Zhang X, Lan L, Yang Y
… +16 more, Guan H, Peng D, Jiang H, Wu Q, Huang R, Liao X, Lin S, Gong D, Huang B, Bellot C, Szécsi J, Bao M, Bendahmane M, Fu X, Wu Z, Pan W
Roses are economically important ornamental plants, with widespread applications in the cut flowers, garden and cosmetics industries. The genomic evolution and diversity of the subgenus Rosa remain understudied, limiting...Roses are economically important ornamental plants, with widespread applications in the cut flowers, garden and cosmetics industries. The genomic evolution and diversity of the subgenus Rosa remain understudied, limiting exploitation of its diversity in breeding. Here we assembled genomes of 23 accessions, comprising 51 haplotypes that capture the subgenus's high genetic diversity. Extensive introgression across accessions from different sections highlights crossbreeding potential. Pangenome analysis revealed 1,801,537 structural variations, providing insights into the genetic basis and key regulators controlling key traits such as continuous flowering, petal number and discoloration. A key finding was the identification of a CCD4 homolog as the main regulator of petal discoloration. Additional subgenomic analysis of the allopolyploid Rosa gallica and the triploid Rosa hybrida 'La France', two important breeding materials of modern roses, revealed their hybrid origins. Overall, this study advances understanding of rose genomics and provides valuable resources for future breeding and trait improvement.
Mendelian randomization has evolved from a niche methodology to a widely adopted research approach. In this Perspective, we briefly present a bibliometric analysis of the Mendelian randomization literature to inform a di...Mendelian randomization has evolved from a niche methodology to a widely adopted research approach. In this Perspective, we briefly present a bibliometric analysis of the Mendelian randomization literature to inform a discussion of how Mendelian randomization studies are conducted and how they do not fully realize the potential of the data and techniques available to empirically examine the reliability of assumptions. We propose that future progress will depend on integrating empirical evidence from molecular, cellular, animal and quasi-experimental studies to assess its assumptions and causal claims. We also highlight how the shifting landscape of genetic and genomic data presents new challenges and opportunities for the Mendelian randomization framework, providing a deeper understanding of causal mechanisms.
Zhou Z, Kim J, Huang AY
… +21 more, Nolan M, Park J, Doan R, Shin T, Miller MB, Bae M, Zhao B, Kim J, Chhouk B, Morillo K, Yeh RC, Kenny C, Neil JE, Lee CZ, Ohkubo T, Ravits J, Ansorge O, Ostrow LW, Lagier-Tourenne C, Lee EA, Walsh CA
Although mutations in many genes cause familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), most cases are sporadic (sALS and sFTD) with unclear etiology. Here we tested whether somatic mutatio...Although mutations in many genes cause familial amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), most cases are sporadic (sALS and sFTD) with unclear etiology. Here we tested whether somatic mutations contribute to sALS and sFTD by deep targeted sequencing of 88 neurodegeneration-related genes in postmortem brain and spinal cord samples from 399 sporadic cases and 144 controls. Predicted deleterious somatic variants in ALS/FTD genes were observed in 2.1% of sporadic cases lacking deleterious germline variants. These variants occurred at very low allele fractions (typically <2%) and were often focal and enriched in disease-affected regions. Analysis of bulk RNA-sequencing data from an additional cohort identified deleterious somatic variants in DYNC1H1 and LMNA, genes associated with pediatric motor neuron degeneration. Targeted long-read sequencing further identified one sFTD case with de novo somatic C9orf72 repeat expansions. Together, these findings suggest that rare, focal somatic variants can contribute to sALS and sFTD and drive widespread neurodegeneration.
