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| Open AccessGraph pangenome captures missing heritability and empowers tomato breeding
A precise catalogue of more than 19 million variants from 838 tomato genomes, including 32 new reference-level genome assemblies, advances the understanding of the heritability of complex traits and demonstrates the power of the graph pangenome in crop breeding.
- Yao Zhou
- , Zhiyang Zhang
- & Sanwen Huang
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Article |
Differential cofactor dependencies define distinct types of human enhancers
The systematic categorization of human enhancers by their cofactor dependencies provides a conceptual framework to understand the sequence and chromatin diversity of enhancers and their roles in different gene-regulatory programmes.
- Christoph Neumayr
- , Vanja Haberle
- & Alexander Stark
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Article
| Open AccessClonal dynamics of haematopoiesis across the human lifespan
Haematopoiesis has high clonal diversity up to about 65 years of age, after which diversity drops precipitously owing to positive selection acting on a handful of clones that expand exponentially throughout adulthood.
- Emily Mitchell
- , Michael Spencer Chapman
- & Peter J. Campbell
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Article
| Open AccessIsland-specific evolution of a sex-primed autosome in a sexual planarian
Assembly and analysis of the Schmidtea mediterranea genome indicate that this planarian’s chromosome 1 may be evolving into a sex chromosome.
- Longhua Guo
- , Joshua S. Bloom
- & Leonid Kruglyak
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News & Views |
A cell atlas for migraine research
The trigeminal nerve has a key role in migraine. An atlas of cell types and gene-expression profiles for cells in this nerve in mice and humans promises to improve our understanding of head pain.
- Philip R. Holland
- & Peter J. Goadsby
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News Explainer |
Why call it BA.2.12.1? A guide to the tangled Omicron family
Nature explores how subvariants are named, and why none of Omicron’s family members has been upgraded to a ‘variant of concern’.
- Amy Maxmen
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Research Highlight |
Vesuvius victim yields first human genome from Pompeii
The skeleton of a man aged 35–40 held enough DNA for scientists to sequence his genome.
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Correspondence |
Regional genomic surveillance networks needed in global south
- Ramy K. Aziz
- , Basant Giri
- & Partha P. Majumder
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Correspondence |
Africa needs more bioinformaticians for population studies
- Ashraf Akintayo Akintola
- , Ui Wook Hwang
- & Abdullahi Tunde Aborode
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News & Views |
The first complete human genome
Sequences of the human genome have typically included gaps in repetitive regions of DNA. A combination of state-of-the-art technologies has now enabled researchers to generate the first complete human genome sequence.
- John T. Lovell
- & Jane Grimwood
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Article
| Open AccessThe mosaic oat genome gives insights into a uniquely healthy cereal crop
Assembly of the hexaploid oat genome and its diploid and tetraploid relatives clarifies the evolutionary history of oat and allows mapping of genes for agronomic traits.
- Nadia Kamal
- , Nikos Tsardakas Renhuldt
- & Nick Sirijovski
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News |
Ancient DNA maps ‘dawn of farming’
Huge collection of genomes charts how hunter-gatherers turned into some of the world’s first farmers in Turkey.
- Ewen Callaway
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Article |
Single-cell eQTL models reveal dynamic T cell state dependence of disease loci
A single-cell Poisson model is used to analyse eQTLs in memory T cells across continuous, dynamic cell states, revealing that the cell context is critical to understanding variation in eQTLs and their association with disease.
- Aparna Nathan
- , Samira Asgari
- & Soumya Raychaudhuri
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A natural mutator allele shapes mutation spectrum variation in mice
Natural variation in the mouse gene Mutyh influences the rate of C>A germline mutations.
- Thomas A. Sasani
- , David G. Ashbrook
- & Kelley Harris
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Article
| Open AccessGenetic and chemotherapeutic influences on germline hypermutation
A study of 21,879 families with rare genetic diseases identifies 12 with 2- to 7-fold excess of germline mutations, most of which are due to DNA repair defects or exposure to mutagenic chemotherapy, although most individuals with a hypermutated genome will not have a genetic disease.
- Joanna Kaplanis
- , Benjamin Ide
- & Matthew Hurles
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Correspondence |
How to ensure the Human Cell Atlas benefits humanity
- Partha Majumder
- , Musa Mhlanga
- & Barbara Wold
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News |
Massive study of pet dogs shows breed does not predict behaviour
Data from more than 18,000 canines show that pedigree is not destiny.
