Biology subjects

Schwartz, U.

Publications and source records attributed to Schwartz, U..

12 recordsLinked to original sources

bioRxiv2026

The SWI/SNF subunit SWI3B functions with the m6A writer complex to establish embryo patterning in Arabidopsis

N6-methyladenosine (m6A) is the most abundant mRNA modification in eukaryotes and is essential for Arabidopsis embryogenesis. However, how m6A mRNA methylation is coordinated with other regulatory pathways during development including embryogenesis remains largely unknown. Here, we report the SWI/SNF chromatin-remodeling subunit SWI3B as a bona fide interactor of the m6A methyltransferase MTA. Like m6A writer mutants, SWI3B is required for early embryo development. We demonstrate that the interaction between MTA and SWI3B is required for MTA function during embryogenesis. MTA and SWI3B are both required to establish the correct expression pattern of WOX8 and proper auxin maxima during early embryogenesis. Transcriptome analysis of isolated embryos from mta, swi3b, and fip37 mutants identified a shared set of upregulated transcripts, including STM as well as several NAC and ERF transcription factors that are normally absent or expressed at very low levels during early embryogenesis. Embryo-specific overexpression of ANAC087 and ERF114 genes phenocopied early embryonic defects observed in mta and swi3b mutants, indicating that their ectopic expression contributes to the observed developmental phenotype. Moreover, SWI3B and MTA are both required for m6A deposition on specific developmental transcripts. Together, our findings uncover a mechanism by which chromatin remodeling and m6A-mediated RNA regulation cooperate to suppress the precocious stability of key developmental regulators, thereby contributing to the establishment of the transcriptional program required for early embryo patterning in Arabidopsis. HighlightsO_LIThe SWI/SNF subunit SWI3B is a functional interactor of the m6A methyltransferase MTA during Arabidopsis embryogenesis C_LIO_LISWI3B and MTA cooperate to establish embryo patterning, WOX8 expression, and auxin maxima C_LIO_LIMTA and SWI3B suppress precocious expression of STM, ANAC087 and ERF114 transcription factors that disrupt early embryo development C_LIO_LISWI3B links chromatin-associated regulation with m6A-mediated control of transcript stability C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=161 HEIGHT=200 SRC="FIGDIR/small/744595v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@1056f76org.highwire.dtl.DTLVardef@1d8b9d6org.highwire.dtl.DTLVardef@190918corg.highwire.dtl.DTLVardef@439ce1_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

bioRxiv2025

Deciphering chromatin architecture and dynamics in Plasmodium falciparum using the nucDetective pipeline

High-resolution analysis of cellular chromatin structure is crucial for uncovering developmental and cell-type-specific regulatory networks. We developed the nucDetective pipeline to provide a comprehensive evaluation of chromatin organisation. This involves assessing nucleosome positioning, occupancy, fuzziness, and array regularity. The pipeline was benchmarked by analysing the chromatin structure of the malaria-causing parasite Plasmodium falciparum (Pf) during its erythrocytic development cycle. Pf is characterised by a unique chromatin landscape, exhibiting unstable nucleosomes and a genomic AT-content exceeding 80%, which presents challenges for standard MNase-seq analysis of chromatin. The nucDetective pipeline provides specific, high-resolution nucleosome profiles for the different asexual stages of Pf, monitoring the dynamics of individual nucleosomes. In contrast to the current view, suggesting an irregular chromatin structure and lack of nucleosomal DNA, we demonstrate that the transcription start sites exhibit typical eukaryotic features, including +1 nucleosomes, nucleosome-free regions upstream, and phased nucleosome arrays downstream of the TSSs. The global mean nucleosome repeat length varies from 176 bp to 185 bp depending on the developmental stage. Stage specific changes in nucleosome positioning occur locally in intergenic regulatory regions, which are characterized by specific histone modifications and variants. Dynamic nucleosomes correlate with DNA accessibility, gene expression and determine the access to transcription factor binding sites in Pf. The highly regular chromatin structure, with stage-specific structural alterations, emphasises the important role of epigenetic mechanisms in regulating the complex life cycles of Pf.

bioinformatics↗

bioRxiv2025

Adenovirus maturation establishes the transcription competent packaging of its genome

