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At least 19 recordsLinked to original sources
PubMed2025

Free energy spectroscopy reveals the mechanistic landscape of chromatin compaction.

Eukaryotic genomic DNA is repeatedly wrapped into nucleosome spools: the basic building block of chromatin. This organization regulates the physical accessibility of the genome to gene transcription, replication, and repair regulatory factors. Chromatin compaction is controlled by multivalent weak interactions, resulting in a complicated conformational landscape that remains challenging to characterize. This work reports a method for characterizing chromatin compaction, Free Energy Spectroscopy (FES), which is based on DNA nanotechnology and transmission electron microscopy. This method experimentally determines the chromatin compaction free energy landscape in terms of end-to-end distance and nucleosome stacking interactions. By deconvolving the free energy landscapes of partially and fully compact tetranucleosomes, FES revealed three separate mechanisms by which linker histones reshape the compaction energetics to condense chromatin. This study establishes FES as a method with the potential to help answer a broad range of mechanistic questions about genome and epigenome function.

DNA nanotechnology↗
PubMed1975

The influence of chromatin compactness on the stoichiometry of the Feulgen-Schiff procedure studied in model films. II. Investigations on films containing condensed or swollen chicken erythrocyte nuclei.

As models for different states of chromatin compactness, nuclei from chicken erythrocytes were isolated and either osmotically swollen or kept as condensed as possible. Both types of nuclei were then fixed and incorporated into polyacrylamide films. Hydrolysis with 5 N HCl and staining with Schiff's reagent of these model films were studied using several parameters. The phosphate content of the films was analyzed as a parameter for the depolymerization losses and the staining with Schiff's reagent as a parameter for the apurinic acid (APA) content. The loss of ultraviolet absorbance from the films and the accumulation of ultraviolet absorbing substances in the hydrolyzing acid were monitored as parameters for the progress of hydrolysis. Conversion of the generated aldehyde groups to APA-Schiff chromophore is shown to take place with the same stoichiometry for both types of nuclei as well as for DNA in model films. It is further shown that the nuclei- and DNA-films are suitable models for investigating the influence of chromatin compactness on the course of the Feulgen-Schiff reaction. For the most compact form of chromatin studied, a very high reduction in staining intensity of up to 40% could be demonstrated after certain normally applied hydrolysis times. This is due primarily to a decrease with a factor of 2.3 of the depurination rate constants of these models (from 0.030/min to 0.013/min). Therefore prolonged hydrolysis periods are required to obtain the same APA concentrations, but then depolymerization processes cause losses of nuclear material. The differences in depurination rates could be explained by a decrease in [H3O]+ in the neighborhood of the purine-sugar linkages, caused by the presence of fixed positive charges form the protein components of the chromatin. These findings may explain the cytophotometrically determined differences in chromophore yield of 10-20% found in the nuclei of cells with different states of compactness of their chromatin. The descending part of the Feulgen hydrolysis curve represents the depolymerization of APA and loss by diffusion of the reaction products. In the Appendix, cytophotometric data of cells have been analyzed to show that this part of the hydrolysis curve may be used to estimate the acid stability of chromatin complexes. The depurination and depolymerization rates found closely correspond with the data obtained from the model films.

Animals↗
PubMed2026

Enhanced chromatin compaction is associated with de novo expression of a nuclear microprotein, global loss of H3 acetylation and local transcriptional changes in retinal rod photoreceptors.

We have limited understanding of how aging alters gene expression and remodels cellular architecture in post-mitotic neurons. The inverted nuclear organization of mouse rod photoreceptors provides a unique model to gain mechanistic insights into age-associated decline in neuronal function. We have generated and integrated multi-omic datasets including 3D-genome topology, histone modifications, chromatin accessibility, DNA methylation and transcriptome of rod photoreceptors from young- and aged-mice. We show that aging drives global chromatin compaction, with regional alterations enriched at active chromatin. Epigenomic and transcriptional changes broadly correlate with chromatin dynamics as validated by high resolution microscopy. We uncover a megabase-sized genomic region with multi-level alterations, including de novo transcription of Gm7239, which encodes a functional microprotein carrying histone acetyltransferase-inhibitor domain. Overexpression of Gm7239 is associated with global loss of histone H3 acetylation, highlighting a potential new axis of genomic regulation in aging. Finally, we identify multiple significant local transcriptional alterations in non-annotated regions and genes associated with age-related macular degeneration. Our studies link age-related chromatin landscape changes with gene expression that may influence rod function and vulnerability to diseases.

