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Targeted genome-modification tools and their advanced applications in crop breeding Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-04-24 Boshu Li, Chao Sun, Jiayang Li, Caixia Gao
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What tubulin can teach us about gene regulation Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-04-24 Olivia S. Rissland
In this Journal Club article, Olivia Rissland describes how a 1987 paper by Don Cleveland and colleagues provided insight into co-translational gene regulation of tubulin.
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Genome assembly in the telomere-to-telomere era Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-04-22 Heng Li, Richard Durbin
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Nuclear mRNA decay: regulatory networks that control gene expression Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-04-18 Xavier Rambout, Lynne E. Maquat
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Natural antisense transcripts as versatile regulators of gene expression Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-04-17 Andreas Werner, Aditi Kanhere, Claes Wahlestedt, John S. Mattick
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Understanding human uniqueness in the pre-genomic era Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-04-15 Jenny Tung
In this Journal Club article, Jenny Tung reflects on a 1975 paper from King and Wilson that emphasized the importance of gene regulatory changes in human evolution.
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A developmental exit from totipotency Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-04-12 Henry Ertl
A paper in Nature Genetics identifies a mechanism involving the transcription factor DUXBL that controls the development of early embryonic mouse cells past stages marked by totipotency.
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SIMPLE-seq to decode DNA methylation dynamics in single cells Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-04-12 Dongsheng Bai, Chenxu Zhu
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Human embryonic genetic mosaicism and its effects on development and disease Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-04-11 Sarah M. Waldvogel, Jennifer E. Posey, Margaret A. Goodell
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Pleiotropy, epistasis and the genetic architecture of quantitative traits Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-04-02 Trudy F. C. Mackay, Robert R. H. Anholt
Pleiotropy (whereby one genetic polymorphism affects multiple traits) and epistasis (whereby non-linear interactions between genetic polymorphisms affect the same trait) are fundamental aspects of the genetic architecture of quantitative traits. Recent advances in the ability to characterize the effects of polymorphic variants on molecular and organismal phenotypes in human and model organism populations
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Genetic variation across and within individuals Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-28 Zhi Yu, Tim H. H. Coorens, Md Mesbah Uddin, Kristin G. Ardlie, Niall Lennon, Pradeep Natarajan
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AIRE targets poised promoters enriched for Z-DNA Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-27 Kirsty Minton
A paper in Nature reports a ‘Z-DNA-anchored’ model for the target specificity of the transcription factor AIRE, involving promoter poising at double-strand breaks.
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Building a catalogue of short tandem repeats in diverse populations Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-27 Ning Xie
Reflecting on the importance of short tandem repeats (STRs) in population genetics, Ning Xie highlights a 2023 publication that characterized genome-wide STR variation in global human genomes to expand our understanding of STR genetic diversity within and across populations.
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Global genomic diversity for All of Us Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-20 Linda Koch
A publication in Nature reports the data release of around 245,000 clinical-grade whole-genome sequences as part of the NIH’s All of Us Research Programme. Several companion papers highlight the value of better capturing global genomic diversity.
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The evolution of modifier genes Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-19 Yoav Ram
In this Journal Club, Yoav Ram recalls how he reconciled results from his own research with the reduction principle through the help of a paper published in PNAS by Altenberg et al.
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Dynamics of ER stress-induced gene regulation in plants Nat. Rev. Genet. (IF 42.7) Pub Date : 2024-03-18 Dae Kwan Ko, Federica Brandizzi
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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.