Fejzo M, Wang X, Tan Q
… +31 more, Zöllner J, Pujol-Gualdo N, Laisk T, Estonian Biobank Research Team, Finer S, van Heel DA, Genes & Health Research Team, Brumpton B, Bhatta L, Hveem K, Jasper EA, Velez Edwards DR, Hellwege JN, Edwards T, Jarvik GP, Luo Y, Khan A, MacGibbon K, Gao Y, Ge G, Averbukh I, Soon E, Angelo M, Magnus P, Johansson S, Njølstad PR, Kim A, Gazal S, Vaudel M, Shu CA, Mancuso N
Most pregnancies are affected by nausea and vomiting, but the most severe form-hyperemesis gravidarum-can be life threatening. Here we performed a multi-ancestry genome-wide association study of hyperemesis gravidarum in...Most pregnancies are affected by nausea and vomiting, but the most severe form-hyperemesis gravidarum-can be life threatening. Here we performed a multi-ancestry genome-wide association study of hyperemesis gravidarum in 10,974 cases and 461,461 controls across European, Asian, African and Latino ancestries. We identified ten associations: four identified previously (GDF15, IGFBP7, PGR and GFRAL) and six additional loci (SLITRK1, SYN3, IGSF11, FSHB, TCF7L2 and CDH9). Downstream analyses revealed GDF15 and TCF7L2 expression primarily in extravillous trophoblasts, with opposing effects for GDF15 between maternal and fetal genotype. Conversely, IGFBP7 and PGR were expressed primarily in maternal spiral arteries, with effects limited to the maternal genome. Selected loci were associated with abnormal pregnancy weight gain, duration, birth weight and pre-eclampsia. Functional studies identified additional associations including antisense IGFBP7-AS1 and protein ACP1. Potential roles for candidate genes in appetite, insulin signaling and brain plasticity provide pathways to explore etiological mechanisms and therapeutic avenues.
Acute cohesin loss causes widespread reorganization of three-dimensional (3D) chromatin architecture but has relatively minor effects on steady-state transcription. It remains unclear whether its role in gene regulation...Acute cohesin loss causes widespread reorganization of three-dimensional (3D) chromatin architecture but has relatively minor effects on steady-state transcription. It remains unclear whether its role in gene regulation becomes more critical during mitotic exit, when 3D chromatin architecture and transcription are globally re-established. To address this, we acutely depleted RAD21 in mouse embryonic stem cells during mitotic exit under self-renewal or differentiation conditions. Here we show that, although most loops failed to reform without cohesin, the few cohesin-independent loops were linked to active promoters, strong enhancers and H3K27ac mitotic bookmarking. Transcriptional changes were only modest, indicating that gene reactivation largely bypasses cohesin. Sensitive genes showed RAD21 promoter binding, a higher number of structural loops and positioning within well-insulated, gene-poor topologically associating domains. During differentiation, cohesin loss impaired activation of a broader set of developmental genes, partly due to defective de novo regulatory interactions. Together, these findings demonstrate context-specific requirements for cohesin in gene activation.
NIPBL promotes chromatin loop extrusion by the cohesin complex until it stalls at convergently oriented CTCF sites, forming structural loops. While a large fraction of loops connecting cis-regulatory elements (CREs) can...NIPBL promotes chromatin loop extrusion by the cohesin complex until it stalls at convergently oriented CTCF sites, forming structural loops. While a large fraction of loops connecting cis-regulatory elements (CREs) can be maintained in cohesin-depleted cells, whether the loop extrusion process contributes to the de novo establishment of CRE loops remains unclear. To address this question, we characterized the formation of structural and CRE loops in NIPBL-depleted cells during the mitosis-to-G1-phase transition. Structural loop formation was impaired proportionally to loop length. Computational modeling supports these observations, suggesting that NIPBL promotes both cohesin loading and extrusion. Notably, most CRE loops, regardless of length, were established normally upon NIPBL degradation. While a subset of contacts among weak CREs were formed with delayed kinetics in NIPBL-depleted cells, generally gene activation was only mildly impaired. Collectively, our findings suggest that postmitotic establishment of regulatory contacts and gene transcription can occur independently of chromatin loop extrusion.
