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Competition between sites of meiotic recombination in snakes Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-12 Kirsty Minton
A study in Science reports that corn snakes use both PRDM9 and promoter-like features to direct meiotic recombination, indicating that these are not mutually exclusive.
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Short tandem repeats — how microsatellites became the currency of forensic genetics Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-11 Bruce Budowle, Antti Sajantila
Short tandem repeats (STRs), also known as microsatellites, are the primary markers of forensic genetics for developing investigative leads in criminal cases and humanitarian efforts. Their variation in length and sequence provides genetic information even in samples of low quantity and quality, enabling high resolution for identification and attribution purposes, and culminating in the development
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The regulatory landscape of chromatin accessibility Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-11 Henry Ertl
A study in Nature Genetics identifies many regulators of genome-wide chromatin accessibility and then reports the mechanistic underpinnings for one of the identified transcription factors.
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Sequence composition changes in short tandem repeats: heterogeneity, detection, mechanisms and clinical implications Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-11 Indhu-Shree Rajan-Babu, Egor Dolzhenko, Michael A. Eberle, Jan M. Friedman
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Genetics of chronic respiratory disease Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-06 Ian Sayers, Catherine John, Jing Chen, Ian P. Hall
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Unveiling the expanding protein universe of life Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-02-29 Hajk-Georg Drost
In this Journal Club, Hajk-Georg Drost highlights a recent study by Pavlopoulos et al. that organizes proteins at tree-of-life scale using massively parallel graph-based clustering.
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How ancient genes form animal body plans Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-04 Hajk-Georg Drost
Hajk-Georg Drost recalls a 2010 publication that used a phylotranscriptomic approach to estimate the age of genes that contribute to the developmental transcriptome across animal species and inspired a subsequent study on the embryonic hourglass in plants.
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Changes in cell-cycle rate drive diverging cell fates Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-01 Kate E. Galloway
Kate Galloway highlights a paper by Kueh et al., who showed that the cell cycle indirectly influences concentrations of the transcription factor PU.1 to stabilize cell-fate trajectories in mice.
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Targeting and engineering long non-coding RNAs for cancer therapy Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-02-29 Michela Coan, Simon Haefliger, Samir Ounzain, Rory Johnson
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The continuum of transcription factor affinities Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-02-27 Carl G. de Boer
Carl G. de Boer highlights a recent paper by Lim et al. on the importance low-affinity transcription factor-binding sites for determining organismal phenotypes.
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Plant pangenomes for crop improvement, biodiversity and evolution Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-02-20 Mona Schreiber, Murukarthick Jayakodi, Nils Stein, Martin Mascher
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The origin and evolution of Wnt signalling Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-02-19 Michaela Holzem, Michael Boutros, Thomas W. Holstein
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Fitness effects of mutations throughout evolution Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-02-16 Henry Ertl
A study in Science uses bacteria from the Long-Term Evolution Experiment to report on how fitness effects of mutations change through evolution.
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Single-cell sequencing of diverse microorganisms Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-02-16 Henry Ertl
Lan et al. report a high-throughput method for single-cell sequencing of diverse microbial communities.
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Sequencing and characterizing short tandem repeats in the human genome Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-02-16 Hope A. Tanudisastro, Ira W. Deveson, Harriet Dashnow, Daniel G. MacArthur
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A TRIP to understand gene regulation Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-02-14 Michael Attwaters
A study in Nature describes how single-cell expression data can be used to understand gene regulatory landscapes in bacteria.
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Genome replication in space and time Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-02-09 Amnon Koren
Amnon Koren recalls two papers from 2001 and 2002 that laid the foundations for a new field by using microarrays to measure DNA replication timing across the genome.
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Metabolic engineering of plant medicines Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-02-09 Vincent Courdavault, Nicolas Papon
Vincent Courdavault and Nicolas Papon highlight two articles in Nature, published in 2006 and 2013, that reported the biosynthesis of a complex natural plant product to treat malaria in engineered yeast.
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Ancient migration and the modern genome Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-02-05 Michael Attwaters
Four papers in Nature describe how ancient European migration patterns have shaped the modern human genome.
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Effects of regulatory variants across pig tissues Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-02-01 Henry Ertl
The Farm Animal GTEx project introduces a new resource for pigs, in which they map genetic variation to differences in gene expression across thousands of samples.
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Transcriptional diversity along the intestinal crypt–villi axis Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-01-30 Kylie R. James
Kylie R. James discusses a paper by Moor et al. that described a transcriptional gradient along the intestinal axis using single-cell RNA sequencing.
