Nature Genetics

💫 @natgenet.nature.com October issue's out! Featuring: ✅insect resistance in wheat ✅rare CNVs analysis in schizophrenia in EAS populations ✅epigenomics in medulloblastoma ✅human brain genetic regulatory atlas ✅chromatin accessibility map of Crohn’s disease & more! www.nature.com/ng/volumes/5...

nature.comEstablishing Polycomb regulatory landscapes in human early development - Nature GeneticsThe authors profile H2AK119ub (H2Aub) in human gametes, two-cell embryos, eight-cell embryos, blastocysts and human embryonic stem cells. Their analysis provides a comprehensive view of H2Aub reprogra...

📢OUT TODAY @natgenet.nature.com 📰Establishing Polycomb regulatory landscapes in human early development. By Xiaoyu Hu, Wei Xie and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comClonal heterogeneity in human pancreatic ductal adenocarcinoma and its impact on tumor progression - Nature GeneticsThis study uses single-cell RNA sequencing and spatial transcriptomics of pancreatic ductal adenocarcinoma tumors to investigate tumor heterogeneity and clonal evolution, providing a valuable resource...

📢PUBLISHED @natgenet.nature.com 📰Clonal heterogeneity in human pancreatic ductal adenocarcinoma and its impact on tumor progression. By Despoina Kalfakakou, Aristotelis Tsirigos, Diane M. Simeone and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comMicronuclear ecDNA constrains tumor cell fitness and is associated with favorable patient survival - Nature GeneticsSingle-micronucleus sequencing and live-cell imaging of cancer cells, as well as analyses of biopsies from patients with neuroblastoma, reveal that ecDNA in micronuclei limits tumor cell fitness and i...

📢PUBLISHED @natgenet.nature.com 📰Micronuclear ecDNA constrains tumor cell fitness and is associated with favorable patient survival. By Lotte Brückner, Anton G. Henssen and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comImputation of fluid intelligence scores reduces ascertainment bias and increases power for analyses of common and rare variants - Nature GeneticsImputing unmeasured fluid intelligence scores in UK Biobank reduces ascertainment bias and increases power for genetic analyses, improving out-of-sample polygenic score performance and identifying rar...

📢PUBLISHED @natgenet.nature.com 📰Imputation of fluid intelligence scores reduces ascertainment bias and increases power for analyses of common and rare variants. By David M. van den Berg, Hilary C. Martin and colleagues. ⬇️ www.nature.com/articles/s41...

fusion-conferences.com5th Epigenetics Conference | Fusion ConferencesHighlighting how chromatin organisation, nuclear architecture, gene regulatory networks, metabolism and RNA-based mechanisms converge to shape cell identity and plasticity across development, homeosta...

📢📢📢 @natgenet.nature.com editor Chiara Anania will be joining the 5th #Epigenetics Conference @fusionconf.bsky.social 📍Lisbon, Portugal 📅1-4 Oct 26 Please feel free to reach out to her if you want to discuss your research! fusion-conferences.com/conference/206

nature.comCCNB1IP1 regulatory evolution underlies gradual increases in cortical size and folding in primates - Nature GeneticsThe authors use tree shrews in multispecies comparisons to identify evolutionary changes in CCNB1IP1 expression associated with primate cortical expansion and folding, and investigate the cis-regulato...

📢PUBLISHED @natgenet.nature.com 📰CCNB1IP1 regulatory evolution underlies gradual increases in cortical size and folding in primates. By Ting Hu, Lei Shi and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comA human single-cell atlas identifies OLR1+ scar-associated macrophages as a potential therapeutic target for chronic liver disease - Nature GeneticsThis study provides a single-cell RNA-sequencing atlas of 77 healthy and chronic liver disease livers and identifies a subpopulation of pro-inflammatory scar-associated macrophages enriched for OLR1 e...