Journal Article↗
PubMed2025

Differential Crosslinking and Contractile Motors Drive Nuclear Chromatin Compaction.

During interphase, a typical cell nucleus features spatial compartmentalization of transcriptionally active euchromatin and repressed heterochromatin domains. In conventional nuclear organization, euchromatin predominantly occupies the nuclear interior, while heterochromatin, which is approximately 50% more dense than euchromatin, is positioned near the nuclear periphery. Peripheral chromatin organization can be further modulated by the nuclear lamina, which is itself a deformable structure. While a number of biophysical mechanisms for compartmentalization within rigid nuclei have been explored, we study a chromatin model consisting of an active, crosslinked polymer tethered to a deformable, polymeric lamina shell. Contractile motors, the deformability of the shell, and the spatial distribution of crosslinks all play pivotal roles in this compartmentalization. We find that a radial crosslink density distribution, even with a small linear differential of higher crosslinking density at the edge of the nucleus, combined with contractile motor activity, drives genomic segregation, in agreement with experimental observations. This arises from contractile motors preferentially drawing crosslinks into their vicinity at the nuclear periphery, forming high-density domains that promote heterochromatin formation. We also find an increased stiffness of nuclear wrinkles given the preferential heterochromatin compaction below the lamina shell, which is consistent with instantaneous nuclear stiffening under applied nanoindentation. We conclude with the potential for experimental validation of our model predictions.

Journal Article↗
PubMed2025

Differential Crosslinking and Contractile Motors Drive Nuclear Chromatin Compaction.

During interphase, a typical cell nucleus features spatial compartmentalization of transcriptionally active euchromatin and repressed heterochromatin domains. In conventional nuclear organization, euchromatin predominantly occupies the nuclear interior, while heterochromatin, which is approximately 50% more dense than euchromatin, is positioned near the nuclear periphery. Peripheral chromatin organization can be further modulated by the nuclear lamina, which is itself a deformable structure. While a number of biophysical mechanisms for compartmentalization within rigid nuclei have been explored, we study a chromatin model consisting of an active, crosslinked polymer tethered to a deformable, polymeric lamina shell. Contractile motors, the deformability of the shell, and the spatial distribution of crosslinks all play pivotal roles in this compartmentalization. We find that a radial crosslink density distribution, even with a small linear differential of higher crosslinking density at the edge of the nucleus, combined with contractile motor activity, drives genomic segregation, in agreement with experimental observations. This arises from contractile motors preferentially drawing crosslinks into their vicinity at the nuclear periphery, forming high-density domains that promote heterochromatin formation. We also find an increased stiffness of nuclear wrinkles given the preferential heterochromatin compaction below the lamina shell, which is consistent with instantaneous nuclear stiffening under applied nanoindentation. We conclude with the potential for experimental validation of our model predictions.

Journal Article↗
PubMed1975

The influence of chromatin compactness on the stoichiometry of the Feulgen-Schiff procedure studied in model films. I. Theoretical kinetics and experiments with films containing isolated deoxyribonucleic acid.

Theoretical considerations on the expected kinetics of the course of the Feulgen-Schiff reaction show that the leveling off of the first part of the Feulgen hydrolysis curve can be explained by the gradual conversion of deoxyribonucleic acid (DNA) to apurinic acid (APA). In addition, depolymerization of DNA caused by the acid used for hydrolysis can account for the decline after a maximum is reached in this curve. With the aid of polyacrylamide model films containing DNA, a detailed study was made both of the process of purine liberation which results in the formation of APA and of the depolymerization processes which cause losses of stainable material. The liberation of purine bases was analyzed by ultraviolet absorbance measurements and by gel chromatography of the neutralized hydrolysing acid. APA concentration was monitored by following the loss of ultraviolet absorbance associated with the purine losses. The depolymerization process was followed by phosphorus determinations. The experimental results were found to be in accordance with the kinetics expected from the theoretical model.

Chemical Phenomena↗
PubMed2025

Molecular dynamics simulations reveal subtle consequences of H3K9 and H3K27 tri-methylation on chromatin constituents.

