Publishing reviews and commentaries across the fields of genetics and genomics. Part of @SpringerNature and @NaturePortfolio.
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📢 Our July issue features a Focus issue on Evolutionary Innovation go.nature.com/4aLqz6f
Read about it in our Editorial "Genetic origins and constraints of evolutionary innovation": go.nature.com/4acWah3
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Chromosomal instability as a driver of cancer progression bit.ly/46G5tDj #Review by Xuelan Chen, Albert S. Agustinus, Jun Li, @melodyDiBona & @Samuel_Bakhoum @MSKCancerCenter
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Histone post-translational modifications — cause and consequence of genome function go.nature.com/3IMiNZ9 #Review by Gonzalo Millán-Zambrano, Adam Burton, Andrew J. Bannister & Robert Schneider @robert_ife @HelmholtzMunich @LMU_Muenchen @unisevilla @cabimer @Cambridge_Uni
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Molecular mechanisms of transgenerational epigenetic inheritance go.nature.com/40mNtL0 #Review by Maximilian H. Fitz-James & Giacomo Cavalli
@CNRS @umontpellier @IGH_MTP
Free to read here: rdcu.be/dBBQc
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To celebrate our upcoming 20-year anniversary, we commissioned a #Viewpoint in which 12 leading researchers reflect on 'The road ahead in genetics and genomics' rdcu.be/b6qQ5 #SharedIt
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Epigenomic marks at cis-regulatory elements and their association with gene expression #Figure from #Review 'Characterizing cis-regulatory elements using single-cell epigenomics' go.nature.com/3o4qCkP by @seb11pr, @kjgaulton & Bing Ren @CEpigenomics @UCSanDiego @UniFreiburg
ALT Schematic representation of epigenetic features associated with different classes of cis-regulatory elements and gene regions. Promoters of expressed genes show high levels of chromatin accessibility, low DNA methylation levels, high levels of H3K4me3 and acetylated lysine residues such as H3K27ac. The histone modification H3K36me3 is found in gene bodies of expressed genes. Gene expression can be modulated by enhancers, which are distal CREs that can be brought in close proximity to the promoter of target genes through the folding of chromatin. Active enhancers are characterized by high chromatin accessibility, low DNA methylation levels, and high H3K4me1 and H3K27ac levels. Repressed genes or heterochromatic regions show high levels of DNA methylation and/or histone marks such as H3K9me3 and H3K27me3.
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It is our absolute pleasure to present to you our latest Nature Milestone project: go.nature.com/3tNKXMT We teamed up with @Nature and @NatureGenet to chart the history of DNA sequencing technologies and their continuously expanding applications in the 21st century
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Structural variation in the sequencing era go.nature.com/2NP87PX #Review by Steve S. Ho, Alexander E. Urban & Ryan E. Mills
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New online! Beyond the black box with biologically informed neural networks bit.ly/3DhWUUH
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The epigenetic basis of cellular heterogeneity go.nature.com/37g8Hir #Review by Benjamin Carter & Keji Zhao
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Principles and methods for transferring polygenic risk scores across global populations go.nature.com/3PbbGQ8 #Review
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Methods for mapping 3D chromosome architecture go.nature.com/2S31aNQ #Review by Rieke Kempfer and @apombo1
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Machine learning methods for variant effect prediction
Decoding disease: from genomes to networks to phenotypes go.nature.com/3fq7VnT #Review by @wongak, Rachel S. G. Sealfon, Chandra L. Theesfeld & @OlgaTroyanskaya @TroyanskayaLab @FlatironCCB @FlatironInst @Princeton @PrincetonHive
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Molecular mechanisms of transgenerational epigenetic inheritance go.nature.com/40mNtL0 #Review by Maximilian H. Fitz-James & Giacomo Cavalli @CNRS @umontpellier @IGH_MTP
Free to read here: rdcu.be/dBBQc
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mRNAs, proteins and the emerging principles of gene expression control go.nature.com/2ByWgSV #Review by Christopher Buccitelli & Matthias Selbach
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#Free for 1 month: Towards a comprehensive catalogue of validated and target-linked human enhancers go.nature.com/2O6ezSC #Review by @MollyGasp, Jacob Tome & @JShendure
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CRISPR functional genomics tools for scalable and multiplexable characterization of genes and gene regulatory elements - A new era in functional genomics screens go.nature.com/3kmuIUy #Review by Laralynne Przybyla & Luke A. Gilbert @UCSF
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Molecular mechanisms of transgenerational epigenetic inheritance go.nature.com/40mNtL0 #Review by Maximilian H. Fitz-James & @giacomo_cavalli
@CNRS @umontpellier @IGH_MTP
