Research Briefing |
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Article
| Open AccessPopulation-specific polygenic risk scores for people of Han Chinese ancestry
The Taiwan Precision Medicine Initiative recruited and genotyped more than half a million Taiwanese participants, almost all of Han Chinese ancestry, and performed comprehensive genomic analyses and developed polygenic risk score prediction models for numerous health conditions.
- Hung-Hsin Chen
- , Chien-Hsiun Chen
- & Cathy S. J. Fann
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Article
| Open AccessFrom genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes
A newly compiled atlas of species-wide structural variants and gene-based and graph pangenomes derived from highly complete assemblies of genomes from 1,086 natural isolates enable integrative genome-scale studies of Saccharomyces cerevisiae.
- Victor Loegler
- , Pia Thiele
- & Joseph Schacherer
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Article |
The evolution of facultative symbiosis in stony corals
Genomic sequencing of the thermotolerant coral species Oculina patagonica, single-cell transcriptomic analyses of symbiotic and non-symbiotic specimens and comparisons with obligate symbiotic coral species reveal adaptations that provide resilience to coral bleaching.
- Shani Levy
- , Xavier Grau-Bové
- & Arnau Sebé-Pedrós
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News Feature |
Faulty mitochondria cause deadly diseases: fixing them is about to get a lot easier
CRISPR-based tools can’t easily access the DNA in these organelles, but researchers are finding other ways in.
- Gemma Conroy
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Research Briefing |
Tracing the ancestry of barley in time and space
The genetic ancestry of domesticated barley has been mapped at high resolution, with each genome segment traced to its wild origins and the date estimated for when it entered the domesticated lineage. The findings reveal a mosaic of contributions from across western and central Asia, shaped by early cultivation and later gene flow.
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Article
| Open AccessSperm sequencing reveals extensive positive selection in the male germline
A combination of whole-genome NanoSeq with deep whole-exome and targeted NanoSeq is used to accurately characterize mutation rates and genes under positive selection in sperm cells.
- Matthew D. C. Neville
- , Andrew R. J. Lawson
- & Raheleh Rahbari
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Career News |
Model organism databases face budget cuts and closures
Beyond the crucial data they contain, these digital archives have provided an important space for academic communities to exchange ideas and resources.
- Amanda Heidt
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News |
US serial killer case opens door to using cutting-edge DNA data in courts
New York trial could set a legal precedent by admitting findings from whole-genome sequencing as evidence.
- Katherine Bourzac
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Research Briefing |
A common chromosome fusion in humans explained
A condition known as Robertsonian translocation occurs when the long arms of two chromosomes join together. The characterization of the fully sequenced and assembled fused chromosomes reveals a common fusion site and how these chromosomes are stably transmitted from cell to cell and passed on from parent to child.
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News |
She lived to 117: what her genes and lifestyle tell us about longevity
Maria Branyas Morera was the oldest person in the world when she died. Scientists analysed her genes, metabolism and more.
- Mariana Lenharo
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Article
| Open AccessA haplotype-based evolutionary history of barley domestication
The evolutionary history of barley is analysed using ancient and modern DNA.
- Yu Guo
- , Murukarthick Jayakodi
- & Martin Mascher
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News & Views |
Ancient DNA clarifies the early history of the Slavs
A study examines the emergence of a group that sparked a fundamental change in lifestyle in Central and Eastern Europe in the sixth century.
- Steffen Patzold
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Article |
Multiple overlapping binding sites determine transcription factor occupancy
A new method enables comprehensive screening and identification of low-affinity DNA binding sites for transcription factors, and reveals that nucleotides flanking high-affinity binding sites create overlapping low-affinity binding sites that modulate transcription factor binding in vivo.
- Shubham Khetan
- , Brent S. Carroll
- & Martha L. Bulyk
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Article
| Open AccessOne mother for two species via obligate cross-species cloning in ants
In a case of obligate cross-species cloning, female ants of Messor ibericus need to clone males of Messor structor to obtain sperm for producing the worker caste, resulting in males from the same mother having distinct genomes and morphologies.
- Y. Juvé
- , C. Lutrat
- & J. Romiguier
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Technology Feature |
Beyond AlphaFold: how AI is decoding the grammar of the genome
Scientists are seeking to decipher the role of non-coding DNA in the human genome, helped by a suite of artificial-intelligence tools.
