Biology subjects

Buck, M. J.

Publications and source records attributed to Buck, M. J..

7 recordsLinked to original sources

bioRxiv2026

A population-scale landscape of the subgingival microbiome reveals divergent routes to periodontal dysbiosis

Periodontitis is an archetypical mucosal inflammatory disease in which microbiome dysbiosis at the tooth-epithelial interface interacts with host genetic and behavioral risk factors to drive immune-mediated tissue destruction. Although subgingival microbiome compositional shifts are thought to parallel disease severity, microbiome variation at the population-level and its relationship to periodontal clinical phenotypes and disease-modifying factors remain poorly defined. Here, we use unsupervised manifold learning to map the compositional landscape of the subgingival microbiome in 1,355 adults spanning periodontal health to severe periodontitis. We identified eight latent microbiome states organized along a branching continuum from eubiosis to dysbiosis. An intermediate microbial configuration marked ecological destabilization and bifurcation into two distinct periodontitis-associated dysbiotic trajectories, distinguished by links to gingival inflammation and smoking. Although the microbiome trajectories broadly tracked periodontal destruction, a minority of individuals showed discordant microbiome-clinical phenotypes, with some individuals with periodontitis retaining otherwise eubiotic microbiomes enriched for low-abundance pathobionts, while some cases of health or mild disease had highly dysbiotic communities, suggesting distinct host susceptibility. Together, these findings define a population-scale ecological landscape of the subgingival microbiome, reveal divergent trajectories to periodontal dysbiosis, and highlight heterogeneity in the relationship between microbial community structure and clinical disease expression.

microbiology↗

bioRxiv2026

Cooperative FOXA1-HNF4A binding emerges from motif spacing and nucleosome architecture

The pioneer factor hypothesis posits that specialized transcription factors access nucleosomal DNA to enable binding of secondary factors, implying a hierarchical mechanism of chromatin opening. However, recent evidence indicates that cooperative binding between pioneer and non-pioneer factors can occur in a context-dependent manner. Here we define the sequence and chromatin features that specify cooperative binding between FOXA1 and HNF4A. Using dual-induction of FOXA1 and HNF4A in naive cells, which lack endogenous expression of either factor, we identify a class of genomic sites that require both factors for binding and reside in initially inaccessible chromatin. A dual-head convolutional neural network finds no novel composite motif at these sites, instead implicating motif arrangement as the distinguishing feature. Cooperative loci are enriched for FOXA1-HNF4A motif pairs spaced 15-60 bp apart, a soft-syntax grammar consistent with nucleosome-mediated cooperativity. This spacing signature recurs at endogenously co-bound sites in HepG2 cells and primary fetal hepatocytes. Using a multiplexed in vitro nucleosome-binding assay (Pioneer-seq), we show that FOXA1 binds nucleosomal DNA more strongly than HNF4A across positions, and that cooperative binding strength on natural nucleosome sequences is predicted primarily by the position of the FOXA1 motif relative to the nucleosome dyad. Together, these results support a model in which positioned nucleosomes act as scaffolds that facilitate cooperative transcription factor binding through spatial motif organization, rather than a barrier one factor clears for the other.

genomics↗

bioRxiv2024

Nucleosome-binding by TP53, TP63, and TP73 is determined by the composition, accessibility, and helical orientation of their binding sites

The p53 family of transcription factors plays key roles in driving development and combating cancer by regulating gene expression. TP53, TP63, and TP73--the three members of the p53 family--regulate gene expression by binding to their DNA binding sites, many of which are situated within nucleosomes. To thoroughly examine the nucleosome-binding abilities of the p53 family, we used Pioneer-seq, a technique that assesses a transcription factors binding affinity to its DNA binding sites at all possible positions within the nucleosome core particle. Using Pioneer-seq, we analyzed the binding affinity of TP53, TP63, and TP73 to 10 p53-family binding sites across the nucleosome core particle. We found that the affinity of TP53, TP63, and TP73 for nucleosomes was largely determined by the positioning of p53-family binding sites within nucleosomes; p53-family members bind strongly to the more accessible edges of nucleosomes but weakly to the less accessible centers of nucleosomes. We also found that the DNA-helical orientation of p53-family binding sites within nucleosomal DNA impacted the nucleosome-binding affinity of p53-family members. The composition of their binding sites also impacted each p53-family members nucleosome-binding affinities only when the binding site was located in an accessible location. Taken together, our results show that the accessibility, composition, and helical orientation of p53-family binding sites collectively determine the nucleosome-binding affinities of TP53, TP63, and TP73. These findings help explain the rules underlying p53-family-nucleosome binding and thus provide requisite insight into how we may better control gene-expression changes involved in development and tumor suppression.

molecular biology↗

bioRxiv2022

Defining transcription factor nucleosome binding with Pioneer-seq

Gene expression requires the targeting of transcription factors (TFs) to regulatory sequences often occluded within nucleosomes. To comprehensively examine TF nucleosome binding, we developed Pioneer-Seq. In Pioneer-seq a library of nucleosomes containing thousands of DNA sequences with TF binding sites in all possible nucleosome orientations is bound to a TF and the protein-nucleosome complex is isolated and quantified. To demonstrate Pioneer-seq we examined nucleosome binding by OCT4, SOX2, KLF4, and c-MYC. Our results demonstrate that KLF4 and SOX2 can bind close to the nucleosome dyad with nucleosome sequence being the major factor regulating TF binding across all studied TFs.