📢PUBLISHED @natgenet.nature.com 📰A human single-cell atlas identifies OLR1+ scar-associated macrophages as a potential therapeutic target for chronic liver disease. By Eleni Papachristoforou, Prakash Ramachandran and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comDefining pathogenic macrophages in the fibrotic niche of human chronic liver disease - Nature GeneticsMonocyte-derived macrophages are central in liver fibrosis pathogenesis, but the specific phenotype of the pro-fibrotic subpopulation is unknown. Using a liver single-cell atlas from 77 patients with ...

✨Don't miss the Research Briefing✨ 📰Defining pathogenic macrophages in the fibrotic niche of human chronic liver disease. ⬇️ www.nature.com/articles/s41...

nature.comGermline homologous recombination deficiency influences TP53-mutant clonal hematopoiesis fitness during platinum and PARP inhibitor treatment - Nature GeneticsThe authors show that platinum is a greater driver of DNA damage response gene-mutant clonal hematopoiesis than poly(ADP-ribose) polymerase inhibitors and that the presence of germline mutations confe...

📢PUBLISHED @natgenet.nature.com 📰Germline homologous recombination deficiency influences TP53-mutant clonal hematopoiesis fitness during platinum and PARP inhibitor treatment. By Jeremy T. Baeten, Kelly L. Bolton and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comGenetics and treatment history influence clonal hematopoiesis risk after PARP inhibitor therapy - Nature GeneticsPARP inhibitors and platinum chemotherapy both promote expansion of blood stem cell clones carrying leukemia-associated mutations, but inherited defects in homologous recombination limit this process....

✨Don't miss the Research Briefing✨ 📰Genetics and treatment history influence clonal hematopoiesis risk after PARP inhibitor therapy. ⬇️ www.nature.com/articles/s41...

nature.comSingle-cell analysis of chromatin accessibility in the human intestine identifies regulatory programs and clarifies genetic associations in Crohn’s disease - Nature GeneticsThis study uses single-cell ATAC–seq to map chromatin accessibility in the intestinal mucosa from patients with Crohn’s disease and healthy controls to characterize regulatory programs associated with...

📢PUBLISHED @natgenet.nature.com 📰Single-cell analysis of chromatin accessibility in the human intestine identifies regulatory programs and clarifies genetic associations in Crohn’s disease. By Yu Zhao, Sebastian Pott and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comGenome-wide mapping of common and rare variant effects on adiposity across childhood - Nature GeneticsGenome-wide analyses identify common and rare variants associated with childhood adiposity, including rare protein-coding variants in ADCY3, CALCR, MC4R, MRAP2, POMC and MYH13 that exhibit stronger ef...

📢PUBLISHED @natgenet.nature.com 📰Genome-wide mapping of common and rare variant effects on adiposity across childhood. By Katherine A. Kentistou, Stefan Johansson and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comEuchromatin forms condensed domains with short active regions on the surface - Nature GeneticsSimulations integrating micro-C and imaging data provide a coherent view of chromatin organization from nucleosomes to clutches to domains, revealing that most regions form compact domains but short r...

📢PUBLISHED @natgenet.nature.com 📰Euchromatin forms condensed domains with short active regions on the surface. By Joseph M. Paggi, Lawrence Y. Long & Bin Zhang ⬇️ www.nature.com/articles/s41...

nature.comAtlas of cell types and regulatory elements underlying human facial diversity - Nature GeneticsSingle-cell transcriptomics, spatial transcriptomics and chromatin accessibility maps of the human craniofacial region in developing embryos provide insights into the mechanisms underlying facial vari...

📢PUBLISHED @natgenet.nature.com 📰Atlas of cell types and regulatory elements underlying human facial diversity. By Alek G. Erickson, @adameykolab.bsky.social and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comHuman facial development atlas illuminates enhancer-based control of facial individuality - Nature GeneticsThe facial skeleton is essential for eating, breathing, kissing, speech and personal identity. Our spatiotemporally resolved cell atlas of human embryonic craniofacial development will facilitate a de...