Erdogdu NU, Guhathakurta S, Oellers R
… +9 more, Shvedunova M, Morin JA, Patrick EM, Seyfferth J, Deboutte W, Gomez-Auli A, Mittler G, Cissé II, Akhtar A
Bromodomain (BD) and extra-terminal domain (BET) proteins are key regulators of RNA polymerase II (Pol II)-mediated transcription and their BDs represent promising drug targets. Yet, the interplay between histone acetyla...Bromodomain (BD) and extra-terminal domain (BET) proteins are key regulators of RNA polymerase II (Pol II)-mediated transcription and their BDs represent promising drug targets. Yet, the interplay between histone acetylation and the chromatin dynamics of individual BET proteins with respect to transcriptional regulation is not fully understood. Here in mouse embryonic stem cells, we uncover an essential role of BRD2 in maintaining Pol II recruitment at promoters through its interaction with TFIID, which becomes particularly critical under the conditions of impaired pause release. Combining rapid protein degradation, chemogenomics and super-resolution microscopy, we show that MOF-mediated histone H4 acetylation promotes BRD2 chromatin association, which in turn enables BRD2 clustering. Accordingly, MOF depletion or deletion of the BRD2's intrinsically disordered region largely recapitulates defects in promoter enrichment and clustering of the transcription machinery observed upon BRD2 loss. Thus, these findings support a model in which histone acetylation-dependent spatiotemporal dynamics of BRD2 coordinate the transcription machinery to regulate transcription initiation.
Genetic variants in RNU4-2, which is transcribed into the U4 small nuclear RNA component of the major spliceosome, were recently shown to cause ReNU syndrome, a prevalent dominant neurodevelopmental disorder (NDD). These...Genetic variants in RNU4-2, which is transcribed into the U4 small nuclear RNA component of the major spliceosome, were recently shown to cause ReNU syndrome, a prevalent dominant neurodevelopmental disorder (NDD). These variants almost exclusively arise de novo and cluster within 18 nucleotides of RNU4-2. Here we describe a new recessive NDD associated with homozygous and compound heterozygous variants in RNU4-2. We identify 38 individuals with biallelic variants outside the 18-nucleotide ReNU syndrome region that cluster within other functionally important elements of U4: Stem II, the k-turn and the Sm protein binding site. We characterize the clinical phenotype in 31 individuals, demonstrating that the recessive disorder is clinically distinct from ReNU syndrome and is associated with distinctive white matter abnormalities, including enlarged perivascular spaces. Finally, we find reduced RNU4-2 transcript levels in individuals with the recessive disorder, suggesting a loss-of-function disease mechanism that is distinct from the mechanism underlying ReNU syndrome. Together, these findings expand the genotypic and phenotypic spectrum of RNU4-2-associated NDDs.
Jang B, Bp K, Tokolyi A
… +14 more, Dredge WH, Ravi A, Jung SH, Naito T, Kim B, Kim MS, Cho M, Park MS, Rosen M, Blanchard J, Humphrey J, Knowles DA, Won HH, Raj T
T cells recognize their target cells through the T cell receptor (TCR). Combining gain-of-function, single-cell and optical high-content screens, we identified RNA-based mechanisms that selectively sensitize target cells...T cells recognize their target cells through the T cell receptor (TCR). Combining gain-of-function, single-cell and optical high-content screens, we identified RNA-based mechanisms that selectively sensitize target cells to TCR-specific T cell cytotoxicity. First, CRISPR activation screens in melanoma cells identify functionally diverse regulators of TCR-specific cytotoxicity, including SAFB, KHDRBS1, MYC, CD44, WNT3A, WNT1 and others. Expressing sensitizing hits in cancer and virally infected cells restores TCR-specific cytotoxicity. Next, we developed in situ Perturb-seq for optical pooled genetic screens with in situ detection of perturbations and spatial transcriptomic readouts. Perturb-seq and in vivo-in situ Perturb-seq show that the hits converge on shared cell-autonomous and intercellular mechanisms, map gene-environment interactions and reveal that Wnt ligands activate T cells. Introducing a scalable approach to decode gene function at the cell and tissue level, the study uncovered context-specific gene functions to restore targeted T cell-based elimination of dysfunctional cells via synthetically lethal, RNA-based interventions.