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Alternative splicing as a source of phenotypic diversity go.nature.com/3yW3Q3V #Review by
@CharJWright, Christopher W. J. Smith & @mel_rosina
@sangerinstitute @darwintreelife @CamZoology @CamBiochem @LabsRna
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New online! Predicting gene expression from DNA sequence using deep learning models bit.ly/4iXE6ZB
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Single-cell genomics meets human genetics go.nature.com/3LjdSmL #Review by @AnnaSECuomo, @aparnanathan, @soumya_boston, @dgmacarthur and @drjosephpowell #singlecellgenetics
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Transposable elements: McClintock’s legacy revisited go.nature.com/3Lq3rxu #Perspective #Essay by @cedricfeschotte
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New online! Structural variants in the 3D genome as drivers of disease bit.ly/44FiIo5
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Genome assembly in the telomere-to-telomere era go.nature.com/4aLqIED #Review by Heng Li @lh3lh3 & Richard Durbin @richard_durbin
@DanaFarber @HarvardDBMI @Cambridge_Uni
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Methods for studying cell–cell interactions and communication go.nature.com/491i6Zi #Review by @eagut, @hmbaghdassarian & @Nathan_E_Lewis
@LewisLabUCSD @UCSanDiegoCPD
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Chromatin-associated RNAs as facilitators of functional genomic interactions go.nature.com/3182fWH #Review by Xiao Li & Xiang-Dong Fu
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DNA methylation in mammalian development and disease go.nature.com/3X14Ali #Review by Zachary D. Smith @YaleMed, Sara Hetzel (@hetzel_s) & Alexander Meissner @MPI_MolGen
Free to read here: rdcu.be/dQEND
@maxplanckpress
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Interrogating epigenetic mechanisms with chemically customized chromatin go.nature.com/3umu7K3 #Review by @HananyaNir, @ShanyKoren & Tom W. Muir @MuirLab @Princeton
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Characterizing cis-regulatory elements using single-cell epigenomics go.nature.com/3o4qCkP #Review by @seb11pr, @kjgaulton & Bing Ren
@CEpigenomics @UCSanDiego @UniFreiburg @Ludwig_Cancer
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New online! Integrating model systems and genomic insights to decipher mechanisms of cancer metastasis bit.ly/3XC0xvy
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Genetic variation across and within individuals go.nature.com/3PFrsTf #Review by @ZhiYu_ACGT, @TimCoorens, Md Mesbah Uddin, Kristin G. Ardlie, @nialljlennon & @pnatarajanmd
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New online! Advances in single-cell DNA sequencing enable insights into human somatic mosaicism bit.ly/3EGIyxQ
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DNA methylation-based biomarkers and the epigenetic clock theory of ageing go.nature.com/2GVjEHy #Review
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New online! Epigenetics and individuality: from concepts to causality across timescales bit.ly/4haZkCL
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New online! Computational analysis of DNA methylation from long-read sequencing bit.ly/4cjxUtl
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Human organs-on-chips for disease modelling, drug development and personalized medicine go.nature.com/3Lfq997 #Review by @DonIngber
Free to read here: rdcu.be/cJOud #SharedIt
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Lineage tracing meets single-cell omics: opportunities and challenges go.nature.com/2UPu2cl Our 2020 #Review by @danwagnerlab and @KleinLabHMS
@harvardmed @UCSF
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Genetic correlations of polygenic disease traits: from theory to practice go.nature.com/2K2Cbad #Review by @wrheenen, Wouter J. Peyrot, Andrew J. Schork, S. Hong Lee & Naomi R. Wray @PCTGenomics
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Phylogenetic tree building in the genomic age go.nature.com/2X2OxDe #Review by @PKapli, @zihengyang & @TelfordLab @UCL #phylogenomics
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Decoding disease: from genomes to networks to phenotypes go.nature.com/3fq7VnT #Review by @wongak, Rachel S. G. Sealfon, Chandra L. Theesfeld & @OlgaTroyanskaya @TroyanskayaLab @FlatironCCB @FlatironInst @Princeton @PrincetonHive
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Long-range enhancer–promoter contacts in gene expression control go.nature.com/3wSCJsO 2019 #Review by @stefanschoenfe1 & @Peter_Fraser1
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New online! Reactivation of retrotransposable elements is associated with environmental stress and ageing bit.ly/4497Z5r
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Variant calling and benchmarking in an era of complete human genome sequences go.nature.com/3mBDrWO #Review by Nathan D. Olson, Justin Wagner, Nathan Dwarshuis, @khmiga, @sedlazeck, @bioetalons & Justin M. Zook @NIST @bcmhouston @ucsc
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Gene regulatory programmes of tissue regeneration go.nature.com/2MFfMz2 #Review by