- Freda Kreier
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Technology Feature |
Base edit your way to better crops
Plant scientists are turning to genome-editing techniques to precisely tailor the productivity and consumer appeal of important crops.
- Michael Eisenstein
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News |
Trove of tumour genomes offers clues to cancer origins
Largest-ever study uncovers patterns of mutations that might pinpoint cancer’s causes.
- Heidi Ledford
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Article |
Somatic genomic changes in single Alzheimer’s disease neurons
Analyses of single-cell whole-genome sequencing data show that somatic mutations are increased in the brain of individuals with Alzheimer’s disease compared to neurotypical individuals, with a pattern of genomic damage distinct from that of normal ageing.
- Michael B. Miller
- , August Yue Huang
- & Christopher A. Walsh
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Are new Omicron subvariants a threat? Here’s how scientists are keeping watch
In South Africa, a network of researchers is studying whether lineages BA.4 and BA.5 escape immunity from COVID-19 vaccines and previous infections.
- Amy Maxmen
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Article
| Open AccessSomatic mutation rates scale with lifespan across mammals
Whole-genome sequencing is used to analyse the landscape of somatic mutation in intestinal crypts from 16 mammalian species, revealing that rates of somatic mutation inversely scale with the lifespan of the animal across species.
- Alex Cagan
- , Adrian Baez-Ortega
- & Iñigo Martincorena
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News & Views |
Genetic origins of schizophrenia find common ground
Two differing approaches that are used to study common and rare genetic causes of schizophrenia reveal convergent clues about the biology underlying this complex disorder.
- Conrad O. Iyegbe
- & Paul F. O’Reilly
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Research Briefing |
Solving the mystery of the missing plasmids in seventh pandemic Vibrio cholerae strains
The pathogen responsible for the continuing seventh cholera pandemic typically lacks self-replicating plasmids. Genetics, cell biology and bioinformatics analyses have identified two DNA-defence systems that protect bacterial populations from plasmids and bacteriophages, and that might have shaped the evolution of modern Vibrio cholerae.
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Article |
Mapping the energetic and allosteric landscapes of protein binding domains
An approach that combines deep mutational scanning with neural network-based thermodynamic modelling is used to provide comprehensive maps of the energetic and allosteric effects of mutations in two common protein domains.
- Andre J. Faure
- , Júlia Domingo
- & Ben Lehner
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News |
Missing genomes, flexible microphone — the week in infographics
Nature highlights three key graphics from the week in science and research.
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Editorial |
The alarming rise of complex genetic testing in human embryo selection
Companies are marketing polygenic risk scores as part of IVF well ahead of a full understanding of the potential benefits — or dangers.
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News Feature |
A more-inclusive genome project aims to capture all of human diversity
Researchers are building a human ‘pangenome’ that would represent the entirety of human genetic variation. But not everyone is ready to sign on.
- Roxanne Khamsi
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Comment |
Africa: sequence 100,000 species to safeguard biodiversity
Build a major genomics resource on the continent to help breeders and conservationists.
- ThankGod Echezona Ebenezer
- , Anne W. T. Muigai
- & Appolinaire Djikeng
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News |
Wide-ranging genetic study of severe COVID finds common risk factors
Genetic variants that are linked to immune signalling, mucus production and other functions increase the risk of critical COVID-19.
- Freda Kreier
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Article |
The evolution, evolvability and engineering of gene regulatory DNA
A framework for studying and engineering gene regulatory DNA sequences, based on deep neural sequence-to-expression models trained on large-scale libraries of random DNA, provides insight into the evolution, evolvability and fitness landscapes of regulatory DNA.
- Eeshit Dhaval Vaishnav
- , Carl G. de Boer
- & Aviv Regev
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News |
How to protect the first ‘CRISPR babies’ prompts ethical debate
Fears of excessive interference cloud proposal for protecting children whose genomes were edited, as He Jiankui’s release from jail looks imminent.
- Smriti Mallapaty
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Research Briefing |
Ancient DNA illuminates how humans travelled and interacted in Stone Age Africa
Archaeologists have various hypotheses for how populations changed in Africa about 50,000 years ago, during the Later Stone Age transition. Now, the earliest available ancient-DNA sequences from sub-Saharan Africa reveal a complex Late Pleistocene population structure, pointing to large shifts in human movement and in patterns of social interaction.