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A whole-genome shotgun approach to human reference genome sequencing Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-02-02 Shinichi Morishita
Shinichi Morishita recalls a seminal publication by Weber and Myers, who in 1997 proposed a direct whole-genome shotgun sequencing approach to tackle the human genome.
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Selection on synonymous sites: the unwanted transcript hypothesis Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-01-31 Sofia Radrizzani, Grzegorz Kudla, Zsuzsanna Izsvák, Laurence D. Hurst
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Inhibitors of bacterial immune systems: discovery, mechanisms and applications Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-01-30 David Mayo-Muñoz, Rafael Pinilla-Redondo, Sarah Camara-Wilpert, Nils Birkholz, Peter C. Fineran
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Packaging and delivery of genome-editing tools Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-01-30 Linda Koch
A study in Nature Biotechnology reports a platform that combines lentivirus capabilities with antibody recognition for targeted cell delivery and genome editing.
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Top predator decline has evolutionary as well as ecological effects Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-01-26 Kirsty Minton
Beer et al. use multiple complementary approaches to show that declining densities of the Tasmanian devil have had evolutionary effects on gene flow and selection in the subordinate predator, the spotted-tail quoll.
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Chromatin loops facilitate co-regulation of paralogues Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-01-25 Henry Ertl
Pollex et al. investigate the mechanisms by which chromatin loops bring together paralogues to coordinate gene expression in Drosophila.
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Horizontal gene transfer in eukaryotes: aligning theory with data Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-01-23 Patrick J. Keeling
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The diversification of methods for studying cell–cell interactions and communication Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-01-18 Erick Armingol, Hratch M. Baghdassarian, Nathan E. Lewis
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The expanding diagnostic toolbox for rare genetic diseases Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-01-18 Kristin D. Kernohan, Kym M. Boycott
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Challenges and best practices in omics benchmarking Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-01-12 Thomas G. Brooks, Nicholas F. Lahens, Antonijo Mrčela, Gregory R. Grant
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Real-time single-molecule imaging of transcriptional regulatory networks in living cells Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-01-09 Dong-Woo Hwang, Anna Maekiniemi, Robert H. Singer, Hanae Sato
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Swapping genes within and beyond our bodies Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-12-20 Mashaal Sohail
Mashaal Sohail reflects on a 2011 Nature study by Smillie et al., which analysed human microbiome data to show that microbial ecology, rather than phylogeny or geography, is a key driver of horizontal gene transfer.
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Efficient computation reveals rare CRISPR–Cas systems Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-12-19 Henry Ertl
A study published in Science develops an efficient mining algorithm to identify and then experimentally characterize many rare CRISPR systems.
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Spatial resolution of host–microbiome interactions Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-12-15 Kirsty Minton
Two papers in Nature Biotechnology report spatial transcriptomic methods for the simultaneous capture of host and microbial genes to study host–microorganism interactions.
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The transition from genomics to phenomics in personalized population health Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-12-13 James T. Yurkovich, Simon J. Evans, Noa Rappaport, Jeffrey L. Boore, Jennifer C. Lovejoy, Nathan D. Price, Leroy E. Hood
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Decoding human genetic variation using a synthetic paradigm Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-12-06 Aashiq H. Kachroo
Aashiq Kachroo highlights a recent paper by van Loggerenberg et al. that demonstrates the experimental power of ‘humanized yeast’ to gain insight into the genetic variants underlying disease.
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Divergence and conservation of the meiotic recombination machinery Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-11-30 Meret Arter, Scott Keeney
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SWI/SNF function compensated by another chromatin remodeller Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-11-27 Henry Ertl
Martin et al. report that the EP400/TIP60 complex can compensate for function of the SWI/SNF complex to remodel chromatin at some promoters.
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Translating genomic advances into biodiversity conservation Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-11-27 Carolyn J. Hogg
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Author Correction: Transposable elements: McClintock's legacy revisited. Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-12-01 Cédric Feschotte
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Context-specific functions of chromatin remodellers in development and disease Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-11-24 Sai Gourisankar, Andrey Krokhotin, Wendy Wenderski, Gerald R. Crabtree
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Including diverse populations enhances the discovery of type 2 diabetes loci Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-11-22 Segun Fatumo
Segun Fatumo highlights a paper by Mahajan et al. that uses a multi-ancestry genome-wide association studies approach to uncover the genetic underpinnings of type 2 diabetes, emphasizing the importance of incorporating diverse populations in such studies.