Adenoviruses are human pathogens that, more recently have gathered interest as tools for human gene therapy and vaccination. During their replication, adenoviruses undergo a critical maturation step culminating in the infectious particle. While the structural changes in the adenovirus protein shell during maturation have been subject to previous research, the maturation of the viral genome with associated proteins (core) remains largely unexplored. Here, we show that the adenovirus core maturation is guided by features embedded in the viral DNA sequence, which primes the genome for transcription. Using DMS-seq to compare the accessibility of the nucleoprotein core structure before and after maturation (using the maturation deficient ts1 mutant), we identified five genomic regions that become specifically decompacted during maturation. These regions are characterized by low GC-content and are evolutionarily conserved across different adenovirus species, independent of protein-coding constraints. We show that adenoviral DNA packaging is guided by a distinct 6.1-bp dinucleotide periodicity pattern that helps position viral chromatin proteins. Core processing during maturation serves a dual purpose: (i) it contributes to capsid uncoating by increasing internal pressure while (ii) simultaneously preparing the chromatin structure of the genome for rapid transcription upon nuclear entry. These findings reveal how sequence-encoded structural information guides adenoviral genome organization and suggest new approaches for optimizing adenoviral vectors used in gene therapy and vaccination.

molecular biology↗

bioRxiv2023

Epigenetic deregulation of IFN and WNT pathways in AT2 cells impairs alveolar regeneration (in COPD)

Chronic lung diseases, including chronic obstructive pulmonary disease (COPD), affect over 500 million people and are a leading cause of death worldwide. A common feature of both chronic and acute lung diseases is altered respiratory barrier integrity and impaired lung regeneration. We hypothesized that alveolar type 2 (AT2) cells, as alveolar epithelial progenitors, will carry molecular alterations that compromise alveolar regeneration in COPD. Sorted AT2 cells from ex-smokers with and without COPD at different disease stages were subjected to RNA sequencing and whole-genome bisulfite sequencing to generate unbiased transcriptome and DNA methylation maps of alveolar progenitors in the lung. Our analysis revealed genome-wide epigenetic changes in AT2 cells during COPD that were associated with global gene expression changes. Integrative data analysis uncovered a strong anti-correlation between gene expression and promoter methylation, suggesting that dysregulation of COPD-associated pathways in AT2 cells may be regulated by DNA methylation. Interferon (IFN) signaling was the top-upregulated pathway associated with the concomitant loss of promoter DNA methylation. Epigenetic regulation of the IFN pathway was validated in both global and targeted DNA demethylation assays in A549 cells. Notably, targeted DNA demethylation of IRF9 triggered upregulation of IFN signaling, mimicking the effects observed in COPD AT2 cells in the profiling data. Our findings suggest that COPD-triggered epigenetic alterations in AT2 cells may impair internal regeneration programs in human lung parenchyma.

cell biology↗

bioRxiv2023

The long non-coding RNA LINC00941 modulates MTA2/NuRD occupancy to suppress premature human epidermal differentiation

Numerous long non-coding RNAs (lncRNAs) were shown to have functional impact on cellular processes such as human epidermal homeostasis. However, the mechanism of action for many lncRNAs remains unclear to date. Here, we report that lncRNA LINC00941 regulates keratinocyte differentiation on an epigenetic level through association with the NuRD complex, one of the major chromatin remodelers in cells. We find that LINC00941 interacts with NuRD-associated MTA2 in human primary keratinocytes. LINC00941 perturbation changes MTA2/NuRD occupancy at bivalent chromatin domains in close proximity to transcriptional regulator genes, including the EGR3 gene coding for a transcription factor regulating epidermal differentiation. Notably, LINC00941 depletion resulted in reduced NuRD occupancy at the EGR3 gene locus, increased EGR3 expression in human primary keratinocytes, as well as increased abundance of EGR3-regulated epidermal differentiation genes in cells and human organotypic epidermal tissue. Our results therefore indicate a role for LINC00941/NuRD in repressing EGR3 expression in non-differentiated keratinocytes, consequentially preventing premature differentiation of human epidermal tissue.

molecular biology↗

bioRxiv2023

The long non-coding RNA MALAT1 modulates NR4A1 expression through a downstream regulatory element in specific cancer-cell-types

Chromatin-associated long non-coding RNAs (lncRNAs) have been shown to define chromatin density, regulate gene expression, and are involved in the initiation and progression of various cancer types. Despite the wealth of studies describing transcriptome changes upon lncRNA modulation, little data is showing the direct effects of lncRNA on regulatory elements (REs) that drive gene expression. Here we explored the molecular mechanism of the chromatin-interacting lncRNA, MALAT1, through RNA- and ATAC-seq, using HeLa cells as a model system. Time-resolved MALAT1 knock-down assays revealed its direct regulation of a limited number of protein-coding genes. Loss of MALAT1 resulted in a substantial loss of chromatin accessibility downstream of the NR4A1 gene, associated with its down-regulation. CRISPR-i assays revealed that this region corresponds to a new downstream RE. Next, using TCGA data, we identified a direct correlation between the expression of NR4A1 and the accessibility of the downstream RE in breast cancer. The molecular mechanism was validated on estrogen receptor (ER) positive breast cancer cells (MCF7) and Pancreatic Duct Epithelioid Carcinoma (PANC1) cells, not showing this effect according to TCGA data. Indeed, MALAT1 regulates the expression of NR4A1 in a cell type-specific manner by changing the accessibility of the downstream RE. MALAT1 exhibits a molecular mechanism that fine-tunes the expression of cancer drivers, like NR4A1, in ER-positive breast cancer cells, but not in other cell types.