Epigenetic modifications of histone tails are key mechanisms of genome regulation. In particular, tri-methylation of lysines (K) 9 and K27 of the histone H3 tail is important for genome silencing. In this work, we explore, using all-atom molecular dynamics simulations, the effect of these two epigenetic marks on the structure and interactions of the H3 tail in several contexts: isolated tails, nucleosomes, chromatosomes, and stacked nucleosomes. Overall, we find that although the isolated tails do not show significant conformational changes upon methylation, a more flexible and extended H3 tail compared to the native tail results in the nucleosome systems, with K9 methylation effects more pronounced. This change could facilitate the interaction of the tail with protein readers like heterochromatin protein 1 or Polycomb group. We also observe that both methylations increase the interactions of the H3 tail with the linker DNA in the context of the chromatosome, producing a chromatosome with tighter linker DNA, which could favor chromatin compaction. For stacked nucleosomes mimicking i±2 zigzag interactions, methylation of either K9 or K27 reduces the interactions of one of the H3 tails with its parental nucleosome and increases its interactions with the nonparental nucleosome, which could also help compact the chromatin fiber. In the three nucleosome-containing systems, we observe an asymmetry between the two tails, especially in the chromatosome, where one tail extends to interact with the linker DNA. This asymmetry modulates the effect that methylation has on each tail. Thus, overall, methylations of K9 and K27 have a subtle but notable impact on the H3 tail structure and its interactions within the chromatin fiber. These results help explain how this epigenetic modification compacts chromatin fibers and promotes longer-range interactions; these changes also guide how to approximate these effects in coarse-grained chromatin models.

Histones↗
PubMed1979

Aberrations of holokinetic chromosomes and associated lethality after x-irradiation of meiotic stages in Tetranychus urticae Koch (acari, tetranychidae).

Chromosomes of the holokinetic organization type were irradiated with X-rays in various stages of meiosis in unfertilized eggs of Tetranychus urticae Koch. Visible cytological aberrations, lethality and sterility were investigated in subsequent generations. Chromosome fragments are the most frequently occurring light-microscopically visible chromosome aberrations; bridges are not formed. Contrary to expectations, the presence of fragments appears to be positively correlated with the occurrence of lethality; loss of fragments, mis-segregation and the measure of damage to the broken chromosome parts are involved. In contrast with monokinetic chromosomes the earliest lethality occurs only after about 10 divisions. The ratios between different embryonic lethality types (early vs. late) differ depending on the stage irradiated: in more compact chromatin, more serious damage (i.e. more early lethality syndromes) is induced than in less compact chromatin. In the progeny of the surviving males, neither translocations nor independent fragments are found; indirect evidence indicated the occasional presence of inversions. The presumptive inversions are induced more frequently in a chromatin-compact stage (metaphase I) than in a less compact one (telophase I).

Animals↗
PubMed1975

[Electron microscopic study of chromatin in maturing lymphocyte nuclei using ammoniacal silver].

By means of the ammoniacal silver reaction, cytochemical properties of the chromatin in white rat lymph node lymphocytes were investigated at different stages of their maturation. Electron dense granules of the reaction product are shown to be localized over the compact chromatin region. The number of granules increases as the amount of compact chromatin enlarges. A possible role of arginine histones in the process of chromatin condensation is suggested, this suggestion being based on the assumption that ammoniacal silver binds with active arginine groups of histones.

Animals↗
PubMed1977

Age-related changes in chromatin of liver cell nuclei of different ploidity.

A comparison of the Feulgen hydrolysis curves and the chromatin compactness of the liver cell nuclei of young and old rats was made. It was found that the rate of DNA depurination and chromatin compactness are higher in the liver cell nuclei of old rats, both in di-and tetraploidal cells. The effect of fixation upon the course of the hydrolysis curves is discussed.

Aging↗
PubMed1979

[Ultrastructure and antigens in differentiation of thymus lymphocytes in human embryogenesis].

Thymus lymphocytes of 7--8-week human embryos have nuclei of irregular form with 1--3 distinct nucleoli characterized by absence of compact chromatin or heterchromatin. The electron-dense cytoplasm of these cells contains polysomes and an insignificant number of mitochondria. No receptors to sheep red blood cells and T antigen are revealed on their surface. In 11--12-week human embryos one can observe a decrease in the size of thymus lymphocytes, appearance of heterochromatin in their nuclei and receptors to sheep red blood cells (79%), and T antigen (60%) on the cell surface. Subsequently the quantity of compact chromatin in thymus lymphoid cells increases, and the cells acquire definitive properties and structure.

Antigens, Surface↗
PubMed2025

MNase-seq to Identify Genome-Wide DNA-Protein Interactions.

Identification of the occupancy of transcription factors (TFs) and nucleosomes across the genome yields insights into the regulation of gene expression patterns. While several independent techniques can be performed and then analyzed in composite to reveal this chromatin landscape, the use of micrococcal nuclease (MNase) digestion can resolve the footprints of nearly all chromatin proteins simultaneously. The protocol below describes the use of MNase to identify chromatin footprints of both TFs and nucleosomes in two vastly different cell types, Mouse embryonic stem cells (mESCs) and sperm, with differing levels of chromatin compaction.

