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Cell Reports May 2024CUX1 is a homeodomain-containing transcription factor that is essential for the development and differentiation of multiple tissues. CUX1 is recurrently mutated or...
CUX1 is a homeodomain-containing transcription factor that is essential for the development and differentiation of multiple tissues. CUX1 is recurrently mutated or deleted in cancer, particularly in myeloid malignancies. However, the mechanism by which CUX1 regulates gene expression and differentiation remains poorly understood, creating a barrier to understanding the tumor-suppressive functions of CUX1. Here, we demonstrate that CUX1 directs the BAF chromatin remodeling complex to DNA to increase chromatin accessibility in hematopoietic cells. CUX1 preferentially regulates lineage-specific enhancers, and CUX1 target genes are predictive of cell fate in vivo. These data indicate that CUX1 regulates hematopoietic lineage commitment and homeostasis via pioneer factor activity, and CUX1 deficiency disrupts these processes in stem and progenitor cells, facilitating transformation.
Topics: Humans; Homeodomain Proteins; Hematopoietic Stem Cells; Chromatin; Repressor Proteins; Transcription Factors; Animals; Mice; Nuclear Proteins; Cell Lineage; Chromatin Assembly and Disassembly; Cell Differentiation; DNA-Binding Proteins; Enhancer Elements, Genetic
PubMed: 38735044
DOI: 10.1016/j.celrep.2024.114227 -
Nature Genetics Jun 2024Chromatin modifications are linked with regulating patterns of gene expression, but their causal role and context-dependent impact on transcription remains unresolved....
Chromatin modifications are linked with regulating patterns of gene expression, but their causal role and context-dependent impact on transcription remains unresolved. Here we develop a modular epigenome editing platform that programs nine key chromatin modifications, or combinations thereof, to precise loci in living cells. We couple this with single-cell readouts to systematically quantitate the magnitude and heterogeneity of transcriptional responses elicited by each specific chromatin modification. Among these, we show that installing histone H3 lysine 4 trimethylation (H3K4me3) at promoters can causally instruct transcription by hierarchically remodeling the chromatin landscape. We further dissect how DNA sequence motifs influence the transcriptional impact of chromatin marks, identifying switch-like and attenuative effects within distinct cis contexts. Finally, we examine the interplay of combinatorial modifications, revealing that co-targeted H3K27 trimethylation (H3K27me3) and H2AK119 monoubiquitination (H2AK119ub) maximizes silencing penetrance across single cells. Our precision-perturbation strategy unveils the causal principles of how chromatin modification(s) influence transcription and dissects how quantitative responses are calibrated by contextual interactions.
Topics: Chromatin; Histones; Epigenome; Humans; Gene Editing; Epigenesis, Genetic; Promoter Regions, Genetic; Chromatin Assembly and Disassembly; Ubiquitination; Histone Code; Transcription, Genetic; Single-Cell Analysis
PubMed: 38724747
DOI: 10.1038/s41588-024-01706-w -
BioRxiv : the Preprint Server For... Apr 2024Acute inflammation, characterized by a rapid influx of neutrophils, is a protective response that can lead to chronic inflammatory diseases when left unresolved....
Acute inflammation, characterized by a rapid influx of neutrophils, is a protective response that can lead to chronic inflammatory diseases when left unresolved. Secretion of LTB -containing exosomes is required for effective neutrophil infiltration during inflammation. In this study, we show that neutrophils release nuclear DNA in a non-lytic, rapid, and repetitive manner, via a mechanism distinct from suicidal NET release and cell death. The packaging of nuclear DNA occurs in the lumen of nuclear envelope (NE)-derived multivesicular bodies (MVBs) that harbor the LTB synthesizing machinery and is mediated by the lamin B receptor (LBR) and chromatin decondensation. Disruption of secreted exosome-associated DNA (SEAD) in a model of sterile inflammation in mouse skin amplifies and prolongs the presence of neutrophils, impeding the onset of resolution. Together, these findings advance our understanding of neutrophil functions during inflammation and the physiological significance of NETs, with implications for novel treatments for inflammatory disorders.