✨Don't miss the Research Briefing✨ 📰Human facial development atlas illuminates enhancer-based control of facial individuality. ⬇️ www.nature.com/articles/s41...

nature.comDivergent medulloblastoma chromatin states disclose KDM2B as a selective dependency - Nature GeneticsEpigenomic analyses of medulloblastoma identify a bivalent/poised enhancer (EnhBiv) chromatin signature enriched for KDM2B binding in Group 3 and Group 4 tumors. Functional work suggests a selective d...

📢PUBLISHED @natgenet.nature.com 📰Divergent medulloblastoma chromatin states disclose KDM2B as a selective dependency. By Ran Tao, Paul A. Northcott and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comBalancing phenotyping depth and representativeness in psychiatric genomics - Nature GeneticsDeep phenotyping can improve diagnostic precision in psychiatric genomics, but it remains susceptible to non-random, partly heritable selection bias that compromises representativeness. Accordingly, a...

📢OUT TODAY @natgenet.nature.com 📰Balancing phenotyping depth and representativeness in psychiatric genomics. A Comment by Woojae Myung, Jisun Ryu & Hong-Hee Won. ⬇️ www.nature.com/articles/s41...

nature.comGenetic factor analysis for characterizing phenome-wide patterns of genetic pleiotropy - Nature GeneticsGenetic factor analysis uses genome-wide association summary statistics to identify shared polygenic factors underlying patterns of cross-trait genetic associations, while automatically determining th...

📢OUT TODAY @natgenet.nature.com 📰Genetic factor analysis for characterizing phenome-wide patterns of genetic pleiotropy. By Jean Morrison, Matthew Stephens and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comGb3 encodes a unique kinase fusion protein conferring greenbug resistance in wheat - Nature GeneticsGb3 encodes an intracellular kinase–pseudokinase protein with a unique MAP3K-like domain that confers resistance to multiple greenbug biotypes in wheat.

📢OUT TODAY @natgenet.nature.com 📰Gb3 encodes a unique kinase fusion protein conferring greenbug resistance in wheat. By Dhondup Lhamo, Steven S. Xu and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comSingle-nucleus atlas of cell-type specific genetic regulation in the human brain - Nature GeneticsMulti-resolution genetic regulatory atlas of the human brain from single-nucleus transcriptomics of 1,384 donors of diverse ancestries reveals cell type-specific regulation underlying genetic risk of ...

📢OUT TODAY @natgenet.nature.com 📰Single-nucleus atlas of cell-type specific genetic regulation in the human brain. By Biao Zeng, Panos Roussos and colleagues. ⬇️ www.nature.com/articles/s41...

Nature Genetics reposted

Kazuhiro Maeshima

@kazu-maeshima.bsky.social

18 Sept

🧬 Our “Behind the Paper” is now online at Nature Communities: “Active chromatin is not simply open—it forms compact domains that cohesin keeps from mixing.” 📖 A short story behind our recent @natgenet.nature.com paper. communities.springernature.com/posts/active... www.nature.com/articles/s41...

nature.comInterpreting human genetic variation at atomic resolution - Nature GeneticsThis Perspective discusses computational structural genomics, a conceptual framework that links genetic variants to three-dimensional molecular structures and their dynamics and function in a cellular...

21 Sept

📢OUT TODAY @natgenet.nature.com 📰Interpreting human genetic variation at atomic resolution. A Perspective by Michael T. Zimmermann & Raul Urrutia. ⬇️ www.nature.com/articles/s41...

nature.comGenetic landscape of an in vivo protein interactome - Nature GeneticsThis study uses budding yeast as a model system to link genetic variants with quantitative changes in protein–protein interaction strength under different environmental perturbations by leveraging a p...

21 Sept

📢OUT TODAY @natgenet.nature.com 📰Genetic landscape of an in vivo protein interactome. By Savandara Besse, Adrian W. R. Serohijos and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comProtein interactions reveal the hidden wiring of the genome - Nature GeneticsA large-scale genetic screen in yeast identifies protein interaction quantitative trait loci (piQTLs), demonstrating that natural genetic variation acts extensively through protein interaction network...