- Jeffrey M. Perkel
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News & Views |
The perplexing body plan of arrow worms decoded
A genome sequence and single-cell atlas of a marine worm species point towards bursts of gene emergence, duplication and loss as the drivers of lineage-specific body traits.
- Thomas D. Lewin
- & Yi-Jyun Luo
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Article
| Open AccessThe genomic origin of the unique chaetognath body plan
Genomic, single-cell transcriptomic and epigenetic analyses show that chaetognaths, following extensive gene loss in the gnathiferan lineage, relied on newly evolved genes and lineage-specific tandem duplications, not caused by a whole-genome duplication event, to shape their distinctive body plan.
- Laura Piovani
- , Daria Gavriouchkina
- & Ferdinand Marlétaz
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News |
These genes can have the opposite effects depending on which parent they came from
New approach finds ‘parent-of-origin’ effects in more than a dozen genes — without the need for parental data.
- Rachel Fieldhouse
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Technology Feature |
Is your AI benchmark lying to you?
Artificial intelligence models are too often assessed against flawed goals — a stumbling block for progress.
- Michael Brooks
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Research Briefing |
Parent-of-origin effects found for gene variants that affect human growth and metabolism
A genome-wide analysis has identified genetic variants that have different effects on human growth and metabolic traits depending on their parental origin. Often, the same variant will push traits in opposite directions depending on its parental origin, in line with a hypothesized conflict between the ‘interests’ of the two parents’ genomes.
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News Feature |
This company claimed to ‘de-extinct’ dire wolves. Then the fighting started
Colossal’s bold announcements have drawn criticism from many scientists, but the billion-dollar firm is not backing down.
- Ewen Callaway
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News & Views |
The tiny mouse lemur could make for a mighty model organism
A cellular atlas for a small, fast-reproducing primate could set the stage for scientists to use it as a model organism that has more human relevance than rodents.
- J. Gray Camp
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Article
| Open AccessA molecular cell atlas of mouse lemur, an emerging model primate
Together with a companion paper, the generation of a transcriptomic atlas for the mouse lemur and analyses of example cell types establish this animal as a molecularly tractable primate model organism.
- Antoine de Morree
- , Iwijn De Vlaminck
- & Mark A. Krasnow
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Article
| Open AccessMouse lemur cell atlas informs primate genes, physiology and disease
Together with an accompanying paper presenting a transcriptomic atlas of the mouse lemur, interrogation of the atlas provides a rich body of data to support the use of the organism as a model for primate biology and health.
- Camille Ezran
- , Shixuan Liu
- & Mark A. Krasnow
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Article
| Open AccessComplex genetic variation in nearly complete human genomes
Using sequencing and haplotype-resolved assembly of 65 diverse human genomes, complex regions including the major histocompatibility complex and centromeres are analysed.
- Glennis A. Logsdon
- , Peter Ebert
- & Tobias Marschall
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Article
| Open AccessPrecisely defining disease variant effects in CRISPR-edited single cells
A plate-based assay called CRAFTseq has been developed that uses ‘multi-omic’ single-cell RNA sequencing and direct genotyping of CRISPR edits to test the functional effects of genetic variants on cell state and function.
- Yuriy Baglaenko
- , Zepeng Mu
- & Soumya Raychaudhuri
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Article
| Open AccessStructural variation in 1,019 diverse humans based on long-read sequencing
Intermediate-coverage long-read sequencing in 1,019 diverse humans from the 1000 Genomes Project, representing 26 populations, enables the generation of comprehensive population-scale structural variant catalogues comprising common and rare alleles.
- Siegfried Schloissnig
- , Samarendra Pani
- & Jan O. Korbel
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News & Views |
Genome doubling fuels ovarian cancer evolution and immune dysregulation
Single-cell analysis reveals the extent of genome doubling in ovarian cancer, its variability and its role in enabling tumours to evade the immune system.
- Nikki L. Burdett
- & Elizabeth L. Christie
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Research Briefing |
Birds use a tiny RNA fragment to balance sex chromosomes
Birds use a unique mechanism to balance gene expression from their sex chromosomes. MiR-2954 is a microRNA that suppresses specific target genes, preventing them from being overexpressed in male birds and ensuring the males’ survival. It is not required in females.
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News & Views |
Weight loss alters adipose tissue beyond just reducing fat
Cellular changes to adipose tissue after weight-loss surgery could point to pathways responsible for the metabolic benefits of this procedure.
