Centromeres are critical for cell division, loading CENH3 or CENPA histone variant nucleosomes, directing kinetochore formation and allowing chromosome segregation1,2. Despite their conserved function, centromere size and structure are diverse across species. To understand this centromere paradox3,4, it is necessary to know how centromeric diversity is generated and whether it reflects ancient trans-species variation or, instead, rapid post-speciation divergence. To address these questions, we assembled 346 centromeres from 66 Arabidopsis thaliana and 2 Arabidopsis lyrata accessions, which exhibited a remarkable degree of intra- and inter-species diversity. A. thaliana centromere repeat arrays are embedded in linkage blocks, despite ongoing internal satellite turnover, consistent with roles for unidirectional gene conversion or unequal crossover between sister chromatids in sequence diversification. Additionally, centrophilic ATHILA transposons have recently invaded the satellite arrays. To counter ATHILA invasion, chromosome-specific bursts of satellite homogenization generate higher-order repeats and purge transposons, in line with cycles of repeat evolution. Centromeric sequence changes are even more extreme in comparison between A. thaliana and A. lyrata. Together, our findings identify rapid cycles of transposon invasion and purging through satellite homogenization, which drive centromere evolution and ultimately contribute to speciation.

• MeSH
• Arabidopsis * genetika   metabolismus   MeSH
• centromera * genetika   metabolismus   MeSH
• genová konverze MeSH
• histony genetika   metabolismus   MeSH
• molekulární evoluce * MeSH
• nukleozomy genetika   metabolismus   MeSH
• satelitní DNA * genetika   MeSH
• transpozibilní elementy DNA * genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• Cid protein, Drosophila MeSH Prohlížeč
• histony MeSH
• nukleozomy MeSH
• satelitní DNA * MeSH
• transpozibilní elementy DNA * MeSH

Male germ cells experience a drastic chromatin remodeling through the nucleo-histone to nucleo-protamine (NH-NP) transition necessary for proper sperm functionality. Post-translational modifications (PTMs) of H4 Lys5, such as acetylation (H4K5ac), play a crucial role in epigenetic control of nucleosome disassembly facilitating protamine incorporation into paternal DNA. It has been shown that butyrylation on the same residue (H4K5bu) participates in temporal regulation of NH-NP transition in mice, delaying the bromodomain testis specific protein (BRDT)-dependent nucleosome disassembly and potentially marking retained nucleosomes. However, no information was available so far on this modification in human sperm. Here, we report a dual behavior of H4K5bu and H4K5ac in human normal spermatogenesis, suggesting a specific role of H4K5bu during spermatid elongation, coexisting with H4K5ac although with different starting points. This pattern is stable under different testicular pathologies, suggesting a highly conserved function of these modifications. Despite a drastic decrease of both PTMs in condensed spermatids, they are retained in ejaculated sperm, with 30% of non-colocalizing nucleosome clusters, which could reflect differential paternal genome retention. Whereas no apparent effect of these PTMs was observed associated with sperm quality, their presence in mature sperm could entail a potential role in the zygote.

• Klíčová slova
• H4K5, acetylation, butyrylation, epigenetic regulation, sperm, sperm chromatin, spermatogenesis,
• MeSH
• acetylace MeSH
• chromatin * metabolismus   MeSH
• histony metabolismus   MeSH
• lidé MeSH
• myši MeSH
• nukleozomy * metabolismus   MeSH
• posttranslační úpravy proteinů MeSH
• protaminy metabolismus   MeSH
• restrukturace chromatinu MeSH
• sperma metabolismus   MeSH
• spermatidy metabolismus   MeSH
• spermatogeneze fyziologie   MeSH
• spermie metabolismus   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• mužské pohlaví MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• chromatin * MeSH
• histony MeSH
• nukleozomy * MeSH
• protaminy MeSH