PubMed: 38712240
DOI: 10.1101/2024.04.21.590456 -
BioRxiv : the Preprint Server For... Apr 2024ICP1, a lytic bacteriophage of , is parasitized by phage satellites, PLEs, which hijack ICP1 proteins for their own horizontal spread. PLEs' dependence on ICP1's DNA...
ICP1, a lytic bacteriophage of , is parasitized by phage satellites, PLEs, which hijack ICP1 proteins for their own horizontal spread. PLEs' dependence on ICP1's DNA replication machinery, and virion components results in inhibition of ICP1's lifecycle. PLEs' are expected to depend on ICP1 factors for genome packaging, but the mechanism(s) PLEs use to inhibit ICP1 genome packaging is currently unknown. Here, we identify and characterize Gpi, PLE's indiscriminate genome packaging inhibitor. Gpi binds to ICP1's large terminase (TerL), the packaging motor, and blocks genome packaging. To overcome Gpi's negative effect on TerL, a component PLE also requires, PLE uses two genome packaging specifiers, GpsA and GpsB, that specifically allow packaging of PLE genomes. Surprisingly, PLE also uses mimicry of ICP1's site as a backup strategy to ensure genome packaging. PLE's site mimicry, however, is only sufficient if PLE can inhibit ICP1 at other stages of its lifecycle, suggesting an advantage to maintaining Gpi, GpsA, and GpsB. Collectively, these results provide mechanistic insights into another stage of ICP1's lifecycle that is inhibited by PLE, which is currently the most inhibitory of the documented phage satellites. More broadly, Gpi represents the first satellite-encoded inhibitor of a phage TerL.
PubMed: 38712175
DOI: 10.1101/2024.04.22.590561 -
Biological Research May 2024Chromatin dynamics is deeply involved in processes that require access to DNA, such as transcriptional regulation. Among the factors involved in chromatin dynamics at...
BACKGROUND
Chromatin dynamics is deeply involved in processes that require access to DNA, such as transcriptional regulation. Among the factors involved in chromatin dynamics at gene regulatory regions are general regulatory factors (GRFs). These factors contribute to establishment and maintenance of nucleosome-depleted regions (NDRs). These regions are populated by nucleosomes through histone deposition and nucleosome sliding, the latter catalyzed by a number of ATP-dependent chromatin remodeling complexes, including ISW1a. It has been observed that GRFs can act as barriers against nucleosome sliding towards NDRs. However, the relative ability of the different GRFs to hinder sliding activity is currently unknown.
RESULTS
Considering this, we performed a comparative analysis for the main GRFs, with focus in their ability to modulate nucleosome sliding mediated by ISW1a. Among the GRFs tested in nucleosome remodeling assays, Rap1 was the only factor displaying the ability to hinder the activity of ISW1a. This effect requires location of the Rap1 cognate sequence on linker that becomes entry DNA in the nucleosome remodeling process. In addition, Rap1 was able to hinder nucleosome assembly in octamer transfer assays. Concurrently, Rap1 displayed the highest affinity for and longest dwell time from its target sequence, compared to the other GRFs tested. Consistently, through bioinformatics analyses of publicly available genome-wide data, we found that nucleosome occupancy and histone deposition in vivo are inversely correlated with the affinity of Rap1 for its target sequences in the genome.
CONCLUSIONS
Our findings point to DNA binding affinity, residence time and location at particular translational positions relative to the nucleosome core as the key features of GRFs underlying their roles played in nucleosome sliding and assembly.