Joseph Goldman & Kenneth Poss @Ken_Poss_lab @RegenerateNext
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Regulation of gene expression by cis-acting long non-coding RNAs go.nature.com/2CNQh9W #Review by Noa Gil and @IgorUlitsky
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Transposable elements in mammalian chromatin organization go.nature.com/3P4wVDI #Review by @lab_lawson, @leung_holden and @twang5 @WUSTLdbbs @WashUGenetics @GenomeInstitute @wustlcrm
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Real-time single-molecule imaging of transcriptional regulatory networks in living cells go.nature.com/4aIpLNQ #Review by Dong-Woo Hwang, Anna Maekiniemi, Robert H. Singer & Hanae Sato
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Pleiotropy, epistasis and the genetic architecture of quantitative traits go.nature.com/3VK75YZ #Review by Trudy Mackay and Robert Anholt @ClemsonScience @ClemsonCHG
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Mechanical regulation of chromatin and transcription go.nature.com/3LCObdZ #Review by @SirioDupont @UniPadova & @WickstromLab @helsinkiuni @MPI_Muenster
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Challenges in unsupervised clustering of single-cell RNA-seq data go.nature.com/2FdxCa2 #Review by @wikiselev , @talandrews & @m_hemberg
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Using genetic data to strengthen causal inference in observational research go.nature.com/2JxVDuM #Review
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From genome-wide associations to candidate causal variants by statistical fine-mapping go.nature.com/2ITwrQ5
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Genetics of human brain development go.nature.com/3KjoBwD #Review by Yi Zhou, Hongjun Song & Guo-li Ming @UPenn_SongMing @Penn @PennMedicine
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Single-cell atlases: shared and tissue-specific cell types across human organs go.nature.com/36P6iyD #Review by @elmentaite, @CDominguezConde, @edenling3 & @teichlab
@sangerinstitute @humancellatlas
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New online! Epigenetic ageing clocks: statistical methods and emerging computational challenges bit.ly/3CiRhVI
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New online! Functional synonymous mutations and their evolutionary consequences bit.ly/43Dlee0
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The genomics of coloration provides insights into adaptive evolution go.nature.com/3ce3cln #Review by @AnnaOrteu and @mel_rosina @Cambridge_Uni
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Best practices for single-cell analysis across modalities go.nature.com/3K1Y3Pv #ExpertRecommendation
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Pan-genomics in the human genome era rdcu.be/b1lAf #Review by @rshermanjhu &
@StevenSalzberg1 #SharedIt
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Integrating genetic and non-genetic determinants of cancer evolution by single-cell multi-omics go.nature.com/2EaExlT #Review by @AnnaEnim, @ChaligneRonan & @landau_lab @NYGenome @WeillCornell @WCM_MeyerCancer
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Long-range enhancer–promoter contacts in gene expression control go.nature.com/2WJp6p8 #Review by Stefan Schoenfelder & @Peter_Fraser1 @BabrahamInst
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The epigenetic basis of cellular heterogeneity go.nature.com/37g8Hir #Review by Benjamin Carter & Keji Zhao
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Methods for mapping 3D chromosome architecture rdcu.be/bZwOW 2020 #Review by Rieke Kempfer and @apombo1 #SharedIt #Freetoread
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Enhancing the accuracy of next-generation sequencing for detecting rare and subclonal mutations ow.ly/fESs30jamjK #review
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Generating specificity in genome regulation through transcription factor sensitivity to chromatin go.nature.com/3PpLm2k #Review by @LukeIsbel, @RalphSGrand & @SchubelerLab @FMIscience
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The splicing mechanism and the spliceosome #Figure from our recent #Review by @MalgorzataRoga1, @clau_vivori & Juan Valcárcel on the regulation of splicing go.nature.com/3BDfNO4 @CRGenomica @UPFBarcelona @TheCrick
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Spatial biology of cancer evolution go.nature.com/3W2m25J #Review by @zaira_sef, @LomakinAI, @Yates_lab & @MoritzGerstung @DKFZ @sangerinstitute
Free to read here: rdcu.be/c1jwe
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Primary structure of histone variants and their influence on nucleosome structure
#Figure from the #Review by Lee H. Wong @MonashUni & David J. Tremethick @JCSMR:
Multifunctional histone variants in genome function go.nature.com/4dDLXcI
Free to read: rdcu.be/dQO4i
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Principal methods for measuring chromatin accessibility: #DNAse-seq #ATAC-seq #MNase-seq #NOMe-seq
Figure from our Review: Chromatin accessibility and the regulatory epigenome rdcu.be/bh1yE by @WJGreenleaf et al.