Transcription elongation factor Spt6 associates with RNA polymerase II (Pol II) and acts as a histone chaperone, which promotes the reassembly of nucleosomes following the passage of Pol II. The precise mechanism of nucleosome reassembly mediated by Spt6 remains unclear. In this study, we used a hybrid approach combining cryo-electron microscopy and small-angle X-ray scattering to visualize the architecture of Spt6 from Saccharomyces cerevisiae. The reconstructed overall architecture of Spt6 reveals not only the core of Spt6, but also its flexible N- and C-termini, which are critical for Spt6's function. We found that the acidic N-terminal region of Spt6 prevents the binding of Spt6 not only to the Pol II CTD and Pol II CTD-linker, but also to pre-formed intact nucleosomes and nucleosomal DNA. The N-terminal region of Spt6 self-associates with the tSH2 domain and the core of Spt6 and thus controls binding to Pol II and nucleosomes. Furthermore, we found that Spt6 promotes the assembly of nucleosomes in vitro. These data indicate that the cooperation between the intrinsically disordered and structured regions of Spt6 regulates nucleosome and Pol II CTD binding, and also nucleosome assembly.

• MeSH
• elektronová kryomikroskopie MeSH
• genetická transkripce MeSH
• histonové chaperony genetika   metabolismus   MeSH
• nukleozomy * genetika   metabolismus   MeSH
• RNA-polymerasa II metabolismus   MeSH
• Saccharomyces cerevisiae - proteiny * metabolismus   MeSH
• Saccharomyces cerevisiae genetika   metabolismus   MeSH
• transkripční elongační faktory metabolismus   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• histonové chaperony MeSH
• nukleozomy * MeSH
• RNA-polymerasa II MeSH
• Saccharomyces cerevisiae - proteiny * MeSH
• SPT6 protein, S cerevisiae MeSH Prohlížeč
• transkripční elongační faktory MeSH

Telomerase, an essential enzyme that maintains chromosome ends, is important for genome integrity and organism development. Various hypotheses have been proposed in human, ciliate and yeast systems to explain the coordination of telomerase holoenzyme assembly and the timing of telomerase performance at telomeres during DNA replication or repair. However, a general model is still unclear, especially pathways connecting telomerase with proposed non-telomeric functions. To strengthen our understanding of telomerase function during its intracellular life, we report on interactions of several groups of proteins with the Arabidopsis telomerase protein subunit (AtTERT) and/or a component of telomerase holoenzyme, POT1a protein. Among these are the nucleosome assembly proteins (NAP) and the minichromosome maintenance (MCM) system, which reveal new insights into the telomerase interaction network with links to telomere chromatin assembly and replication. A targeted investigation of 176 candidate proteins demonstrated numerous interactions with nucleolar, transport and ribosomal proteins, as well as molecular chaperones, shedding light on interactions during telomerase biogenesis. We further identified protein domains responsible for binding and analyzed the subcellular localization of these interactions. Moreover, additional interaction networks of NAP proteins and the DOMINO1 protein were identified. Our data support an image of functional telomerase contacts with multiprotein complexes including chromatin remodeling and cell differentiation pathways.

• Klíčová slova
• Arabidopsis, chromatin, folding, mitochondria, protein–protein interaction, replication, telomerase, transport,
• MeSH
• Arabidopsis metabolismus   MeSH
• genetická transkripce MeSH
• Golgiho aparát metabolismus   MeSH
• homeostáza telomer MeSH
• mapy interakcí proteinů MeSH
• mitochondrie metabolismus   MeSH
• multiproteinové komplexy metabolismus   MeSH
• nukleozomy metabolismus   MeSH
• peptidy metabolismus   MeSH
• posttranskripční úpravy RNA genetika   MeSH
• proteiny huseníčku chemie   metabolismus   MeSH
• proteiny vázající telomery metabolismus   MeSH
• regulace genové exprese u rostlin MeSH
• replikace DNA MeSH
• restrukturace chromatinu MeSH
• ribozomy metabolismus   MeSH
• telomerasa metabolismus   MeSH
• vazba proteinů MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• multiproteinové komplexy MeSH
• nukleozomy MeSH
• peptidy MeSH
• proteiny huseníčku MeSH
• proteiny vázající telomery MeSH
• telomerasa MeSH