Topics: Nucleosomes; Chromatin Assembly and Disassembly; Adenosine Triphosphatases; Saccharomyces cerevisiae Proteins; Transcription Factors; Saccharomyces cerevisiae; Histones; DNA-Binding Proteins
PubMed: 38704609
DOI: 10.1186/s40659-024-00500-6 -
Current Opinion in Genetics &... Jun 2024Polycomb-associated chromatin and pericentromeric heterochromatin form genomic domains important for the epigenetic regulation of gene expression. Both Polycomb... (Review)
Review
Polycomb-associated chromatin and pericentromeric heterochromatin form genomic domains important for the epigenetic regulation of gene expression. Both Polycomb complexes and heterochromatin factors rely on 'read and write' mechanisms, which, on their own, are not sufficient to explain the formation and the maintenance of these epigenetic domains. Microscopy has revealed that they form specific nuclear compartments separated from the rest of the genome. Recently, some subunits of these molecular machineries have been shown to undergo phase separation, both in vitro and in vivo, suggesting that phase separation might play important roles in the formation and the function of these two kinds of repressive chromatin. In this review, we will present the recent advances in the field of facultative and constitutive heterochromatin formation and maintenance through phase separation.
Topics: Heterochromatin; Epigenesis, Genetic; Polycomb-Group Proteins; Chromatin; Animals; Humans; Histones; Chromatin Assembly and Disassembly; Phase Separation
PubMed: 38701672
DOI: 10.1016/j.gde.2024.102201 -
Cell Reports May 2024During cell fate transitions, cells remodel their transcriptome, chromatin, and epigenome; however, it has been difficult to determine the temporal dynamics and...
During cell fate transitions, cells remodel their transcriptome, chromatin, and epigenome; however, it has been difficult to determine the temporal dynamics and cause-effect relationship between these changes at the single-cell level. Here, we employ the heterokaryon-mediated reprogramming system as a single-cell model to dissect key temporal events during early stages of pluripotency conversion using super-resolution imaging. We reveal that, following heterokaryon formation, the somatic nucleus undergoes global chromatin decompaction and removal of repressive histone modifications H3K9me3 and H3K27me3 without acquisition of active modifications H3K4me3 and H3K9ac. The pluripotency gene OCT4 (POU5F1) shows nascent and mature RNA transcription within the first 24 h after cell fusion without requiring an initial open chromatin configuration at its locus. NANOG, conversely, has significant nascent RNA transcription only at 48 h after cell fusion but, strikingly, exhibits genomic reopening early on. These findings suggest that the temporal relationship between chromatin compaction and gene activation during cellular reprogramming is gene context dependent.
Topics: Humans; Cellular Reprogramming; Chromatin Assembly and Disassembly; Histones; Single-Cell Analysis; Transcriptional Activation; Octamer Transcription Factor-3; Chromatin; Nanog Homeobox Protein; Induced Pluripotent Stem Cells
PubMed: 38700983
DOI: 10.1016/j.celrep.2024.114170 -
Open Biology May 2024The nucleolus is the most prominent liquid droplet-like membrane-less organelle in mammalian cells. Unlike the nucleolus in terminally differentiated somatic cells,...
The nucleolus is the most prominent liquid droplet-like membrane-less organelle in mammalian cells. Unlike the nucleolus in terminally differentiated somatic cells, those in totipotent cells, such as murine zygotes or two-cell embryos, have a unique nucleolar structure known as nucleolus precursor bodies (NPBs). Previously, it was widely accepted that NPBs in zygotes are simply passive repositories of materials that will be gradually used to construct a fully functional nucleolus after zygotic genome activation (ZGA). However, recent research studies have challenged this simplistic view and demonstrated that functions of the NPBs go beyond ribosome biogenesis. In this review, we provide a snapshot of the functions of NPBs in zygotes and early two-cell embryos in mice. We propose that these membrane-less organelles function as a regulatory hub for chromatin organization. On the one hand, NPBs provide the structural platform for centric and pericentric chromatin remodelling. On the other hand, the dynamic changes in nucleolar structure control the release of the pioneer factors (i.e. double homeobox (Dux)). It appears that during transition from totipotency to pluripotency, decline of totipotency and initiation of fully functional nucleolus formation are not independent events but are interconnected. Consequently, it is reasonable to hypothesize that dissecting more unknown functions of NPBs may shed more light on the enigmas of early embryonic development and may ultimately provide novel approaches to improve reprogramming efficiency.