21 Sept

✨Don't miss the N&V✨ 📰Protein interactions reveal the hidden wiring of the genome. By Jing Hou & Joseph Schacherer. ⬇️ www.nature.com/articles/s41...

nature.comPan-genome-based resequencing of 2,320 accessions reveals structural variations and accelerates breeding advances in cultivated peanut - Nature GeneticsPan-genome analyses of cultivated peanut using 10 newly assembled genomes, along with whole-genome resequencing of 2,320 germplasm accessions, highlight structural variations and loci associated with ...

15 Sept

📢OUT TODAY @natgenet.nature.com 📰Pan-genome-based resequencing of 2,320 accessions reveals structural variations and accelerates breeding advances in cultivated peanut. By Yiyang Liu, Shubo Wan and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comType 1 interferon perturbates clonal competition by reshaping human blood development - Nature GeneticsSingle-cell multiomics of blood stem cells from patients with myeloproliferative neoplasms revealed that interferon-α normalizes blood counts by augmenting lymphoid differentiation and modulates clona...

15 Sept

📢OUT TODAY @natgenet.nature.com 📰Type 1 interferon perturbates clonal competition by reshaping human blood development. By Chhiring Lama, Anna Nam and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comContribution of copy number variants to schizophrenia in East Asian populations - Nature GeneticsGenomic analyses in populations of East Asian ancestry identify rare copy number variants associated with schizophrenia. Meta-analyses with populations of European ancestry identify additional risk lo...

14 Sept

📢PUBLISHED @natgenet.nature.com 📰Contribution of copy number variants to schizophrenia in East Asian populations. By Yu Chen, Hailiang Huang and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comCohesin prevents local mixing of condensed euchromatic domains in living human cells - Nature GeneticsSingle-nucleosome imaging/tracking and super-resolution three-dimensional structured illumination microscopy within euchromatic regions show that cohesin-mediated loops constrain condensed euchromatic...

14 Sept

📢PUBLISHED @natgenet.nature.com 📰Cohesin prevents local mixing of condensed euchromatic domains in living human cells. By Masa A. Shimazoe, Kazuhiro Maeshima and colleagues. ⬇️ www.nature.com/articles/s41...

14 Sept

📢 @natgenet.nature.com September issue's out! Featuring: ✅myeloid cells in AD ✅multiple sclerosis multiancestry GWAS & multiomics ✅functional AI-designed enhancers in mice ✅hPTMs cross species profiling with iChIP2 ✅data integration with SCIGMA and much more! ⬇️ www.nature.com/ng/volumes/5...

nature.comGenome-wide association analyses of gestational phenotypes identify context-specific genetic effects - Nature GeneticsGenome-wide analyses in up to 121,579 pregnant women from China identify genetic associations across 111 phenotypes, including gestation-specific effects and interactions with gestational timing.

📢PUBLISHED @natgenet.nature.com 📰Genome-wide association analyses of gestational phenotypes identify context-specific genetic effects. By Siyang Liu, Fengxiang Wei and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comIntrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants - Nature GeneticsIntrinsically disordered regions impose regulatory restraints on gene-activating demethylases, limiting chromatin engagement and preserving genomic stability. This function is a key determinant of the...

📢PUBLISHED @natgenet.nature.com 📰Intrinsically disordered regions restrain genomic targeting of RNA and histone demethylases in mammals and plants. By Liudan Jiang, Chuan He and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comPangenome-resolved structural variation drives adaptation and trait evolution in cucumber - Nature GeneticsPangenome analyses of chromosome-scale genome assemblies for 125 diverse cucumber accessions highlight structural variation shaped by selection for geographical adaptation, fruit-length diversificatio...