Animals↗
PubMed2025

Epigenetic Histone β-Hydroxybutyrylation Contributes to Renoprotection by β-Hydroxybutyrate in the Dahl Rat.

BACKGROUND: Previously, we demonstrated that the ketone body, β-hydroxybutyrate, is a potent antihypertensive and reno-protective metabolite in Dahl Salt-Sensitive rats. However, the mechanism by which β-hydroxybutyrate confers these beneficial effects is understudied. Here we focused on determining whether the reno-protective effect of β-hydroxybutyrate is due to its known ability to epigenetically remodel chromatin via histone β-hydroxybutyrylation. METHODS: We used the same animal protocol previously used for the discovery of the reno-protective effect of β-hydroxybutyrate. Briefly, postweaning, male and female Dahl Salt-Sensitive rats were split into 2 groups and supplemented with or without 1,3-butanediol for 6 weeks. At euthanasia, circulating β-hydroxybutyrate was quantitated. Renal homogenates were examined for histone 3 lysine 9 β-hydroxybutyrylation, chromatin occupancy, transcriptomic and proteomic profiles with validations. RESULTS: Rats supplemented with 1,3-butanediol had higher circulating β-hydroxybutyrate, renal histone β-hydroxybutyrylation, and significant remodeling of chromatin. Notably, regions of the genome associated with lipid catabolism were predominantly in an open chromatin configuration, leading to active transcription and translation. The most highly upregulated gene actively transcribed and translated was Hmgcs2 (3-hydroxy-3-methylglutaryl CoA synthase 2), a gene responsible for the biosynthesis of β-hydroxybutyrate in mitochondria. In contrast, regions with more compact chromatin structures contained immune function genes, Ptprc (protein tyrosine phosphatase receptor type C) and Lcp1 (lymphocyte cytosolic protein 1), which were suppressed. CONCLUSIONS: These results reveal that renal epigenetic histone β-hydroxybutyrylation is a novel mechanism by which transcriptional regulation of both energy metabolism and immune function occur concomitantly and contribute to renoprotection in the hypertensive Dahl rat.

Animals↗
PubMed2025

Ketone body mediated histone β-hydroxybutyrylation is reno-protective.

Starvation, intermittent fasting and exercise, all of which are recommended lifestyle modifiers share a common metabolic signature, ketogenesis to generate the ketone bodies, predominantly β-hydroxybutyrate. β-hydroxybutyrate exerts beneficial effects across various contexts, preventing or mitigating disease. We hypothesized that these dynamic health benefits of β-hydroxybutyrate might stem from its ability to regulate genome architecture through chromatin remodeling via histone β-hydroxybutyrylation, thereby influencing the transcriptome. Focusing on the kidney, which is an end organ protected by β-hydroxybutyrate, we examined histone β-hydroxybutyrylation-mediated chromatin remodeling. Notably, regions of the genome associated with lipid catabolism were predominantly in an open chromatin configuration, leading to active transcription and translation. Significant β-hydroxybutyrylation was observed in the kidneys and the most highly upregulated gene actively transcribed and translated was 3-hydroxy-3-methyglutaryl CoA Synthase 2 (Hmgcs2), a gene responsible for the biosynthesis of β-hydroxybutyrate in mitochondria. In contrast, regions with more compact chromatin structures were enriched with genes related to immune function such as protein tyrosine phosphatase receptor type C (Ptprc) and lymphocyte cytosolic protein 1 (Lcp1), which exhibited reduced transcription and translation. These results reveal that renal epigenetic histone β-hydroxybutyrylation is a novel mechanism by which transcriptional regulation of both energy metabolism and immune function occur concomitantly to protect kidneys and lower hypertension.

Blood pressure↗
PubMed2025

Chromatin state dynamics of autosomes and the B chromosome during spermatogenesis in Pseudococcus viburni.

