNAs, transcript of a key gene for the biosynthesis of abscisic acid, via protein phase separation.
- Huaijun Wang
- , Tiantian Ye
- & Lizhong Xiong
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Article
| Open AccessDynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry
Subgenome dominance is widely observed in allopolyploid species, but the molecular mechanisms remain unclear. Here, the authors generate genome-wide map of accessible chromatin regions (ACRs) in allo-octoploid cultivated strawberry and reveal that dynamics of the ACRs play an important role in its subgenome dominance.
- Chao Fang
- , Ning Jiang
- & Jiming Jiang
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Article
| Open AccessMapping human tissues with highly multiplexed RNA in situ hybridization
Application of multiplexed RNA in situ mapping techniques to human tissues remains challenging. Here, the authors report DART-FISH, a padlock probe-based technology capable of profiling large numbers of genes in centimetre-sized human tissue sections.
- Kian Kalhor
- , Chien-Ju Chen
- & Kun Zhang
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Article
| Open AccessStrong positive selection biases identity-by-descent-based inferences of recent demography and population structure in Plasmodium falciparum
Identity-by-descent (IBD) is used to infer malaria parasite population demography, but positive selection imposed by drug pressure can bias IBD estimates. This study shows that strong selection distorts IBD distributions impacting downstream inferences and presents an approach to correct these biases.
- Bing Guo
- , Victor Borda
- & Shannon Takala-Harrison
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Article
| Open AccessExtended stop codon context predicts nonsense codon readthrough efficiency in human cells
Stop codon readthrough, the ribosomal bypass of mRNA nonsense codons, has therapeutic potential for diseases caused by nonsense mutations. Here, the authors used machine learning to define readthrough-conducive mRNA sequences and predict specific CFTR alleles likely amenable to readthrough therapy.
- Kotchaphorn Mangkalaphiban
- , Lianwu Fu
- & Allan Jacobson
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Article
| Open AccessGenetic gains underpinning a little-known strawberry Green Revolution
Cultivated strawberry is a hybrid species with a 250-year domestication history. Here, the authors use genomic prediction and a historically important breeding population to show that the introduction of photoperiod-insensitive hybrids and genetic gains from breeding have been catalysts for a strawberry Green Revolution.
- Mitchell J. Feldmann
- , Dominique D. A. Pincot
- & Steven J. Knapp
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Article
| Open AccessGenetic imputation of kidney transcriptome, proteome and multi-omics illuminates new blood pressure and hypertension targets
Genetic mechanisms of blood pressure regulation remain poorly defined. Here, the authors perform a kidney multi-omics study to identify 399 kidney effector genes, 11 miRNAs and 97 proteins for blood pressure and hypertension.
- Xiaoguang Xu
- , Chachrit Khunsriraksakul
- & Maciej Tomaszewski
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Article
| Open AccessWheat powdery mildew resistance gene Pm13 encodes a mixed lineage kinase domain-like protein
Wheat powdery mildew is one of the most destructive diseases threatening global wheat production. Here, the authors report the cloning of powdery mildew resistance gene Pm13 from the wild wheat species Aegilops longissima encoding a mixed lineage kinase domain-like (MLKL) protein.
- Huanhuan Li
- , Wenqiang Men
- & Wenxuan Liu
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Article
| Open AccessSCGB1D2 inhibits growth of Borrelia burgdorferi and affects susceptibility to Lyme disease
The genetic basis of susceptibility to Lyme disease is largely unknown. Here, the authors discover a risk locus in the gene encoding the protein Secretoglobin family 1D member 2, which is expressed in skin and affects infection by the bacteria that causes Lyme disease in vitro and in vivo.
- Satu Strausz
- , Erik Abner
- & Hanna M. Ollila
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Article
| Open AccessDynamics of extrachromosomal circular DNA in rice
Comparing to other biological systems, our understanding of plant extrachromosomal circular DNA (eccDNA) is limited. Here, the authors profile eccDNA from six rice tissues and investigate eccDNA characteristics, formation mechanisms, distribution, and functional implications.
- Jundong Zhuang
- , Yaoxin Zhang
- & Tingting Lu
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Article
| Open AccessIntegrative genomic analyses identify candidate causal genes for calcific aortic valve stenosis involving tissue-specific regulation
Here the authors report 20 novel genomic risk loci for calcific aortic valve stenosis, the most common heart valve disorder. Using RNA sequencing in 500 human aortic valves, they prioritize candidate causal genes including TWIST1, a gene involved in endothelial-mesenchymal transition.