During homologous recombination, Dbl2 protein is required for localisation of Fbh1, an F-box helicase that efficiently dismantles Rad51-DNA filaments. RNA-seq analysis of dbl2Δ transcriptome showed that the dbl2 deletion results in upregulation of more than 500 loci in Schizosaccharomyces pombe. Compared with the loci with no change in expression, the misregulated loci in dbl2Δ are closer to long terminal and long tandem repeats. Furthermore, the misregulated loci overlap with antisense transcripts, retrotransposons, meiotic genes and genes located in subtelomeric regions. A comparison of the expression profiles revealed that Dbl2 represses the same type of genes as the HIRA histone chaperone complex. Although dbl2 deletion does not alleviate centromeric or telomeric silencing, it suppresses the silencing defect at the outer centromere caused by deletion of hip1 and slm9 genes encoding subunits of the HIRA complex. Moreover, our analyses revealed that cells lacking dbl2 show a slight increase of nucleosomes at transcription start sites and increased levels of methylated histone H3 (H3K9me2) at centromeres, subtelomeres, rDNA regions and long terminal repeats. Finally, we show that other proteins involved in homologous recombination, such as Fbh1, Rad51, Mus81 and Rad54, participate in the same gene repression pathway.

• MeSH
• centromera MeSH
• histonový kód MeSH
• homologní rekombinace * MeSH
• nukleozomy metabolismus   MeSH
• proteiny buněčného cyklu antagonisté a inhibitory   metabolismus   MeSH
• regulace genové exprese u hub * MeSH
• represorové proteiny fyziologie   MeSH
• Schizosaccharomyces pombe - proteiny antagonisté a inhibitory   metabolismus   fyziologie   MeSH
• Schizosaccharomyces genetika   MeSH
• transkripční faktory antagonisté a inhibitory   metabolismus   MeSH
• umlčování genů * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• Dbl2 protein, S pombe MeSH Prohlížeč
• hip1 protein, S pombe MeSH Prohlížeč
• nukleozomy MeSH
• proteiny buněčného cyklu MeSH
• represorové proteiny MeSH
• Schizosaccharomyces pombe - proteiny MeSH
• Slm9 protein, S pombe MeSH Prohlížeč
• transkripční faktory MeSH

OBJECTIVE: While circulating nucleosome levels are high in obese mouse models, it is unknown where these nucleosomes originate from and whether they are a marker of cardio-metabolic health in humans. Here, we aimed to determine whether an association exists between circulating nucleosomes and the risk of developing obesity, metabolic syndrome (MetS) and/or a dysfunctional cardiovascular performance. METHODS: We randomly selected 120 participants of the Kardiovize Brno 2030 study across three BMI strata: BMI 18-25, 25-30, and > 30. We assessed the association between circulating nucleosome levels and the risk of obesity, MetS, and poor cardiovascular health. We then cultured human neutrophils, adipocytes, and hepatoma cells to study nucleosome origins in a fat-rich environment. RESULTS: Circulating nucleosome levels positively correlated with BMI (R = 0.602, p < 0.05), fatty liver index (R = 0.622, p < 0.05), left ventricular mass (R = 0.457, p < 0.05), and associated with MetS (p < 0.001) and poor cardiovascular health (p < 0.001). Incubating neutrophils with 1-10 μM free fatty acids triggered nucleosome production without concomitant cell death. Nucleosomes were not produced during pre-adipocyte differentiation or upon incubation of hepatic cells with palmitic acid. CONCLUSIONS: Neutrophils are a bona fide source of circulating nucleosomes in an obesogenic environment and in overweight/obese patients. High nucleosome levels are associated with MetS and cardiovascular performance, and might represent novel candidate biomarkers for cardio-metabolic health.

• Klíčová slova
• Cardiovascular disease, Epigenetics, Liquid biopsy, Metabolic health, Nucleosome,
• MeSH
• buňky Hep G2 MeSH
• dospělí MeSH
• index tělesné hmotnosti MeSH
• kardiovaskulární nemoci etiologie   MeSH
• kultivované buňky MeSH
• lidé středního věku MeSH
• lidé MeSH
• metabolický syndrom krev   komplikace   MeSH
• nadváha krev   komplikace   metabolismus   MeSH
• neutrofily cytologie   metabolismus   MeSH
• nukleozomy metabolismus   MeSH
• obezita krev   komplikace   metabolismus   MeSH
• senioři MeSH
• tukové buňky cytologie   metabolismus   MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• nukleozomy MeSH