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Mouse genome rewriting with human DNA for disease modelling Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-11-22 Kirsty Minton
Zhang et al. describe mSwAP-In, a platform for large-scale, efficient, biallelic and ‘scarless’ genome editing in mice.
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Weaponized genomics: potential threats to international and human security Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-11-22 Subhayan Chattopadhyay, Tony Ingesson, Alberto Rinaldi, Oscar Larsson, J. J. Widen, Jessica Almqvist, David Gisselsson
Genetic technologies are revolutionizing human health. In parallel, geopolitical instability has prompted renewed discussions on the risks of DNA technology being weaponized in international conflict. With today’s changing security environment, we argue that risk assessments must be broadened from genetically targeted weapons to a series of new domains. Geopolitical instability has prompted renewed
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Interrogating epigenetic mechanisms with chemically customized chromatin Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-11-20 Nir Hananya, Shany Koren, Tom W. Muir
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Non-coding RNAs in disease: from mechanisms to therapeutics Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-11-15 Kinga Nemeth, Recep Bayraktar, Manuela Ferracin, George A. Calin
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WNT regulator controls stripe patterning Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-11-10 Henry Ertl
Johnson et al. identify a WNT regulator that underlies the development and evolution of distinct colour patterning in the African striped mouse.
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Scrambling the genome in cancer: causes and consequences of complex chromosome rearrangements Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-11-08 Ksenia Krupina, Alexander Goginashvili, Don W. Cleveland
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A genetic atlas of the human blood proteome Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-11-01 Michael Attwaters
Three papers in Nature report on the largest open-access plasma proteomics dataset to date, a valuable resource for understanding human disease and the identification of drug targets.
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De novo genes: from non-genic to genic Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-10-26 Li Zhao
Li Zhao recalls a 2006 paper by Levine et al. that, by identifying a handful of de novo genes, outlined a potentially universal process of de novo gene birth and propelled forward this field of research.
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Controlling organoid gene expression with light Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-10-23 Henry Ertl
Legnini et al. report in Nature Methods their new optogenetic method for controlling gene expression in organoids that can be coupled with single-cell and spatial transcriptomics.
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Genomics for monitoring and understanding species responses to global climate change Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-10-20 Louis Bernatchez, Anne-Laure Ferchaud, Chloé Suzanne Berger, Clare J. Venney, Amanda Xuereb
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Inborn errors of immunity: an expanding universe of disease and genetic architecture Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-10-20 Yemsratch T. Akalu, Dusan Bogunovic
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Predicting variant pathogenicity with AlphaMissense Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-10-11 Kirsty Minton
Reporting in Science, a team from Google DeepMind describe AlphaMissense, a tool to predict the pathogenicity of missense variants.
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Nuclear genome influences mitochondrial DNA Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-10-06 Henry Ertl
A paper in Nature finds that nuclear genetic variation can influence heteroplasmy and the human mitochondrial genome.
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The evolutionary tale of lactase persistence in humans Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-09-25 Luis B. Barreiro
Luis Barreiro highlights a 2007 paper by Tishkoff et al. that identified genetic variants associated with lactose persistence in East African populations, representing one of the first examples of convergent evolution in humans.
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Genomic surveillance for antimicrobial resistance — a One Health perspective Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-09-25 Steven P. Djordjevic, Veronica M. Jarocki, Torsten Seemann, Max L. Cummins, Anne E. Watt, Barbara Drigo, Ethan R. Wyrsch, Cameron J. Reid, Erica Donner, Benjamin P. Howden
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Pioneer factors — key regulators of chromatin and gene expression Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-09-22 Martha L. Bulyk, Jacques Drouin, Melissa M. Harrison, Jussi Taipale, Kenneth S. Zaret
Pioneer factors are a group of transcription factors with important roles in gene regulation during development. Their unique ability to bind to compacted chromatin, promoting its remodelling for gene expression, sets them apart from other regulatory proteins and makes them essential players in cellular differentiation, fate determination and reprogramming. Here, we have tasked five experts with discussing
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Sequencing to save the Kākāpō Nat. Rev. Genet. (IF 42.7) Pub Date : 2023-09-25 Michael Attwaters
Guhlin et al. sequenced the genomes of almost the entire extant population of the critically-endangered kākāpō, revealing genetic variants for fitness-related traits that can inform conservation strategies.