Tao XY, Tan C, Liu Y
… +91 more, Wang Y, Raza A, He J, Wang L, Xia K, Yan Y, Liao S, Jiang W, Qu Y, Xu B, Zhou Y, Yang X, Roy S, Denton M, Tucker M, Able J, Gilliham M, Langridge P, Hu HW, He JZ, Zhao C, Zhou M, Mir RR, Chitikineni A, Li C, Zhang P, Trethowan R, Ding Y, Zhang J, Franks P, Wu Q, Ye L, Wang Y, Wu F, Zhang G, Cai S, Shen Q, Jiang H, Chen G, Zhou Y, Song C, Zhang Y, Ma W, Li X, Guo W, Zeng J, He X, Liu W, Feng X, Zhang R, Li G, Cao X, Liu S, Liu Q, Chen J, Zhang X, Liu L, Zeng F, Deng F, Qin Y, Zhu X, Shabala S, Tee EE, Schnurbusch T, Mascher M, Wu H, Spannagl M, Xin M, Gou J, Brar G, Xue D, Wang W, Reynolds M, Zhao Y, Liu Z, Krugman T, Sakata Y, Yee S, Chan K, Pogson B, Zhang Y, Marchant DB, Siddique KHM, Fang X, Chen A, Henry R, Boden SA, Varshney RK, Xu SC, Xu X, Chen ZH
Wheat is a major staple crop for over one-third of the world's population, crucial for global food security, economic stability and cultural traditions. Recently, single-cell and spatial omics approaches have transformed...Wheat is a major staple crop for over one-third of the world's population, crucial for global food security, economic stability and cultural traditions. Recently, single-cell and spatial omics approaches have transformed biological discovery, primarily in medical and animal sciences, and they are now beginning to be applied in plant research. Here we summarize the technical innovations and feasibility of spatial omics applications in wheat research, particularly for understanding developmental and environmental responses, thereby potentially enhancing wheat breeding. We highlight how these tools can reveal spatial and temporal patterns in gene expression, cellular heterogeneity and tissue organization in wheat. Furthermore, we propose developing a spatially resolved single-cell atlas of wheat across its life cycle to facilitate breakthroughs in basic research and potential applications in breeding. To achieve these goals, we advocate for a Wheat Spatial Omics Consortium to foster worldwide collaboration for overcoming barriers and developing sustainable and climate-resilient wheat.
Hop PJ, Kooyman M, Kenna BJ
… +86 more, Zwamborn RAJ, van Eijk KR, Wang Y, van Dijk CH, Bekema E, van Rheenen W, Beele P, van Vugt JJFA, Project MinE ALS sequencing Consortium, NYGC ALS Consortium, FALS sequencing Consortium, GTAC Consortium, Khleifat AA, Iacoangeli A, Cooper-Knock J, Smith BN, Topp S, van der Kooi AJ, Fominykh V, Drory V, Lerner Y, Shovman Y, Rowe DB, Williams KL, McLaughlin RL, Hurt J, Huang Y, Chen CY, Tsai E, Runz H, Aronica E, Groen EJN, van Es MA, Pasterkamp RJ, Farhan SMK, Garton FC, McRae AF, McCombe PA, Henderson RD, Fan D, Šlachtová L, Høyer H, Nishimura AL, Cauchi RJ, Brylev L, Rogelj B, Koritnik B, Zidar J, Salas T, Mora Pardina JS, Gotkine M, Povedano M, Corcia P, Vourc'h P, Couratier P, Weber M, Kiernan MC, Pamphlett R, Blair IP, de Carvalho M, Başak NA, Ingre C, Andersen PM, Zinman L, Rogaeva E, MacKenzie IR, Dupre N, Rouleau GA, Traynor BJ, Ticozzi N, Chiò A, Silani V, Hardiman O, Phatnani H, Harms MB, Dalgard CL, Glass JD, Landers JE, Van Damme P, Morrison KE, Shaw PJ, Shaw CE, Al-Chalabi A, van den Berg LH, Kenna KP, Veldink JH
Amyotrophic lateral sclerosis (ALS) is a heritable disorder where rare variants with low-to-moderate penetrance are thought to dominate genetic risk. To identify such rare variants, we harmonized and analyzed exome data...Amyotrophic lateral sclerosis (ALS) is a heritable disorder where rare variants with low-to-moderate penetrance are thought to dominate genetic risk. To identify such rare variants, we harmonized and analyzed exome data from 22 cohorts, totaling 17,919 individuals with ALS and 200,703 controls across discovery and replication phases. Rare variant analyses identified several new risk genes, with replication confirming association of YKT6 and supporting HTR3C, GBGT1 and KNTC1. We also provide strong, independent validation for genes with limited previous evidence: ARPP21, DNAJC7 and CFAP410. Notably, in ARPP21, we identified a new high-effect variant (p.P747L) and confirmed that p.P563L is an ALS-associated variant leading to an aggressive disease course. Beyond new discoveries, our analyses largely recapitulated the known genetic architecture of ALS, identifying risk variants in over 20% of cases and supporting a cumulative oligogenic risk model. These findings highlight new translational targets and show that rare variant analyses capture substantially more genetic risk than common variant genome-wide association studies.