The mealybug Pseudococcus viburni is a plant-feeding insect with a non-Mendelian genetic system known as paternal genome elimination (PGE). In PGE, males eliminate their paternally inherited chromosomes during meiosis, transmitting only the maternal genome to the next generation. This involves genome-wide imprinting, where paternal chromosomes are heterochromatinised in embryogenesis and throughout adulthood. In this species, a non-essential B chromosome can escape paternal genome elimination, thereby enhancing its transmission rate to the next generation. Previous studies show that the B chromosome escapes elimination by changing its chromatin compaction during meiosis to resemble that of maternal chromosomes. Although the exact mechanism underlying this change is poorly understood. Here we investigated histone methylation and acetylation modifications, as well as the Heterochromatin Protein 1 (HP1), to characterise differences between maternal, paternal and B chromosomes during male meiosis of P. viburni. Maternal and paternal chromosomes show distinct histone modification patterns, with marks associated with euchromatin present on maternal chromosomes and marks associated with heterochromatin present on paternal chromosomes. We then identified key histone modification changes that coincide with chromatin remodelling of the B chromosome, which allows it to segregate with maternal chromosomes. In addition, we showed that these chromatin modifications occur regardless of the parental origin of the B chromosome. Overall, our findings support the role of histone modifications for proper chromosome segregation during meiosis in mealybugs and provide insight into the mechanisms by which the B chromosome exploits PGE for its preferential transmission.

Animals↗
PubMed2026

Bovine Colostrum-Derived Extracellular Vesicles Impair Cancer Cell Proliferation Through Transcriptional Dysregulation.

Milk-derived extracellular vesicles (EVs) are a promising source of molecules with therapeutic potential. Bovine colostrum is particularly enriched in EVs, which carry cargo of proteins involved in immune regulation, development and cellular signalling. Some studies have explored their role as bioactive anti-cancer agents, however, their mechanistic effects remain underexplored. Here, we show that colostrum-derived EVs (Col-EVs) exert anti-proliferative effects in gastrointestinal cancer models, including cell lines and patient-derived organoids, which is independent of apoptosis induction. Using a multi-modal approach combining proteomics, imaging and functional assays, we demonstrate that Col-EVs induce a reversible growth-arrest state, characterized by widespread transcriptional and RNA-processing dysregulation, chromatin compaction, nuclear reorganization and cytoskeletal remodelling. Proteomic analyses reveal that Col-EV treatment disrupts key components of the transcriptional machinery and cell cycle regulatory pathways, effects that are reversible upon EV withdrawal and can be rescued pharmacologically using an EZH2 inhibitor. Col-EVs enhance the sensitivity of cancer cells as well to DNA-targeting chemotherapies such as 5-fluorouracil, indicating their potential as modulatory adjuvants rather than cytotoxic agents. Overall, our findings reveal that Col-EVs can reversibly suppress cancer cell proliferation by reprogramming transcriptional and nuclear architecture, offering a natural, biocompatible strategy for modulating tumour growth and sensitizing cancer cells to conventional therapies.

Extracellular Vesicles↗
PubMed1978

The organization, composition and matrix of hepatocyte nuclei exposed to alpha-amanitin.

Alterations in the structure and molecular composition of avian hepatocyte nuclei were compared following administration in vivo of lethal and sub-lethal doses of alpha-amanitin. This toxin interferes with extranucleolar transcription by direct inhibition of RNA polymerase II activity. the resultant effects include: extensive condensation of chromatin, displacement of nucleoplasmic contents and fragmentation of nucleoli. Changes in nuclear morphology were quantitated by stereometry and related to variations in RNA and residual, non-histone proteins (NHP). Gross alterations in nuclear structure and depletion of RNA and NHP levels were of similar magnitude with both doses of amanitin. The effects were fully reversible, however, with a minimal dose but terminal with a lethal dose. DNA and histone protein levels remained unchanged at all stages. These results imply that the process of transciption may itself keep and/or maintain chromatin in a dispersed state, and that in the absence of transcription chromatin naturally condenses. Modification of nuclear proteins may be necessary only to maintain chromatin compacted permanently or for extended periods of time. A model of nuclear organization is proposed to incorporate these considerations and to identify the probable location of the nuclear matrix in situ.

Amanitins↗
PubMed1978

A study of an endogenous nucleolytic reaction and of the action micrococcal nuclease and DNAase I on a salt-soluble, compact form of chromatin.

The endogenous nucleolytic reaction occurring in rabbit thymus nuclear lysates has been studied at extended incubation times (up to 4 h). Production of nucleosomal polymers containing multiples of 205 base pairs of DNA was observed. The stability of the bands and the low release (1%) of acid-soluble nucleotides indicated there was only a small fraction of sensitive DNA between the subunits. The salt-soluble chromatin formed in the endogenous reaction at short incubation times (14--24 min) and purified over Sephadex G-200 has been treated with micrococcal nuclease and DNAase I. With micrococcal nuclease, nucleosomal polymers containing multiples of 201 base pairs of DNA were formed. Extensive digestion reaveled a core subunit containing 145 base pairs of DNA. With DNAase I only random degradation was observed and nucleosomal complexes were not produced.

Animals↗