molecular biology↗

bioRxiv2020

Targeted Next Generation Sequencing in Saccharomyces cerevisiae Reveals Complex Mutation Profiles in the Presence of Mismatch Repair and Ribonucleotide Reductase Mutations that Compromise the Fidelity of DNA Replication

Distinct mutation signatures arise from environmental exposures and/or from defects in metabolic pathways that promote genome stability. The presence of a particular mutation signature in a cell or a tumor can therefore predict the underlying mechanism of mutagenesis, which, in practice, may be clinically important. These insults to the genome often alter dNTP pools, which itself impacts replication fidelity. Therefore, the impact of altered dNTP pools should be considered when making mechanistic predictions based on mutation signatures. We developed a targeted deep-sequencing approach on the CAN1 gene in Saccharomyces cerevisiae to define information-rich mutational profiles associated with distinct rnr1 backgrounds that alter replication fidelity by elevating dNTP levels.. The mutation spectra of rnr1Y285F and rnr1Y285A alleles were characterized previously; our analysis was consistent with this prior work but the sequencing depth achieved in our study allowed a significantly more robust and nuanced computational analysis of the variants observed, generating profiles that integrated information about mutation spectra, position effects, and sequence context. This approach revealed novel, genotype-specific mutation profiles in the presence of even modest changes in dNTP pools. Furthermore, we identified broader sequence contexts and specific nucleotide motifs that influenced variant profiles in different rnr1 backgrounds, which allowed us to make specific mechanistic predictions about the impact of altered dNTP pools on replication fidelity.

genetics↗

bioRxiv2018

Feasibility of constructing multi-dimensional genomic maps of juvenile idiopathic arthritis

BackgroundJuvenile idiopathic arthritis (JIA) is one of the most common chronic conditions of childhood. Like many common chronic human illnesses, JIA likely involves complex interactions between genes and the environment, mediated by the epigenome. Such interactions are best understood through multi-dimensional genomic maps that identify critical genetic and epigenetic components of the disease. However, constructing such maps in a cost-effective way is challenging, and this challenge is further complicated by the challenge of obtaining biospecimens from pediatric patients at time of disease diagnosis, prior to therapy, as well as the limited quantity of biospecimen that can be obtained from children,particularly those who are unwell. In this paper, we demonstrate the feasibility and utility of creating multi-dimensional genomic maps for JIA from limited sample numbers.\n\nMethodsTo accomplish our aims, we used an approach similar to that used in the ENCODE and Roadmap Epigenomics projects, which used only 2 replicates for each component of the genomic maps. We used genome-wide DNA methylation sequencing, whole genome sequencing on the Illumina 10x platform, RNA sequencing, and chromatin immunoprecipitation-sequencing for informative histone marks (H3K4me1 and H3K27ac) to construct a multi-dimensional map of JIA neutrophils, a cell we have shown to be important in the pathobiology of JIA.\n\nResultsThe epigenomes of JIA neutrophils display numerous differences from those from healthy children. DNA methylation changes, however, had only a weak effect on differential gene expression. In contrast, H3K4me1 and H3K27ac, commonly associated with enhancer functions, strongly correlated with gene expression. Furthermore, although unique/novel enhancer marks were associated with insertion-deletion events (indels) identified on whole genome sequencing, we saw no strong association between epigenetic changes and underlying genetic variation. The initiation of treatment in JIA is associated with a re-ordering of both DNA methylation and histone modifications, demonstrating the plasticity of the epigenome in this setting.\n\nConclusionsThese findings, generated from a small number of patient samples, demonstrate how multidimensional genomic studies may yield new understandings of biology of JIA and provide insight into how therapy alters gene expression patterns.

genomics↗

bioRxiv2018

Defining p53 pioneering capabilities with competitive nucleosome binding assays

Accurate gene expression requires the targeting of transcription factors (TFs) to regulatory sequences often occluded within nucleosomes. The ability to target a transcription factor binding site (TFBS) within a nucleosome has been the defining characteristic for a special class of TFs known as pioneer factors. Recent studies suggest p53 functions as a pioneer factor that can target its TFBS within nucleosomes, but it remains unclear how p53 binds to nucleosomal DNA. To comprehensively examine p53 nucleosome binding we competitively bound p53 to multiple in vitro formed nucleosomes containing a high or low-affinity p53 TFBS located at differing translational and rotational positions within the nucleosome. Stable p53-nucleosome complexes were isolated and quantified using next generation sequencing. Our results demonstrate p53 binding is limited to nucleosome edges with significant binding inhibition occurring within 50-bp of the nucleosome dyad. Binding site affinity only affects p53 binding for TFBS located outside the nucleosome core at the same nucleosomal positions. Furthermore, p53 has strong non-specific nucleosome binding facilitating its interaction with chromatin. Our in vitro findings were confirmed by examining p53 induced binding in a cell line model, showing induced binding at nucleosome edges flanked by a nucleosome free region. Overall, our results suggest that the pioneering capabilities of p53 are driven by non-specific nucleosome binding with specific binding at nucleosome edges.

genomics↗