Biology subjects

Dennis, J. H.

Publications and source records attributed to Dennis, J. H..

6 recordsLinked to original sources

bioRxiv2025

Nucleosome positioning and sensitivity suggest novel functional organization of the purple sea urchin (Strongylocentrotus purpuratus) genome

The eukaryotic nucleosome is the fundamental subunit of chromatin and plays functional roles in DNA templated processes, including replication and transcription. In eukaryotic promoters, nucleosome organization is highly structured, with nucleosomes occupying canonical positions flanking the transcription start site (TSS), thereby regulating access of the transcriptional machinery to the underlying DNA. We determine whether this canonical distribution is present in the purple sea urchin, Strongylocentrotus purpuratus, a species of ecological importance and a model organism for developmental biology and climate science. We used titrations of micrococcal nuclease to produce high throughput maps of nucleosome distribution and sensitivity to digestion from female urchin gonad tissue. Unlike yeast, flies, zebrafish, maize, mice or humans, urchins have extended nucleosome repeat lengths and lack a nucleosome depleted region over TSSs. Urchin promoters are dominated by strongly positioned and highly occupied +1 and +2 nucleosomes which are most prominent in highly expressed genes. Additionally, urchin promoters exhibit distinct patterns of susceptibility to nuclease digestion, with heightened sensitivity upstream of the TSS and limited resistance to nuclease digestion. Discretely positioned sensitive nucleosomes were enriched in promoters of highly expressed genes, suggesting a relationship between nucleosome sensitivity and transcriptional regulation. Collectively, we present a comprehensive overview of the unique interplay between nucleosome positioning and chromatin sensitivity in sea urchins. Our study not only provides a better understanding of dynamics of gene expression in a key developmental organism, but also reveals potential heterogeneity in a key structural property of chromatin previously thought to be homogeneous in model eukaryotes. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/653534v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@c724dforg.highwire.dtl.DTLVardef@45c163org.highwire.dtl.DTLVardef@19b6043org.highwire.dtl.DTLVardef@1ccf475_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

SARS-CoV-2 nucleocapsid uniquely disrupts chromatin over pathophysiologically relevant gene promoters

SARS-CoV-2, the causative agent of COVID-19, is a positive-sense, single-stranded RNA virus that causes a spectrum of disease severity, from asymptomatic infection to severe illness to long-term sequelae. Similar to other human coronaviruses, SARS-CoV-2 proteins modulate host genomic responses through epigenomic modifications, facilitating viral replication and immune evasion. While the nucleocapsid protein is well known for its role in RNA stability and immune modulation, its impact on host chromatin organization remains unclear. To investigate this, we generated stable human alveolar cell lines expressing nucleocapsid proteins from endemic and pandemic human coronaviruses. Our analysis revealed that nucleocapsid proteins from all tested coronaviruses induced changes in nucleosome positioning and occupancy at specific gene promoters involved in coagulation pathways, hormone signaling, and innate immune responses. Additionally, SARS-CoV-2-specific alterations were identified in genes dysregulated in severe infections, suggesting a direct role for epigenomic modifications in disease pathophysiology. We also observed extensive changes in nucleosome susceptibility to nuclease digestion in SARS-CoV and SARS-CoV-2 samples that were not observed in common cold cell lines. Promoters with altered sensitivity and resistance to nuclease were linked to innate immune, metabolic, olfactory, and signaling pathways known to be dysregulated in severe COVID-19 and post-acute sequelae (PASC). These findings demonstrate that nucleocapsid protein expression alters chromatin structure at specific loci, implicating viral proteins in host genome dysregulation. Furthermore, we identified both shared and unique chromatin targets of SARS-CoV-2 and common cold coronaviruses, highlighting pathways for further investigation and potential therapeutic intervention. ImportanceHost chromatin is known to be modulated by coronaviruses during infections. However, the role of the nucleocapsid protein in these alterations are unknown. Here, we show that nucleocapsids from seven human coronaviruses alter nucleosome distribution and susceptibility to enzymatic digestion over specific gene promoters in a human lung cell line. Nucleocapsids from SARS-CoV and SARS-CoV-2 have the most prominent effects which are seen over genes involved in immune responses, metabolism, hormone signaling, and other pathways that are known to be dysregulated in severe COVID-19 and post-acute sequelae of COVID-19. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/639619v2_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@d97a79org.highwire.dtl.DTLVardef@1f7d5c3org.highwire.dtl.DTLVardef@1f312f0org.highwire.dtl.DTLVardef@1606a56_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

Transient alterations in nucleosome distribution and sensitivity to nuclease define the THP-1 monocyte to macrophage transition

The monocyte to macrophage transition is marked by alterations to both the structure and function of the genome, including changes in histone post-translational modifications, DNA methylation, 3D nuclear architecture, and expression of lineage specific genes. The nucleosome is the fundamental organizational unit of the eukaryotic genome and underpins both genome structure and function. However, nucleosome dynamics at promoters, which are essential for transcriptional regulation, are understudied in cellular differentiation. We conducted high-resolution chromatin structure profiling at promoters in the THP-1 cell line at eight different time points spanning PMA-induced monocyte to macrophage differentiation. We found that fewer than 10% of nucleosomes within promoters were redistributed during differentiation and only a subset of these were associated with immediate transcriptional alterations. Nucleosomes within the promoters of PMA-responsive genes were strongly positioned prior to differentiation and experienced minimal alterations during differentiation thus implying the existence of a pre-differentiation primed chromatin state. Additionally, we observed pronounced alterations in nucleosome sensitivity to MNase digestion within one hour of PMA-induced differentiation and the emergence of a highly resistant phenotype in fully differentiated cells. We found that resistance is correlated with active chromatin marks, transcription factor binding, gene expression, and higher order chromatin structure demonstrating that it is a useful measure of both genome structure and function. Together this suggests that, unlike more stable nucleosome distribution, transient sensitivity alterations may underpin new genomic functions in differentiating cells. Our results offer a framework for understanding how chromatin structural alterations potentiate cellular differentiation in a monocyte model and use methodology that is widely applicable to other systems. Summary sentenceNucleosome distribution is largely static during PMA induced monocyte differentiation while nucleosome sensitivity is highly dynamic and is associated with gene expression, active chromatin marks, transcription factor binding, and higher order chromatin structure.