Chromatin adopts a diversity of regular and irregular fiber structures in vitro and in vivo. However, how an array of nucleosomes folds into and switches between different fiber conformations is poorly understood. We report the 9.7 Å resolution crystal structure of a 6-nucleosome array bound to linker histone H1 determined under ionic conditions that favor incomplete chromatin condensation. The structure reveals a flat two-start helix with uniform nucleosomal stacking interfaces and a nucleosome packing density that is only half that of a twisted 30-nm fiber. Hydroxyl radical footprinting indicates that H1 binds the array in an on-dyad configuration resembling that observed for mononucleosomes. Biophysical, cryo-EM, and crosslinking data validate the crystal structure and reveal that a minor change in ionic environment shifts the conformational landscape to a more compact, twisted form. These findings provide insights into the structural plasticity of chromatin and suggest a possible assembly pathway for a 30-nm fiber.

• Klíčová slova
• 30-nm fiber, chromatin, cryo-EM, crystallography, histone H1, linker histone, nucleosome array,
• MeSH
• DNA chemie   genetika   metabolismus   MeSH
• elektronová kryomikroskopie MeSH
• Escherichia coli genetika   metabolismus   MeSH
• exprese genu MeSH
• genetické vektory chemie   metabolismus   MeSH
• histony chemie   genetika   metabolismus   MeSH
• hydroxylový radikál chemie   MeSH
• interakční proteinové domény a motivy MeSH
• klonování DNA MeSH
• konformace proteinů, alfa-helix MeSH
• konformace proteinů, beta-řetězec MeSH
• krystalografie rentgenová MeSH
• lidé MeSH
• molekulární modely MeSH
• multimerizace proteinu MeSH
• nukleozomy chemie   metabolismus   ultrastruktura   MeSH
• osmolární koncentrace MeSH
• protein 1 vytvářející nukleozómy chemie   genetika   metabolismus   MeSH
• rekombinantní proteiny chemie   genetika   metabolismus   MeSH
• vazba proteinů MeSH
• vazebná místa MeSH
• Xenopus laevis MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA MeSH
• histony MeSH
• hydroxylový radikál MeSH
• nukleozomy MeSH
• protein 1 vytvářející nukleozómy MeSH
• rekombinantní proteiny MeSH

Psoriasis is a multifactorial chronic inflammatory disease. We aimed to examine blood levels of nucleosomes derived from apoptotic cells, nucleosomal cell-free DNA (cfDNA) and immune-inflammatory biomarkers tumor necrosis factor-α (TNF-α), C-reactive protein (CRP), and interleukin 6 (IL-6) in psoriatic subjects. The study included 28 patients with exacerbated psoriasis vulgaris and 22 controls. The clinical and laboratory investigations included the determination of PASI score, BMI, cfDNA (by real-time PCR), nucleosomes, TNF-α, CRP, and IL-6. The range of PASI score in psoriatic patients was 10-34 (median 19). In the patients, we found significantly elevated levels (p < 0.001) of cfDNA, nucleosomes, TNF-α, CRP, and IL-6. We did not find any significant relationship between the analyzed parameters in either group (i.e., experimental or control). Elevated levels of the biomarkers of inflammation (TNF-α, CRP, and IL-6) and the indicators of apoptosis (cfDNA, circulating nucleosomes) proved that exacerbated psoriasis vulgaris is associated with a high degree of systemic inflammatory responses and dysregulated apoptotic pathways.

• Klíčová slova
• Apoptosis, Cell-free DNA, Inflammation, Nucleosomes, Psoriasis,
• MeSH
• apoptóza MeSH
• biologické markery krev   MeSH
• C-reaktivní protein analýza   MeSH
• dospělí MeSH
• interleukin-6 krev   MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladý dospělý MeSH
• nukleozomy genetika   metabolismus   MeSH
• progrese nemoci MeSH
• psoriáza krev   patologie   MeSH
• senioři MeSH
• stupeň závažnosti nemoci MeSH
• TNF-alfa krev   MeSH
• volné cirkulující nukleové kyseliny krev   MeSH
• zánět MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mladý dospělý MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• biologické markery MeSH
• C-reaktivní protein MeSH
• IL6 protein, human MeSH Prohlížeč
• interleukin-6 MeSH
• nukleozomy MeSH
• TNF-alfa MeSH
• volné cirkulující nukleové kyseliny MeSH

