Germ cell differentiation in the male testis involves extensive phenotypic, transcriptional, and epigenetic modifications, which are essential for producing functional spermatozoa. Among all organs, the testis exhibits the highest baseline physiological levels of L-2-hydroxyglutarate (L-2HG), yet its role in male germ cell development remains unknown. Here, we reveal that L-2HG is synthesized during the pachytene and diplotene stages of meiosis by the testis-specific enzyme lactate dehydrogenase C (LDHC). Surprisingly, LDHC translocates into the nucleus, localizing along the synaptonemal complex and at centromeres. L-2HG, produced by LDHC, regulates centromere condensation and heterochromatin organization via multiple mechanisms, including chromocenter clustering, centromere and chromocenter condensation, and modulation of satellite RNA expression. These effects are rapid, specific to L-2HG, and independent of histone methylation changes. Acute depletion of L-2HG in vivo results in centromere dysfunction and activation of the spindle assembly checkpoint (SAC), suggesting the possible role of this metabolite in ensuring proper chromosome segregation.

Fungi have NOD-Like receptors (NLRs), homologous to the innate immune receptors found in animals, plants and bacteria. Fungal NLRs are characterized by a great variability of domain organizations, but the identity of the nucleotide-binding domains, the genomic localization, and the factors associated with variation in the composition of repertoires of fungal NLRs are not yet fully understood. To better understand the variability of fungal NLR repertoires and the underlying determinants, we conducted a thorough analysis of genome data from the ascomycete order Sordariales. Using similarity searches based on hidden Markov models profiles for canonical N-terminal, nucleotide-binding, or C-terminal domains, we characterized 4613 NLRs in 82 Sordariales taxa. By examining the Helical Third section of the nucleotide-binding domains, we substantially improved their annotation. We demonstrated that fungi have NACHT domains of both NAIP-like and TLP1-like types, similar to animals. We found that the number of NLR genes was highly variable among Sordariales families, and independent of the stringency of defense mechanisms against genomic repeat elements. NLRs were organized in clusters in the majority of taxa, and the strong correlation between the number of NLRs and the number of NLR clusters suggested that organizing in clusters may contribute to repertoire diversification. Our work highlights the similarity of fungal and animal NLRs in terms of nucleotide-binding domain types, and between fungal and plant NLRs in terms of genomic organization in clusters. Our findings will aid in the comparative analysis of the patterns and processes of diversification of NLR repertoires in various lineages of fungi and between the different kingdoms and domains of life.

The spatial organization of the genome is crucial for its function and integrity. Although the ring-like SMC complex condensin II has a well-documented role in organizing mitotic chromosomes, its function in interphase chromatin structure has remained more enigmatic. Using a combination of Oligopaint fluorescence in situ hybridization (FISH) and Hi-C, we show that altering condensin II levels in diploid Drosophila cells significantly changes chromosome architecture at large length scales between chromatin compartments. Notably, condensin II overexpression disrupts the robust boundary between heterochromatin and euchromatin, leading to interactions that span entire chromosomes. These interactions occur independent from transcriptional changes, suggesting that the mechanisms driving compartment formation and their interactions might be distinct aspects of genome organization. Our results provide new insights into the dynamic nature of chromosome organization and underscore the importance of condensin II in maintaining genomic stability.

Transcriptional regulation by binding of transcription factors to palindromic sequences in promoter regions is a fundamental process in bacteria. Some transcription factors have multiple dimeric DNA-binding domains, in principle enabling interaction with higher-order DNA structures; however, mechanistic and structural insights into this phenomenon remain limited. The Pseudomonas putida toxin-antitoxin (TA) system Xre-RES has an unusual 4:2 stoichiometry including two potential DNA-binding sites, compatible with a complex mechanism of transcriptional autoregulation. Here, we show that the Xre-RES complex interacts specifically with a palindromic DNA repeat in the promoter in a 1:1 molar ratio, leading to transcriptional repression. We determine the 2.7 Å crystal structure of the protein-DNA complex, revealing an unexpected asymmetry in the interaction and suggesting the presence of a secondary binding site, which is supported by structural prediction of the binding to the intact promoter region. Additionally, we show that the antitoxin can be partially dislodged from the Xre-RES complex, resulting in Xre monomers and a 2:2 Xre-RES complex, neither of which repress transcription. These findings highlight a dynamic, concentration-dependent model of transcriptional autoregulation, in which the Xre-RES complex transitions between a non-binding (2:2) and a DNA-binding (4:2) form.

The transcription factors TFEB and TFE3 modulate expression of lysosomal, autophagic, and metabolic genes to restore energy and cellular homeostasis in response to a variety of stress conditions. Since their role during vertebrate development is less characterized, we used CRISPR/Cas9 to deplete tfeb, tfe3a, and tfe3b in zebrafish. The simultaneous lack of these genes compromised embryo survival during early development, with an almost complete lethality of the larvae by 8-10 dpf. The knockout animals showed apoptosis in brain and retina and alterations in pancreas, liver, and gut. Exocrine pancreas presented the most severe defects, with accumulation of abnormal zymogen granules leading to acinar atrophy in embryos and pancreatitis-like phenotypes in adults; likely due to a block of the autophagy machinery implicated in removal of damaged granules. Knockout animals displayed increased susceptibility to oxidative and heat-shock stress. Our work reveals an essential role of Tfeb and Tfe3 in maintaining cellular and tissue homeostasis during development.