📢PUBLISHED @natgenet.nature.com 📰Pangenome-resolved structural variation drives adaptation and trait evolution in cucumber. By Jiantao Guan, Shengping Zhang and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comGenome-wide association analyses of borderline personality disorder identify 11 loci and highlight shared risk with mental and somatic disorders - Nature GeneticsGenome-wide association analyses identify risk variants for borderline personality disorder and find genetic correlations with psychiatric disorders, behavioral traits and somatic diseases.

📢PUBLISHED @natgenet.nature.com 📰Genome-wide association analyses of borderline personality disorder identify 11 loci and highlight shared risk with mental and somatic disorders. By Fabian Streit, Stephanie H. Witt and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comSUMOylation fine-tunes DNMT1 to silence viral mimicry transcripts - Nature GeneticsDNMT1 binds unmethylated CpG islands at active genes and, upon catalytic inhibition, redistributes to partially methylated, inaccessible regions, triggering viral mimicry via endogenous retroelements ...

💫Don't miss the N&V by Priscillia Lhoumaud & @maxvcg.bsky.social 📰SUMOylation fine-tunes DNMT1 to silence viral mimicry transcripts. ⬇️ www.nature.com/articles/s41...

nature.comSUMOylation enhances DNMT1 function to repress mega-intergenic RNAs and viral mimicry - Nature GeneticsThis study uses a highly selective inhibitor to elucidate DNMT1’s specific functions and their regulation. Notably, RFN4-mediated SUMOylation enhances DNMT1 mobility and DNA methylation, thereby promo...

📢PUBLISHED @natgenet.nature.com 📰SUMOylation enhances DNMT1 function to repress mega-intergenic RNAs and viral mimicry. By Brian J. Liddicoat, Jesse J. Balic, @mafdawson.bsky.social and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comPromoter strength and position govern promoter competition through transcript-dependent insulation - Nature GeneticsBy inserting diverse promoters at the mouse Sox2 locus, Koska et al. show that promoter strength, position and transcript length tune promoter competition through transcription-dependent insulation, i...

📢PUBLISHED @natgenet.nature.com 📰Promoter strength and position govern promoter competition through transcript-dependent insulation. By Mervenaz Koska, Joanna Wysocka and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comPioneer transcription factors direct tissue-specific cohesin chromatin entry and three-dimensional genome organization - Nature GeneticsAnalyses in prostate cancer cell lines show that FOXA1 mediates tissue-specific recruitment of NIPBL to chromatin to orchestrate three-dimensional genome organization, acting in concert with ETS1 and ...

📢PUBLISHED @natgenet.nature.com 📰Pioneer transcription factors direct tissue-specific cohesin chromatin entry and three-dimensional genome organization. By Song Wang, Haiyang Guo and colleagues. ⬇️ www.nature.com/articles/s41...

Nature Genetics reposted

Luca Giorgetti lab @FMI

@lucagiorgetti.bsky.social

nature.comThe genomic position of an enhancer modulates bursting dynamics of the cognate promoter - Nature GeneticsWe show that, in a genomic locus with minimal complexity, the distance between promoter and enhancer modulates the frequency of clustered transcriptional bursts. Thus, besides the nucleotide sequence,...

Thank you @natgenet.nature.com for this nice Research Briefing www.nature.com/articles/s41... on our recent paper reporting live-cell measurements of Sox2 promoter bursting kinetics when varying its genomic distance from the SCR enhancer 👉 www.nature.com/articles/s41...

nature.comLongitudinal changes in DNA methylation in IDH-mutant glioma fuel disease progression through altered cell state differentiation - Nature GeneticsThe authors use single-cell multi-omics to interrogate longitudinal samples of isocitrate dehydrogenase mutant gliomas. Their analyses couple progression and hypomethylation with changes in differenti...

💫PUBLISHED @natgenet.nature.com 📰Longitudinal changes in DNA methylation in IDH-mutant glioma fuel disease progression through altered cell state differentiation. By @masashi-nomura.bsky.social, @landau.bsky.social, Mario L. Suvà and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comA progeria syndrome links DNA hypermethylation to age-related pathology - Nature GeneticsThis study investigates the consequences of hypermethylation in a progeria syndrome caused by gain-of-function DNMT3A mutations, finding effects on adult stem cell function.