Topics: Animals; Humans; Mice; Cell Nucleolus; Chromatin; Chromatin Assembly and Disassembly; Embryonic Development; Gene Expression Regulation, Developmental; Zygote
PubMed: 38689555
DOI: 10.1098/rsob.230358 -
Nucleic Acids Research Jun 2024Senescent cells can influence the function of tissues in which they reside, and their propensity for disease. A portion of adult human pancreatic beta cells express the...
Senescent cells can influence the function of tissues in which they reside, and their propensity for disease. A portion of adult human pancreatic beta cells express the senescence marker p16, yet it is unclear whether they are in a senescent state, and how this affects insulin secretion. We analyzed single-cell transcriptome datasets of adult human beta cells, and found that p16-positive cells express senescence gene signatures, as well as elevated levels of beta-cell maturation genes, consistent with enhanced functionality. Senescent human beta-like cells in culture undergo chromatin reorganization that leads to activation of enhancers regulating functional maturation genes and acquisition of glucose-stimulated insulin secretion capacity. Strikingly, Interferon-stimulated genes are elevated in senescent human beta cells, but genes encoding senescence-associated secretory phenotype (SASP) cytokines are not. Senescent beta cells in culture and in human tissue show elevated levels of cytoplasmic DNA, contributing to their increased interferon responsiveness. Human beta-cell senescence thus involves chromatin-driven upregulation of a functional-maturation program, and increased responsiveness of interferon-stimulated genes, changes that could increase both insulin secretion and immune reactivity.
Topics: Humans; Insulin-Secreting Cells; Cellular Senescence; Chromatin Assembly and Disassembly; Interferons; Insulin Secretion; Insulin; Chromatin; Cyclin-Dependent Kinase Inhibitor p16; Cells, Cultured; Senescence-Associated Secretory Phenotype; Transcriptome; Single-Cell Analysis
PubMed: 38682582
DOI: 10.1093/nar/gkae313 -
Polymers Apr 2024The development of sustainable materials from the valorization of waste is a good alternative to reducing the negative environmental impact of plastic packaging. The...
Valorization of Cork Stoppers, Coffee-Grounds and Walnut Shells in the Development and Characterization of Pectin-Based Composite Films: Physical, Barrier, Antioxidant, Genotoxic, and Biodegradation Properties.
The development of sustainable materials from the valorization of waste is a good alternative to reducing the negative environmental impact of plastic packaging. The objectives of this study were to develop and characterize pectin-based composite films incorporated with cork or cork with either coffee grounds or walnut shells, as well as to test the films' genotoxicity, antioxidant properties, and biodegradation capacity in soil and seawater. The addition of cork, coffee grounds, or walnut shells modified the films' characteristics. The results showed that those films were thicker (0.487 ± 0.014 mm to 0.572 ± 0.014 mm), more opaque (around 100%), darker (L* = 25.30 ± 0.78 to 33.93 ± 0.84), and had a higher total phenolic content (3.17 ± 0.01 mg GA/g to 4.24 ± 0.02 mg GA/g). On the other hand, the films incorporated only with cork showed higher values of elongation at break (32.24 ± 1.88% to 36.30 ± 3.25%) but lower tensile strength (0.91 ± 0.19 MPa to 1.09 ± 0.08 MPa). All the films presented more heterogeneous and rougher microstructures than the pectin film. This study also revealed that the developed films do not contain DNA-reactive substances and that they are biodegradable in soil and seawater. These positive properties could subsequently make the developed films an interesting eco-friendly food packaging solution that contributes to the valorization of organic waste and by-products, thus promoting the circular economy and reducing the environmental impact of plastic materials.
PubMed: 38674972
DOI: 10.3390/polym16081053