Leitão E, Santini A, Cogne B
… +225 more, Essid M, Athanasiadou M, LaFlamme CW, Marijon P, Bernard V, Jousselin K, Chatron N, Barcia G, Keren B, Mignot C, Charles P, Besnard T, Paluch R, de Sainte Agathe JM, Almanza Fuerte EP, Sengupta S, Milh M, Ramond F, Allan T, An I, Araujo C, Arpin S, Austin-Tse C, Auvin S, Baer S, Bahi-Buisson N, Bak M, Barth M, Baulac S, Bednarek-Weirauch N, Begemann M, Bennett MF, Bensabath U, Bézieau S, Bhouri R, Biehler M, Hammer TB, Bogoin J, Bonanno E, Boussion S, Bris C, Brosseau-Beauvir A, Bruel AL, Briand-Suleau A, Buratti J, Celse T, Chambon P, Chemaly N, Chesneau B, Colin E, Colmard M, Colson C, Conrad S, Courtin T, Creveaux I, Cullier AC, Dang LT, de Saint Martin A, de Vanssay de Blavous Legendre C, Demeer B, Denommé-Pichon AS, Diekhoff P, DiTroia S, Doco-Fenzy M, Dubourg C, Dubucs C, Ducreux S, Dufour L, Duquet R, Durand B, El Chehadeh S, Elbracht M, Faivre L, Faoucher M, Faudet A, Forlani S, Fradin M, Gaignard P, Ganne B, Garde A, Géraud J, Gill D, Goldenberg A, Grabli D, Grisel C, Gueden S, Gueguen P, Guerrot AM, Guichet A, Haack TB, Härting N, Häusler MG, Heide S, Herget T, Héron B, Héron D, Herwig J, Heulin M, Holling T, Houdayer C, Isidor B, Jacquette A, Januel L, Jean-Marçais N, Kaiser FJ, Kaya S, King C, Konyukh M, Kraft F, Krause J, Kirstetter R, Kuechler A, Kurth I, Kutsche K, Labalme A, Laloy JS, Laugel V, Le Bricquir F, Lèbre AS, Lebrun M, Leguern E, Levy J, Lieffering N, Lyonnet S, Lüthy K, Macdonald SMW, Mansour-Hendili L, Maraval J, Marquardt I, Mattausch C, Mercier S, Messaoud O, Morel G, Mortreux J, Munnich A, Nabbout R, Nambot S, Navarro V, Neale A, Nguyen L, Nizon M, Nowak F, O'Leary MC, Odent S, Ojeda NM, Olin V, Olivieri S, Õunap K, Pais LS, Panagiotakaki E, Patat O, Perrin-Sabourin L, Petit F, Philippe C, Piton A, Planes M, Poirsier C, Pouzet A, Prouteau C, Quéméner-Redon S, Renaud M, Richard AC, Rio M, Rivier C, Robin-Renaldo F, Rollier P, Rossi M, Roubertie A, Ruault V, Rupin-Mas M, Saugier-Veber P, Saunier A, Saneto R, Sarrazin E, Sarret C, Schaefer E, Schluth-Bolard C, Schneider A, Schumann I, Seplyarskiy VB, Spranger S, Smol T, Sturm M, Sunyaev SR, Sperelakis-Beedham B, Stenton SL, Stock F, Tharreau M, Torun D, Toulouse J, Thiyagarajah H, Valence S, Valleix S, Van-Gils J, Villard L, Ville D, Villeneuve N, Vitobello A, Waernessyckle A, Wagner J, Weber Y, Wieczorek D, Witkowski T, Yadavilli M, Yammine T, Zaafrane-Khachnaoui K, Zaki MS, Ziegler A, Bramswig NC, Lermine A, Nicolas G, Gleeson JG, Sadleir LG, Hildebrand MS, Scheffer IE, Whiffin N, O'Donnell-Luria A, Mefford HC, Blanc P, Thevenon J, Charbonnier C, Charenton C, Depienne C, Lesca G, Nava C