📢PUBLISHED @natgenet.nature.com 📰A progeria syndrome links DNA hypermethylation to age-related pathology. By Dan Sarni, Andrew Jackson and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comMultiscale analysis and functional validation of the cellular and genetic determinants of skeletal disease - Nature GeneticsThe study integrates cross-species single-cell and genomic analyses with functional validations to map the endosteal bone compartment, revealing musculoskeletal-disease-relevant cell types and transcr...

✨PUBLISHED @natgenet.nature.com 📰Multiscale analysis and functional validation of the cellular and genetic determinants of skeletal disease. By Ryan C. Chai, John P. Kemp and colleagues. ⬇️ www.nature.com/articles/s41...

Nature Genetics reposted

Luca Giorgetti lab @FMI

@lucagiorgetti.bsky.social

15 July

Our preprint is now out in @natgenet.nature.com ! doi.org/10.1038/s415... We measured Sox2 promoter bursting dynamics with the SCR enhancer positioned at different distances within a genomic locus devoid of confounding effects in mESC: Main findings in the 🧵 below:

doi.orgEnhancer control of promoter activity and variability via frequency modulation of clustered transcriptional bursts - Nature GeneticsTünnermann et al. use live-cell imaging to study promoter activity under the control of an enhancer inserted at different genomic distances. RNA production from the promoter occurs in clusters of tran...

Luca Giorgetti lab @FMI@lucagiorgetti.bsky.social

Celebrating 10 years of our lab with a new preprint: www.biorxiv.org/content/10.1... How does enhancer location within a TAD control transcriptional bursts from a cognate promoter? Experiments by Jana Tünnermann and modelling by Gregory Roth

📢@natgenet.nature.com July issue's out! Featuring: ✅special focus on BRCA1 and BRAC2 ✅in vivo Perturb-seq of MDD risk genes ✅human vaginal microbiome genomic landscape ✅Chron's Disease single-cell RNA seq atlas ✅a graph-based mung bean pan-genome and much more! ⬇️ www.nature.com/ng/volumes/5...

springernature.wd3.myworkdayjobs.comAssociate or Senior Editor, Nature GeneticsJob Title: Associate or Senior Editor, Nature Genetics Location: Shanghai, Beijing, Madrid, Milan or Pune, Hybrid Working Model Application Deadline: Aug 3rd, 2026 About Springer Nature Springer Natur...

9 July

@natgenet.nature.com is looking to hire a Cancer editor! Please repost and share with your contacts! This is a rare and exciting opportunity. springernature.wd3.myworkdayjobs.com/SpringerNatu...

nature.comInterpretable, flexible and spatially aware integration of multiple spatial transcriptomics datasets from diverse sources - Nature GeneticsINSPIRE addresses challenges to integrating diverse spatial transcriptomics datasets by combining deep learning with non-negative matrix factorization, revealing shared and context-specific spatial ge...

28 Apr

📢PUBLISHED @natgenet.nature.com 📰 Interpretable, flexible and spatially aware integration of multiple spatial transcriptomics datasets from diverse sources By Jia Zhao, Hongyu Zhao and colleagues. ⬇️ www.nature.com/articles/s41...

nature.comTumor DNA methylation subtypes predict immunotherapy outcomes in pleural mesothelioma patients in the NIBIT-EPI-MESO study - Nature GeneticsProfiling of pleural mesothelioma samples from 91 patients identifies four DNA methylation subtypes that correlate with response to immune checkpoint inhibition and survival

28 Apr

📢 PUBLISHED @natgenet.nature.com 📰Tumor DNA methylation subtypes predict immunotherapy outcomes in pleural mesothelioma patients in the NIBIT-EPI-MESO study By Luana Calabrò, Michele Ceccarelli, Michele Maio and colleagues. ⬇️ www.nature.com/articles/s41...