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Transposable elements in mammalian chromatin organization go.nature.com/4amBz7Q #Review by @lab_lawson, @leung_holden and @twang5
@WUSTLdbbs @WashUGenetics @GenomeInstitute @wustlcrm
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New online! Diversity and consequences of structural variation in the human genome bit.ly/4g1ZQSQ
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Clinical cancer genomic profiling go.nature.com/3fbZ8GG #Review by @CDebyaniPhD and @DSolit @sloan_kettering @MSKPathology @MskccCMO
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Context-specific functions of chromatin remodellers in development and disease go.nature.com/3uEDqF0 #Review by @saigourisankar, @AKrokhotin, @wendywenderski & Gerald R. Crabtree @Stanford
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The interface between metabolism and epigenetic regulation of transcription go.nature.com/2u0m5F7 Figure for talks ow.ly/d/6yOc
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New online! Tracing the evolution of sequencing into the era of genomic medicine bit.ly/45lEYUB
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Targeting and engineering long non-coding RNAs for cancer therapy go.nature.com/49zHhmm #Review by @CoanMichela, Simon Haefliger, Samir Ounzain @ispiyou & @_Rory_Johnson_ @ucddublin
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Shaping faces: genetic and epigenetic control of craniofacial morphogenesis go.nature.com/3H50tMz #Review by @LiciaSelleri & Filippo M. Rijli @FMIscience
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Computational methods for analysing multiscale 3D genome organization go.nature.com/3Lhb4Xb #Review by @zocean636, @LoreBonimba, @muyu_wendy_yang, @NCITomMisteli, @faucla & @jmuiuc @4DNucleome @CMUCompBio @SCSatCMU @UCLA @UCLAQCBio @theNCI
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Transposable elements in mammalian chromatin organization go.nature.com/4amBz7Q #Review by @lab_lawson, @leung_holden and @twang5
@WUSTLdbbs @WashUGenetics @GenomeInstitute @wustlcrm
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Transposable elements shape the evolution of mammalian development go.nature.com/3xr4W4H #Review by @dorotheasenft and @todd_macfarlan
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Long-read human genome sequencing and its applications go.nature.com/3h73Wfh #Review by
@glennis_logsdon, @mrvollger & Evan Eichler
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New online! Cell-type deconvolution methods for spatial transcriptomics bit.ly/43hY2AT
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New online! Simultaneous single-cell sequencing of RNA and DNA at scale with DEFND-seq bit.ly/4ddqzfj
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Human embryonic genetic mosaicism and its effects on development and disease go.nature.com/4avnc1e #Review by Sarah M. Waldvogel, Jennifer E. Posey @poseypod & Margaret A. Goodell @Goodell_Lab @bcmhouston
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New online! Genomics of schizophrenia, bipolar disorder and major depressive disorder bit.ly/455kG1G
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Free to read: Review on analysing DNA methylation data go.nature.com/2QzZnLX by @aetesch & @carolinerelton #Bioinformatics #EWAS #Epigenomics #Statistics
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Gene–environment interactions in human health go.nature.com/3UXaIsJ #Review by Esther Herrera-Luis @EstherHL5, Kelly Benke, Heather Volk, Christine Ladd-Acosta @GnomeChris & Genevieve L. Wojcik @genandgenes @JohnsHopkinsEPI
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Genomic surveillance for antimicrobial resistance — a One Health perspective go.nature.com/3ZAlaIn #Review by @steve_djo, @VMJarocki, @torstenseemann, @maxcummins1, @AnneEWatt, @BarbaraDrigo, @EthanWyrsch, @camreid90, @EricaDonner1 & @BenjaminHowden
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New online! Intrinsically disordered regions as facilitators of the transcription factor target search bit.ly/413Q2SO
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Free for 1 month: Towards a genomics-informed, real-time, global pathogen surveillance system go.nature.com/2yXBmdA #review by @jennifergardy& @pathogenomenick
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Transitioning single-cell genomics into the clinic go.nature.com/3oHN0EG #Perspective by @drjenlim, @chin_venessa, @FairfaxKirsten, @Moutinho_C, Dan Suan, Hanlee Ji & @drjosephpowell @GarvanInstitute @CellularFutures @kinghorncancer @UNSW @UTAS_ @StanfordMed @Stanford
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