Small nuclear RNAs (snRNAs) are essential components of the spliceosome. De novo variants in snRNA genes RNU4-2 (ReNU syndrome), RNU5B-1 and RNU2-2 have been linked to dominant neurodevelopmental disorders (NDDs), reveal...Small nuclear RNAs (snRNAs) are essential components of the spliceosome. De novo variants in snRNA genes RNU4-2 (ReNU syndrome), RNU5B-1 and RNU2-2 have been linked to dominant neurodevelopmental disorders (NDDs), revealing a large unexpected contribution of noncoding RNA genes to genetic diseases. Here, through international collaborations, we analyze systematically 200 potentially functional snRNA genes in a French cohort of 34,329 people with rare disorders. We report RNU2-2 variants in 141 individuals, including 35 with recurrent dominant pathogenic variants and 91 affected members from 73 families with biallelic variants. Recessive RNU2-2 NDD is at least twice as frequent as the dominant form and often involves a de novo variant in trans with an inherited allele, consistent with the high mutability of snRNA genes. Dominant and recessive RNU2-2 NDDs share overlapping clinical features, with frequent epilepsy. Blood transcriptomics and DNA methylation analyses revealed subtle, variant-specific effects on splicing and episignatures. Our results support a gradient-of-impact model bridging dominant and recessive inheritance, and establish RNU2-2 variants as a principal contributor to NDDs, nearly as prevalent as ReNU syndrome.
Jackson A, Blakes AJM, Alhaddad B
… +59 more, Henry OJ, Delgado-Vega AM, Wall E, Abdelhadi O, Agrawal S, Bakur K, Blair E, Brady AF, Brittain H, Chandler KE, Clarke N, Danelli M, Drinkall N, Duba I, Elmslie F, Ellingford J, Ewans LJ, Fennell AP, Gazdagh G, Heller SP, Hammarsjö A, Karrman K, Kini U, Lesko N, Lindstrand A, Macintosh R, Mansour S, Menzies L, Metcalfe K, Milhench A, Nashef L, O'Keefe RT, Pacheco NP, Palmer EE, Parida A, Prescott K, Redman M, Renieri A, Fallerini C, Rizzo CL, Sachdev R, Simons C, Sisodiya SM, Stewart H, Stödberg T, Banos-Pinero B, Taylan F, Thomas HB, Tinella F, Wiafe S, Wedell A, Whiffin N, Walker S, Rius R, Chae JH, Nordgren A, Alkuraya F, Lord J, Banka S
Neurodevelopmental disorders (NDDs) affect 2-4% of the population, are predominantly genetic and remain unsolved in ~50% of individuals. We show that rare biallelic variants in RNU2-2 are enriched and over-transmitted in...Neurodevelopmental disorders (NDDs) affect 2-4% of the population, are predominantly genetic and remain unsolved in ~50% of individuals. We show that rare biallelic variants in RNU2-2 are enriched and over-transmitted in individuals with unresolved NDDs. We define a recessive RNU2-2 syndrome, delineate its unique genetic architecture and show that it manifests clinically as a severe developmental and epileptic encephalopathy. We find that candidate biallelic variants are significantly correlated with reduced U2-2 abundance, implicating compromised transcript stability as a probable pathomechanism. We identify a decreased ratio of U2-2 to its paralog U2-1 as a potential diagnostic biomarker for this condition. We show that the recessive RNU2-2 syndrome is genetically, clinically and mechanistically distinct from the dominant RNU2-2 disorder. Within our cohort, the recessive RNU2-2 syndrome emerges as by far the most frequent recessive NDD, greatly disproportionate to the small genomic footprint of this non-protein-coding gene.