genomics↗

bioRxiv2025

Dynamic nucleosome redistribution and increases innucleosome sensitivity underpin THP-1 macrophage response to LPS

Macrophages detect lipopolysaccharide (LPS) through toll-like receptor 4 (TLR-4) on the cell surface which initiates a signaling cascade resulting in the recruitment of regulatory factors to chromatin and subsequent expression of chemokine and cytokine genes. Primary response genes, marked by poised promoters and enhancers, are rapidly expressed after LPS stimulation, and their gene products activate secondary response genes via paracrine and autocrine signaling pathways. While the signaling cascades following macrophage activation are well understood, the dynamics of nucleosome architecture and regulatory factor binding in promoter regions during early and late LPS responses remain unclear. Here, we stimulated THP-1 derived macrophages with LPS and assessed nucleosome distribution and MNase sensitivity across promoters at eight time points spanning primary and secondary responses. We found that while nucleosome distribution was static over most promoters, LPS stimulation resulted in transient remodeling of a subset of immune and DNA repair gene promoters. We also observed distinct MNase sensitivity alterations in two phases which aligned with early and late gene expression patterns. Notably, while most Pol II promoters showed altered chromatin sensitivity, only a subset exhibited transcriptional changes, suggesting that widespread alterations in nucleosome distribution and sensitivity occur at promoters with or without alterations in gene expression. These findings provide new temporal insights into the transient and long-term effects of immune stimulation on promoter architecture and offer a methodological framework for additional time-resolved studies of chromatin remodeling in other systems. Summary sentenceFollowing LPS stimulation, a subset of nucleosomes in macrophage immune promoters undergo transient redistribution, whereas the majority of nucleosomes show changes in MNase sensitivity that are largely uncoupled from gene expression. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/637695v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@198f47org.highwire.dtl.DTLVardef@dab80org.highwire.dtl.DTLVardef@1769d0corg.highwire.dtl.DTLVardef@40be27_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical abstract.C_FLOATNO LPS stimulation of THP-1 derived macrophages leads to altered nucleosome occupancy and positioning within a subset of promoters which are enriched for LPS response genes. Altered distribution patterns permit regulatory factor binding and gene expression. The majority of promoters have altered nucleosome sensitivity with a trend towards increased sensitivity after LPS stimulation. Altered sensitivity results in regulatory factor binding and expression of LPS response genes. C_FIG

genomics↗

bioRxiv2022

Nucleosome sensitivity distinguishes colon polyps based on their transformation status

One of the keys to eliminating the personal and financial costs of cancer lies in the early detection of the disease. Consequently, effective cancer interventions increasingly rely on our understanding of the earliest cellular and nuclear events that lead to oncogenic transformation. Colorectal cancer, the third most prevalent cancer in the United States, results from the transformation of polyps. Our group demonstrated that the alteration of chromatin organization is a pivotal event in this oncogenic transformation. Here, we analyze the differences of the nucleosomal sensitivity to mocroccocal nuclease (MNase) between histopathologically matched pre-cancerous polyps taken from patients that did not develop cancer (cancer-free polyps, CFP) and those that did develop cancer (cancer-associated polyps, CAP). We produced high-resolution nucleosome distribution and nucleosome sensitivity maps from each of the five CFP patient samples and three CAP patient samples. We show that nucleosome distribution is largely invariant between CFP and CAP samples. Nucleosome sensitivity, however, is a powerful analysis that can identify genomic locations that distinguish CFP from CAP. We have identified more than 1000 genomic locations with altered nucleosomal sensitivity that discriminate between CAP and CFP. Furthermore, we show that these genomic locations with altered nucleosomal sensitivity between CFP and CAP include genes that play critical roles in oncogenic transformation. We propose that nucleosome sensitivity serves as a robust biomarker indicating the oncogenic potential of precancerous polyps and could be used for the early detection of polyps that will become cancerous.

molecular biology↗

bioRxiv2019

MNase profiling of promoter chromatin in S. typhimurium-stimulated GM12878 cells reveals dynamic and response-specific nucleosome architecture

The nucleosome is the primary unit of chromatin structure and commonly imputed as a regulator of nuclear events, although the exact mechanisms remain unclear. Recent studies have shown that certain nucleosomes can have different sensitivities to micrococcal nuclease (MNase) digestion, resulting in the release of populations of nucleosomes dependent on the concentration of MNase. Mapping MNase sensitivity of nucleosomes at transcription start sites genome-wide reveals an important functional nucleosome organization that correlates with gene expression levels and transcription factor binding. In order to understand nucleosome distribution and sensitivity dynamics during a robust genome response, we mapped nucleosome position and sensitivity using multiple concentrations of MNase. We use the innate immune response as a model system to understand chromatin-mediated regulation. Herein we demonstrate that stimulation of a human lymphoblastoid cell line (GM12878) with heat-killed Salmonella typhimurium (HKST) results in widespread nucleosome remodeling of response-specific loci. We further show that the response alters the sensitivity of promoter nucleosomes. Finally, we correlate the increased sensitivity with response-specific transcription factor binding. These results indicate that nucleosome distribution and sensitivity dynamics are integral to appropriate cellular response and pave the way for further studies that will deepen our understanding of the specificity of genome response.

genomics↗