Chromatin Assembly Factor 1 (CAF-1) is a major nucleosome assembly complex which functions particularly during DNA replication and repair. Here we studied how the nucleosome landscape changes in a CAF-1 mutant in the model plant Arabidopsis thaliana. Globally, most nucleosomes were not affected by loss of CAF-1, indicating the presence of efficient alternative nucleosome assemblers. Nucleosomes that we found depleted in the CAF-1 mutant were enriched in non-transcribed regions, consistent with the notion that CAF-1-independent nucleosome assembly can compensate for loss of CAF-1 mainly in transcribed regions. Depleted nucleosomes were particularly enriched in proximal promoters, suggesting that CAF-1-independent nucleosome assembly mechanisms are often not efficient upstream of transcription start sites. Genes related to plant defense were particularly prone to lose nucleosomes in their promoters upon CAF-1 depletion. Reduced nucleosome occupancy at promoters of many defense-related genes is associated with a primed gene expression state that may considerably increase plant fitness by facilitating plant defense. Together, our results establish that the nucleosome landscape in Arabidopsis is surprisingly robust even in the absence of the dedicated nucleosome assembly machinery CAF-1 and that CAF-1-independent nucleosome assembly mechanisms are less efficient in particular genome regions.

• Klíčová slova
• Arabidopsis thaliana, CAF-1, GSE87421, chromatin, plant defense,
• MeSH
• Arabidopsis genetika   imunologie   metabolismus   MeSH
• chromatin genetika   MeSH
• faktor 1 pro uspořádání chromatinu genetika   metabolismus   MeSH
• imunita rostlin genetika   MeSH
• mutace MeSH
• nukleozomy genetika   metabolismus   MeSH
• oprava DNA genetika   MeSH
• počátek transkripce MeSH
• promotorové oblasti (genetika) genetika   MeSH
• replikace DNA genetika   MeSH
• restrukturace chromatinu genetika   MeSH
• sekvenční analýza DNA MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• chromatin MeSH
• faktor 1 pro uspořádání chromatinu MeSH
• nukleozomy MeSH

The incorporation of histone H3 with an acetylated lysine 56 (H3K56ac) into the nucleosome is important for chromatin remodeling and serves as a marker of new nucleosomes during DNA replication and repair in yeast. However, in human cells, the level of H3K56ac is greatly reduced, and its role during the cell cycle is controversial. Our aim was to determine the potential of H3K56ac to regulate cell cycle progression in different human cell lines. A significant increase in the number of H3K56ac foci, but not in H3K56ac protein levels, was observed during the S and G2 phases in cancer cell lines, but was not observed in embryonic stem cell lines. Despite this increase, the H3K56ac signal was not present in late replication chromatin, and H3K56ac protein levels did not decrease after the inhibition of DNA replication. H3K56ac was not tightly associated with the chromatin and was primarily localized to active chromatin regions. Our results support the role of H3K56ac in transcriptionally active chromatin areas but do not confirm H3K56ac as a marker of newly synthetized nucleosomes in DNA replication.

• Klíčová slova
• Cell cycle, Chromatin, DNA replication, H3K56ac, Mammalian cells, Nucleosome,
• MeSH
• buněčný cyklus genetika   fyziologie   MeSH
• chromatin metabolismus   MeSH
• G2 fáze genetika   MeSH
• histony metabolismus   MeSH
• HL-60 buňky MeSH
• hmotnostní spektrometrie MeSH
• lidé MeSH
• nukleozomy metabolismus   MeSH
• replikace DNA genetika   fyziologie   MeSH
• S fáze genetika   MeSH
• Saccharomyces cerevisiae - proteiny genetika   metabolismus   MeSH
• Saccharomyces cerevisiae genetika   metabolismus   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• chromatin MeSH
• histony MeSH
• nukleozomy MeSH
• Saccharomyces cerevisiae - proteiny MeSH