The detection of founder pathogenic variants, those observed in high frequency only in a group of individuals with increased inter-relatedness, can help improve delivery of health care for that community. We identified 16 groups with shared ancestry, based on genomic segments that are shared through identity by descent (IBD), in New York City using the genomic data of 25,366 residents from the All Of Us Research Program and the Mount Sinai BioMe biobank. From these groups we defined 7 as founder populations, mostly communities currently under-represented in medical genomics research, such as Puerto Rican and Garifuna. The enrichment analysis of ClinVar pathogenic or likely pathogenic (P/LP) variants in each group identified 201 of these damaging variants across the seven founder populations. We confirmed disease-causing variants previously reported to occur at increased frequencies in Ashkenazi Jewish and Puerto Rican genetic ancestry groups, but most of the damaging variants identified have not been previously associated with any such founder populations, and most of these founder populations have not been described to have increased prevalence of the associated rare disease. Twenty-two of 47 variants meeting Tier 2 prenatal screening criteria (1/100 carrier frequency within these founder groups) have never previously been reported. We show how population structure studies can provide insights into rare diseases disproportionately affecting under-represented founder populations, delivering a health care benefit but also a potential source of stigmatization of these communities, who should be part of the decision-making about implementation into health care delivery.

The effect of high percentage spliced in (hiPSI) TTN truncating variants (TTNtvs) on risk of dilated cardiomyopathy (DCM) has historically been studied among population subgroups defined by genetic similarity to European reference populations. This has raised questions about the effect of TTNtvs in diverse populations, especially among individuals genetically similar to African reference populations. To determine the effect of TTNtvs on cardiovascular disease risk, we leveraged whole exome sequencing and electronic health record data from 43,731 Penn Medicine Biobank (PMBB) participants recruited from across the Penn Medicine healthcare system. Fraction of genetic similarity to the 1000 Genomes Project (1000G) African (AFR) reference population was determined using ADMIXTURE analysis. Logistic regression was performed to evaluate the association of hiPSI TTNtvs with prevalent DCM and atrial fibrillation (Afib), and linear regression was used to evaluate the association with reduced left ventricular ejection fraction (LVEF) either using dichotomized genetically similar population subgroup analysis or integrating ADMIXTURE population fraction. When individuals were assigned to population subgroups based on genetic similarity to the 1000G reference populations, hiPSI TTNtvs conferred significant risk of DCM among those genetically similar to the 1000G European (EUR) reference population (OR=6.12, 95% confidence intervals [CI] 4.33 to 8.65, P < 0.001) and individuals genetically similar to the AFR reference population (OR=3.44, 95% CI 1.97 to 5.99, P < 0.001). These results were consistent when considering the effect of change in fraction of similarity to the African reference population by ADMIXTURE as a continuous variable. Similar results were observed for the effect of TTNtvs on Afib and LVEF. Our findings demonstrate that TTNtvs are associated with increased risk of DCM, reduced LVEF, and Afib among a diverse cohort. There is no significant difference in effect of TTNtvs across fractions of similarity to the AFR reference population suggesting genetic background should not be considered when screening individuals for titin-related cardiovascular disease.

Plant responses to salt stress involve regulatory networks integrating ion transport, hormonal signaling, and root system architecture remodeling. A key adaptive mechanism is the regulation of sodium (Na⁺) transport by Class 1 HKT1 transporters, which compertamentalize Na⁺ in non-photosynthetic tissues. High HKT1 expression reduces Na+ accumulation in shoots, leading to increased salt tolerance, but simultaneously results in reduced lateral root development. In this study, we explored transcriptional responses that are altered by high HKT1 expression in root stelle in two Arabidopsis backgrounds, Col-0 and C24. We identified TMAC2, a negative ABA regulator, and TIP2:2, a tonoplast aquaporin, as key modulators of root development under salt stress. While TIP2:2 function was conserved, TMAC2 exhibited genotype-specific effects on ABA accumulation and HKT1-mediated salt sensitivity. Co-expression of TMAC2 and HKT1 in Col-0 upregulated ABI4 and ABI5, linking Na⁺ transport to ABA signaling. Our findings underscore genetic context in shaping salt responses and provide molecular targets for enhancing root plasticity under stress.

Climate change poses a major challenge for both natural and cultivated species. Genomic tools are increasingly used in both conservation and breeding to identify adaptive loci that can be used to guide management in future climates. Here, we study the utility of climate and genomic data for identifying promising alleles using common gardens of a large, geographically diverse sample of traditional maize varieties to evaluate multiple approaches. First, we used genotype data to predict environmental characteristics of germplasm collections to identify varieties that may be pre-adapted to target environments. Second, we used environmental GWAS (envGWAS) to identify loci associated with historical divergence along climatic gradients. Finally, we compared the value of environmental data and envGWAS-prioritized loci to genomic data for prioritizing traditional varieties. We find that maize yield traits are best predicted by genome-wide relatedness and population structure, and that incorporating envGWAS-identified variants or environment-of-origin data provide little additional predictive information. While our results suggest that environmental data provide limited benefit in predicting fitness-related phenotypes, environmental GWAS is nonetheless a potentially powerful approach to identify individual novel loci associated with adaptation, especially when coupled with high density genotyping.