cell biology↗

bioRxiv2022

Optimized MNase-seq pipeline reveals a novel gene regulation via differential nucleosome stability

Micrococcal nuclease sequencing (MNase-seq) is the state-of-the-art method for determining chromatin structure and nucleosome positioning. Data analysis is complex due to the AT-dependent sequence bias of the endonuclease, and the requirement for high sequencing depth. Here, we present the newly developed nucleosome-based MNase accessibility (nucMACC) pipeline unveiling the regulatory chromatin landscape by measuring nucleosome accessibility and stability. nucMACC represents the first systematic, and genome-wide approach for detecting unstable ("fragile") nucleosomes. We characterized the regulatory nucleosomal landscape in D. melanogaster and S. cerevisiae. Two functionally distinct sets of promoters were identified, one associated with an unstable nucleosome and the other being nucleosome depleted. Chromatin structure analysis shows that unstable nucleosomes present intermediate states of nucleosome remodeling, preparing inducible genes for transcriptional activation in response to stimuli or stress. The presence of unstable nucleosomes correlates with RNA polymerase II proximal pausing. The nucMACC pipeline offers unparalleled precision and depth in nucleosome research and is a valuable tool for future nucleosome studies. TeaserThe nucMACC pipeline quantifies the local and global functional alterations of chromatin structure.

bioinformatics↗

bioRxiv2022

HMGN5, an RNA or Nucleosome binding protein - potentially switching between the substrates to regulate gene expression

The packaging of DNA into chromatin and its compaction within cells renders the underlying DNA template un-accessible for processes like transcription, replication and repair. Active mechanisms as chromatin modifying activities or the association with non-coding RNAs can de-condense chromatin, rendering it accessible for the DNA dependent processes. High mobility group proteins (HMG) are small architectural chromatin proteins that were shown to contribute to the regulation of chromatin accessibility and condensation. Here we show that HMGN5, a member of the HMGN family that is capable to de-compact chromatin exhibits a novel RNA binding domain that overlaps with its nucleosome binding domain (NBD). HMGN5 binds exclusively to nucleosomes or RNA, suggesting that molecular function relies on switching between these two substrates. We show the specific binding of HMGN5 to regulatory regions and at the same time to bind the RNA of the genes it tends to activate. Furthermore, HMGN5 co-localizes and directly interacts with CTCF, suggesting a cooperative role of both proteins in organizing higher order structures of chromatin and active chromatin domains.

molecular biology↗

bioRxiv2022

High-resolution epigenetic profiling identifies novel regulators of COPD in human lung fibroblasts

Patients with chronic obstructive pulmonary disease (COPD) are still waiting for curative treatments. Considering the environmental cause of COPD (e.g., cigarette smoke) and disease phenotypes, including stem-cell senescence and impaired differentiation, we hypothesized that COPD will be associated with altered epigenetic signaling in lung cells. We generated genome-wide DNA methylation maps at single CpG resolution of primary human lung fibroblasts (HLFs) isolated from distal parenchyma of ex-smoker controls and COPD patients, with both mild and severe disease. The epigenetic landscape is markedly changed in lung fibroblasts across COPD stages, with DNA methylation changes occurring predominantly in regulatory regions, including promoters and enhancers. RNA sequencing of matched fibroblasts demonstrated dysregulation of genes involved in proliferation, DNA repair, and extracellular matrix organization. Notably, we identified epigenetic and transcriptional dysregulation already in mild COPD patients, providing unique insights into early disease. Integration of profiling data identified 110 candidate regulators of disease phenotypes, including epigenetic factors. Using phenotypic screens, we verified the regulator capacity of multiple candidates and linked them to repair processes in the human lung. Our study provides first integrative high-resolution epigenetic and transcriptomic maps of human lung fibroblasts across stages of COPD. We reveal novel transcriptomic and epigenetic signatures associated with COPD onset and progression and identify new candidate regulators involved in the pathogenesis of chronic respiratory diseases. The presence of various epigenetic factors among the candidates demonstrates that epigenetic regulation in COPD is an exciting research field that holds promise for novel therapeutic avenues for patients.