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Article
| Open AccessTDP-43 represses cryptic exon inclusion in the FTD–ALS gene UNC13A
TDP-43 controls an exon splicing event in UNC13A that results in the inclusion of a cryptic exon associated with frontotemporal dementia and amyotrophic lateral sclerosis.
- X. Rosa Ma
- , Mercedes Prudencio
- & Aaron D. Gitler
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Technology Feature |
Revealing chromosome contours, one dot at a time
Methods that meld imaging with sequencing are uncovering the organizational principles of the genome — and how it influences cell fates.
- Amber Dance
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Research Briefing |
Molecular map of the human blood–brain barrier reveals links to Alzheimer’s disease
A method for isolating and analysing the elusive cells of the blood–brain barrier is used to map the expression of genes in the blood vessels of the human brain. Unravelling the molecular basis of this vasculature expands our understanding of overall brain health, disease and treatment.
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Article |
Single-cell dissection of the human brain vasculature
A study describes single-cell characterization of the human cerebrovasculature, revealing human-specific transcriptomic signatures and providing insights into transcriptional changes associated with Huntington’s disease.
- Francisco J. Garcia
- , Na Sun
- & Myriam Heiman
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Research Highlight |
A reindeer’s yearning to travel can be read in its genes
The fingerprint of the last ice age can still be seen in the genomes of reindeer that make long migrations.
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Article
| Open AccessEarly prediction of preeclampsia in pregnancy with cell-free RNA
Analyses of circulating cell-free RNA (cfRNA) in blood samples from pregnant mothers identify changes in gene expression that could be used in liquid biopsy tests to identify and monitor individuals who are at risk of preeclampsia.
- Mira N. Moufarrej
- , Sevahn K. Vorperian
- & Stephen R. Quake
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Article |
Brahma safeguards canalization of cardiac mesoderm differentiation
The BAF chromatin-remodelling complex ATPase gene Brm safeguards cell identity during directed cardiogenesis of mouse embryonic stem cells.
- Swetansu K. Hota
- , Kavitha S. Rao
- & Benoit G. Bruneau
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Technology Feature |
Seven technologies to watch in 2022
Our fifth annual round-up of the tools that look set to shake up science this year.
- Michael Eisenstein
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Editorial |
The ‘war on cancer’ isn’t yet won
The US National Cancer Act of 1971 has fostered tremendous progress in our understanding of the biology that underlies cancer. However, scientific and social challenges remain.
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News & Views |
Important genomic regions mutate less often than do other regions
Genomic regions that are crucial for the viability and reproduction of the model plant Arabidopsis thaliana are enriched with molecular features that are associated with a reduced rate of mutation.
- Jianzhi Zhang
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News & Views |
A blood test to predict complications of pregnancy
Cell-free RNA transcripts in maternal blood can be analysed to monitor the progression of pregnancy and to predict a potentially harmful pregnancy-specific condition called pre‑eclampsia.
- Lydia L. Shook
- & Andrea G. Edlow
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Technology Feature |
Terra takes the pain out of ‘omics’ computing in the cloud
The web-based tool allows scalable, user-friendly computation across multiple data sets
- Jeffrey M. Perkel
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Comment |
Two years of COVID-19 in Africa: lessons for the world
Africa urgently needs to guarantee its own health security.
- Christian T. Happi
- & John N. Nkengasong
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News & Views |
Bronze Age genomes reveal migration to Britain
The genomes of hundreds of individuals who lived in Great Britain and in continental Europe during the Bronze Age provide evidence for a migration of people from the continent to southern Britain between 1000 and 875 bc.
- Daniel G. Bradley
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News |
Omicron blindspots: why it’s hard to track coronavirus variants
Researchers are rapidly sequencing the genomes of virus samples worldwide, but shortcomings in the global surveillance system make the task a challenge.
- Amy Maxmen
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Article |
Spatial genomics enables multi-modal study of clonal heterogeneity in tissues
A technique using barcoded beads for DNA sequencing within tissue sections enables spatial resolution of tumour clonal heterogeneity and can be multiplexed with other analytical techniques for analysis of complex cellular phenotypes.
- Tongtong Zhao
- , Zachary D. Chiang
- & Fei Chen