- Evan D. Rosen
- & Margo P. Emont
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Article
| Open AccessA haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum
A study describes the assembly and analysis of a haplotype-resolved pangenome of bulbous barley with the potential to improve domesticated barley and illustrates its use in evolutionary research and trait mapping.
- Jia-Wu Feng
- , Hélène Pidon
- & Martin Mascher
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News |
Turbocharged ‘killer’ cells show promise for autoimmune disease
Experimental treatment could offer a safer, cheaper alternative to CAR-T-cell therapies for disorders such as lupus.
- Heidi Ledford
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Research Briefing |
A genome from ancient Egypt
The genome of a man buried at Nuwayrat in Middle Egypt about 4,500–4,800 years ago has been sequenced. Compared with published genomes of ancient individuals, most of the man’s ancestry best matches those of older individuals from North Africa, although around one-fifth best matches those of earlier ones from Mesopotamia. The study marks 40 years of progress in ancient-DNA research.
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First human genome from ancient Egypt sequenced from 4,800-year-old teeth
Forty years after the first effort to extract mummy DNA, researchers have finally generated a full genome sequence from an ancient Egyptian.
- Ewen Callaway
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Perspective |
The Somatic Mosaicism across Human Tissues Network
The Somatic Mosaicism across Human Tissues Network aims to create a reference catalogue of somatic mosaicism across different tissues and cells within individuals.
- Tim H. H. Coorens
- , Ji Won Oh
- & Yuqing Wang
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Technology Feature |
’We couldn’t live without it’: the UCSC Genome Browser turns 25
After a quarter of a century, the website remains an essential tool for navigating the genome and understanding its structure, function and clinical impact.
- Michael Eisenstein
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News & Views |
Deciphering how dog roses with an odd chromosome copy number sexually reproduce
Most sexually reproducing species have an even chromosome copy number, but the dog rose does not. What explains its unusual pattern of chromosome inheritance?
- Adrián Gonzalo
- & Joiselle B. Fernandes
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News |
DeepMind’s new AlphaGenome AI tackles the ‘dark matter’ in our DNA
Tool aims to solve the mystery of non-coding sequences — but is still in its infancy.
- Ewen Callaway
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News |
‘Super-healing’ animals inspire human treatments
Studies of the regenerative powers of worms, zebrafish and lizards suggest ways to improve recovery in people.
- Smriti Mallapaty
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News & Views |
Investigating the molecular ‘scars’ of PTSD in the human brain
Trauma leaves traces in the brain. A study of alterations in gene regulation in the brains of people with post-traumatic stress disorder offers insights into its biology.
- Arturo Marroquin Rivera
- & Benoit Labonté
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Research Briefing |
Neolithic matrilineal society in ancient China
Studies of ancient DNA have generally found that societies in Neolithic and Bronze Age Eurasia were organized around the male line. However, investigation of the Fujia archaeological site in eastern China reveals a Neolithic community organized around two maternal clans — suggesting that this prehistoric society traced its ancestry through the maternal line.
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Article
| Open AccessBimodal centromeres in pentaploid dogroses shed light on their unique meiosis
Insights into the dogrose genome and centromeres explain their ability to achieve stable sexual reproduction.
- V. Herklotz
- , M. Zhang
- & C. M. Ritz
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Article |
In vivo mapping of mutagenesis sensitivity of human enhancers
Human enhancers contain a high density of sequence features that are required for their normal in vivo function.
- Michael Kosicki
- , Boyang Zhang
- & Len A. Pennacchio
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News & Views |
Fetal and parental genomes offer mechanistic insights into pregnancy loss
Genomic analyses of mother–father–fetus trios after early pregnancy loss uncover contributions from chromosomal abnormalities and subtle genetic variants.
- Ziyue Gao
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News Q&A |
Genomics pioneer fired from firm he founded: ‘It was not easy to domesticate me’
Kári Stefánsson, who last month left the Icelandic genetics company deCODE, spoke to Nature about his legacy.
- Ewen Callaway
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News |
Black Death bacterium has become less lethal after genetic tweak
Reducing the number of copies of one gene in the pathogen could also make it more transmissible.
- Rachel Fieldhouse
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News |
This ancient pathogen became deadlier when humans started wearing wool
Ancient genomes reveal that a bacterial fever jumped from human-borne ticks to lice around the time wool textiles became common.
- Ewen Callaway
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News |
World’s first personalized CRISPR therapy given to baby with genetic disease
Treatment seems to have been effective, but it is not clear whether such bespoke therapies can be widely applied.
- Heidi Ledford