Nucleic Acids Research最新文献

The AlphaFold Protein Structure Database (AFDB) is the largest repository of accurately predicted structures with taxonomic labels. Despite providing predictions for over 214 million UniProt entries, the AFDB does not cover viral sequences, severely limiting their study. To address this, we created the Big Fantastic Virus Database (BFVD), a repository of 351 242 protein structures predicted by applying ColabFold to the viral sequence representatives of the UniRef30 clusters. By utilizing homology searches across two petabases of assembled sequencing data, we improved 36% of these structure predictions beyond ColabFold's initial results. BFVD holds a unique repertoire of protein structures as over 62% of its entries show no or low structural similarity to existing repositories. We demonstrate how a substantial fraction of bacteriophage proteins, which remained unannotated based on their sequences, can be matched with similar structures from BFVD. In that, BFVD is on par with the AFDB, while holding nearly three orders of magnitude fewer structures. BFVD is an important virus-specific expansion to protein structure repositories, offering new opportunities to advance viral research. BFVD can be freely downloaded at bfvd.steineggerlab.workers.dev and queried using Foldseek and UniProt labels at bfvd.foldseek.com.

CRISPR-based DNA adenine base editors (ABEs) hold remarkable promises to address human genetic diseases caused by point mutations. ABEs were developed by combining CRISPR-Cas9 with a transfer RNA (tRNA) adenosine deaminase enzyme and through directed evolution, conferring the ability to deaminate DNA. However, the molecular mechanisms driving the efficient DNA deamination in the evolved ABEs remain unresolved. Here, extensive molecular simulations and biochemical experiments reveal the biophysical basis behind the astonishing base editing efficiency of ABE8e, the most efficient ABE to date. We demonstrate that the ABE8e's DNA deaminase domain, TadA8e, forms remarkably stable dimers compared to its tRNA-deaminating progenitor and that the strength of TadA dimerization is crucial for DNA deamination. The TadA8e dimer forms robust interactions involving its R98 and R129 residues, the RuvC domain of Cas9 and the DNA. These locking interactions are exclusive to ABE8e, distinguishing it from its predecessor, ABE7.10, and are indispensable to boost DNA deamination. Additionally, we identify three critical residues that drive the evolution of ABE8e toward improved base editing by balancing the enzyme's activity and stability, reinforcing the TadA8e dimer and improving the ABE8e's functionality. These insights offer new directions to engineer superior ABEs, advancing the design of safer precision genome editing tools.

Response to spatiotemporal variation in selection gradients resulted in signatures of polygenic adaptation in human genomes. We introduce RAISING, a two-stage deep learning framework that optimizes neural network architecture through hyperparameter tuning before performing feature selection and prediction tasks. We tested RAISING on published and newly designed simulations that incorporate the complex interplay between demographic history and selection gradients. RAISING outperformed Phylogenetic Generalized Least Squares (PGLS), ridge regression and DeepGenomeScan, with significantly higher true positive rates (TPR) in detecting genetic adaptation. It reduced computational time by 60-fold and increased TPR by up to 28% compared to DeepGenomeScan on published data. In more complex demographic simulations, RAISING showed lower false discoveries and significantly higher TPR, up to 17-fold, compared to other methods. RAISING demonstrated robustness with least sensitivity to demographic history, selection gradient and their interactions. We developed a sliding window method for genome-wide implementation of RAISING to overcome the computational challenges of high-dimensional genomic data. Applied to African, European, South Asian and East Asian populations, we identified multiple genomic regions undergoing polygenic selection. Notably, ∼70% of the regions identified in Africans are unique, with broad patterns distinguishing them from non-Africans, corroborating the Out of Africa dispersal model.

Heterochromatin plays a critical role in regulating gene expression and maintaining genome integrity. While structural and enzymatic components have been linked to heterochromatin establishment, a comprehensive view of the underlying pathways at diverse heterochromatin domains remains elusive. Here, we developed a systematic approach to identify factors involved in heterochromatin silencing at pericentromeres, subtelomeres and the silent mating type locus in Schizosaccharomyces pombe. Using quantitative measures, iterative genetic screening and domain-specific heterochromatin reporters, we identified 369 mutants with different degrees of reduced or enhanced silencing. As expected, mutations in the core heterochromatin machinery globally decreased silencing. However, most other mutants exhibited distinct qualitative and quantitative profiles that indicate heterochromatin domain-specific functions, as seen for example for metabolic pathways affecting primarily subtelomere silencing. Moreover, similar phenotypic profiles revealed shared functions for subunits within complexes. We further discovered that the uncharacterized protein Dhm2 plays a crucial role in heterochromatin maintenance, affecting the inheritance of H3K9 methylation and the clonal propagation of the repressed state. Additionally, Dhm2 loss resulted in delayed S-phase progression and replication stress. Collectively, our systematic approach unveiled a landscape of domain-specific heterochromatin regulators controlling distinct states and identified Dhm2 as a previously unknown factor linked to heterochromatin inheritance and replication fidelity.