- Sébastien Thériault
- , Zhonglin Li
- & Yohan Bossé
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Article
| Open AccessDistinguishing preferences of human APOBEC3A and APOBEC3B for cytosines in hairpin loops, and reflection of these preferences in APOBEC-signature cancer genome mutations
Human APOBEC3A (A3A) and APOBEC3B (A3B) proteins convert cytosines in hairpin loops to uracils and cause mutations with differing preferences for loop sizes and sequences. Examination of human tumor mutations reflects largely the preferences of A3A, not A3B.
- Yasha Butt
- , Ramin Sakhtemani
- & Ashok S. Bhagwat
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Article
| Open AccessIntegrative cross-omics and cross-context analysis elucidates molecular links underlying genetic effects on complex traits
Genetic effects on functionally related ‘omic’ traits often co-occur in relevant cellular contexts, such as tissues. Here, the authors introduce X-ING, an integrative analysis method for cross-omics, cross-context associations based on summary-level data. Application to quantitative trait locus analysis yields insights into complex disease/trait mechanisms.
- Yihao Lu
- , Meritxell Oliva
- & Lin S. Chen
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Article
| Open AccessThe chromatin factors SET-26 and HCF-1 oppose the histone deacetylase HDA-1 in longevity and gene regulation in C. elegans
SET-26, HCF-1, HDA-1 are factors that help package DNA and regulate gene expression. Here, the authors find that SET-26 recruits HCF-1 to specific locations along the genome, where they antagonize the activity of HDA-1. Together, they maintain balanced gene expression and longevity in C. elegans.
- Felicity J. Emerson
- , Caitlin Chiu
- & Siu Sylvia Lee
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Article
| Open AccessA transposon insertion in the promoter of OsUBC12 enhances cold tolerance during japonica rice germination
Japonica rice generally has greater capacity for low temperatures germination (LTG) than indica rice. Here, the authors report an E2 ubiquitin-conjugating enzyme-encoding gene OsUBC12 can increase LTG in japonica rice by negatively regulate ABA signaling via promoting the proteasomal degradation of OsSnRK1.1.
- Chuanzhong Zhang
- , Hongru Wang
- & Jun Fang
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Article
| Open AccessNatural variation in OsMYB8 confers diurnal floret opening time divergence between indica and japonica subspecies
Florets of indica rice open earlier than japonica rice, hindering utilization of the cross subspecies heterosis. Here, the authors show that an OsMYB8-OsJAR1 module regulates diurnal floret opening time divergences between the two subspecies.
- Yajun Gou
- , Yueqin Heng
- & Rongxin Shen
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Article
| Open AccessBiallelic NAA60 variants with impaired N-terminal acetylation capacity cause autosomal recessive primary familial brain calcifications
Most individuals with primary familial brain calcification (PFBC) remain genetically unsolved. Here the authors show that NAA60 biallelic variants cause PFBC, likely via reduced N-terminal acetylation and SLC20A2 levels with impaired phosphate uptake.
- Viorica Chelban
- , Henriette Aksnes
- & Henry Houlden
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Article
| Open AccessIdentifying regulators of aberrant stem cell and differentiation activity in colorectal cancer using a dual endogenous reporter system
Aberrant stem cell-like activity and impaired differentiation are central to the development of colorectal cancer. Here, authors develop a dual endogenous reporter system to identify functional regulators of aberrant stem cell and differentiation programs, showing that SMARCB1 restricts differentiation, and nominating other regulators with therapeutic potential.
- Sandor Spisak
- , David Chen
- & Nilay S. Sethi
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Article
| Open AccessYTHDF2 governs muscle size through a targeted modulation of proteostasis
This study highlights the role of YTHDF2, a protein that recognizes m6A-modified RNA, in determining muscle size. The authors show a post-transcriptional mechanism regulating muscle catabolism and growth, prompting interest to address muscle wasting.
- Christopher J. Gilbert
- , Charles P. Rabolli
- & Federica Accornero
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Article
| Open AccessGWAS reveals determinants of mobilization rate and dynamics of an active endogenous retrovirus of cattle
Endogenous retroviruses constitute 5–10% of mammalian genome space. This study characterize the bovine ERVK[2-1- LTR] clade showing that its activity varies between individuals as a function of the number of inherited autonomous elements, yet that most de novo insertions are non-autonomous elements lacking functional genes.
- Lijing Tang
- , Benjamin Swedlund
- & Carole Charlier
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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
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