cell biology↗

bioRxiv2020

A pVII positioning code determines the dynamics of Adenoviral nucleoprotein structure and primes it for early gene activation

Within the virion, adenovirus DNA associates with the virus-encoded, protamine-like structural protein pVII. Whether this association is organized, and how genome packaging changes during infection and subsequent transcriptional activation is currently unknown. Here, we combined RNA-seq, MNase-seq, ChIP-seq and single genome imaging during early adenovirus infection to unveil the structure- and time-resolved dynamics of viral chromatin changes as well as their correlation with gene transcription. Our MNase mapping data indicates that the viral genome is arranged in precisely positioned nucleoprotein particles (Adenosomes), like nucleosomes. We identified 238 Adenosomes, being positioned by a DNA sequence code and protecting about 60 to 70bp of DNA. The incoming genome is more accessible at early gene loci that undergo additional chromatin de-condensation upon infection. Histone H3.3 containing nucleosomes specifically replace pVII at distinct genomic sites and at the transcription start sites of early genes. Acetylation of H3.3 is predominant at the transcription start sites, preceding transcriptional activation. Based on our results we propose a central role for the viral pVII nucleoprotein-architecture, which is required for the dynamic structural changes during early infection, including the regulation of nucleosome assembly prior to transcription initiation. Our study thus may aid the rational development of recombinant adenoviral vectors exhibiting sustained expression in gene therapy.

microbiology↗

bioRxiv2020

Versatile workflow for cell type resolved transcriptional and epigenetic profiles from cryopreserved human lung.

The complexity of the lung microenvironment together with changes in cellular composition during disease progression make it exceptionally hard to understand the molecular mechanisms leading to the development of chronic lung diseases. Although recent advances in cell type resolved and single-cell sequencing approaches hold great promise for studying complex diseases, their implementation greatly relies on local access to fresh tissue, as traditional methods to process and store tissue do not allow viable cell isolation. To overcome these hurdles, we developed a novel, versatile workflow that allows long-term storage of human lung tissue with high cell viability, permits thorough sample quality check before cell isolation, and is compatible with next generation sequencing-based profiling, including single-cell approaches. We demonstrate that cryopreservation is suitable for isolation of multiple cell types from different lung locations and is applicable to both healthy and diseased tissue, including COPD and tumor samples. Basal cells isolated from cryopreserved airways retain the ability to differentiate, indicating that cellular identity is not altered by cryopreservation. Importantly, using RNA sequencing (RNA-seq) and Illumina EPIC Array, we show that genome-wide gene expression and DNA methylation signatures are preserved upon cryopreservation, emphasizing the suitability of our workflow for -omics profiling of human lung cells. In addition, we obtained high-quality single-cell RNA sequencing data of cells isolated from cryopreserved human lung, demonstrating that cryopreservation empowers single-cell approaches. Overall, thanks to its simplicity, our cryopreservation workflow is well-suited for prospective tissue collection by academic collaborators and biobanks, opening worldwide access to human tissue.

cell biology↗

bioRxiv2018

Characterizing higher order structures of chromatin in human cells

Packaging of DNA into chromatin regulates DNA accessibility and, consequently, all DNA-dependent processes, such as transcription, recombination, repair, and replication. The nucleosome is the basic packaging unit of DNA forming arrays that are suggested, by biochemical studies, to fold hierarchically into ordered higher-order structures of chromatin. This defined organization of chromatin has been recently questioned using microscopy techniques, proposing a rather irregular structure. To gain more insight into the principles of chromatin organization, we applied an in situ differential MNase-seq strategy and analyzed in silico the results of complete and partial digestions of human chromatin. We investigated whether different levels of chromatin packaging exist in the cell. Thus, we assessed the accessibility of chromatin within distinct domains of kb to Mb genomic regions by utilizing statistical data analyses and computer modelling. We found no difference in the degree of compaction between domains of euchromatin and heterochromatin or between other sequence and epigenomic features of chromatin. Thus, our data suggests the absence of differentially compacted domains of higher-order structures of chromatin. Moreover, we identified only local structural changes, with individual hyper-accessible nucleosomes surrounding regulatory elements, such as enhancers and transcription start sites. The regulatory sites per se are occupied with structurally altered nucleosomes, exhibiting increased MNase sensitivity. Our findings provide biochemical evidence that supports an irregular model of large-scale chromatin organization.

genomics↗