The establishment of long-lasting immunity against pathogens is facilitated by the germinal center (GC) reaction, during which B cells increase their antibody affinity and differentiate into antibody-secreting cells (ASC) and memory cells. These events involve modifications in chromatin packaging that orchestrate the profound restructuring of gene expression networks that determine cell fate. While several chromatin remodelers were implicated in lymphocyte functions, less is known about SMARCA5. Here, using ribosomal pull-down for analyzing translated genes in GC B cells, coupled with functional experiments in mice, we identified SMARCA5 as a key chromatin remodeler in B cells. While the naive B cell compartment remained unaffected following conditional depletion of Smarca5, effective proliferation during B cell activation, immunoglobulin class switching, and as a result GC formation and ASC differentiation were impaired. Single-cell multiomic sequencing analyses revealed that SMARCA5 is crucial for facilitating the transcriptional modifications and genomic accessibility of genes that support B cell activation and differentiation. These findings offer novel insights into the functions of SMARCA5, which can be targeted in various human pathologies.
- MeSH
- adenosintrifosfatasy MeSH
- aktivace lymfocytů imunologie MeSH
- B-lymfocyty * metabolismus imunologie MeSH
- buněčná diferenciace * MeSH
- chromozomální proteiny, nehistonové * metabolismus genetika MeSH
- myši inbrední C57BL MeSH
- myši MeSH
- přesmyk imunoglobulinových tříd genetika MeSH
- restrukturace chromatinu * MeSH
- zárodečné centrum lymfatické uzliny * imunologie metabolismus MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- adenosintrifosfatasy MeSH
- chromozomální proteiny, nehistonové * MeSH
- Smarca5 protein, mouse MeSH Prohlížeč
Changes in the cellular redox balance that occur during plant responses to unfavourable environmental conditions significantly affect a myriad of redox-sensitive processes, including those that impact on the epigenetic state of the chromatin. Various epigenetic factors, like histone modifying enzymes, chromatin remodelers, and DNA methyltransferases can be targeted by oxidative posttranslational modifications. As their combined action affects the epigenetic regulation of gene expression, they form an integral part of plant responses to (a)biotic stress. Epigenetic changes triggered by unfavourable environmental conditions are intrinsically linked with primary metabolism that supplies intermediates and donors, such acetyl-CoA and S-adenosyl-methionine, that are critical for the epigenetic decoration of histones and DNA. Here, we review the recent advances in our understanding of redox regulation of chromatin remodelling, dynamics of epigenetic marks, and the interplay between epigenetic control of gene expression, redox signalling and primary metabolism within an (a)biotic stress context.
- Klíčová slova
- abiotic stress, epigenetics, redox signalling,
- MeSH
- epigeneze genetická * MeSH
- fyziologický stres MeSH
- oxidace-redukce * MeSH
- regulace genové exprese u rostlin MeSH
- restrukturace chromatinu * MeSH
- rostliny * metabolismus genetika MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
Several cancer core regulatory circuitries (CRCs) depend on the sustained generation of DNA accessibility by SWI/SNF chromatin remodelers. However, the window when SWI/SNF is acutely essential in these settings has not been identified. Here we used neuroblastoma (NB) cells to model and dissect the relationship between cell-cycle progression and SWI/SNF ATPase activity. We find that SWI/SNF inactivation impairs coordinated occupancy of non-pioneer CRC members at enhancers within 1 hour, rapidly breaking their autoregulation. By precisely timing inhibitor treatment following synchronization, we show that SWI/SNF is dispensable for survival in S and G2/M, but becomes acutely essential only during G1 phase. We furthermore developed a new approach to analyze the oscillating patterns of genome-wide DNA accessibility across the cell cycle, which revealed that SWI/SNF-dependent CRC binding sites are enriched at enhancers with peak accessibility during G1 phase, where they activate genes involved in cell-cycle progression. SWI/SNF inhibition strongly impairs G1-S transition and potentiates the ability of retinoids used clinically to induce cell-cycle exit. Similar cell-cycle effects in diverse SWI/SNF-addicted settings highlight G1-S transition as a common cause of SWI/SNF dependency. Our results illustrate that deeper knowledge of the temporal patterns of enhancer-related dependencies may aid the rational targeting of addicted cancers.
Cancer cells driven by runaway transcription factor networks frequently depend on the cellular machinery that promotes DNA accessibility. For this reason, recently developed small molecules that impair SWI/SNF (or BAF) chromatin remodeling activity have been under active evaluation as anti-cancer agents. However, exactly when SWI/SNF activity is essential in dependent cancers has remained unknown. By combining live-cell imaging and genome-wide profiling in neuroblastoma cells, Cermakova et al. discover that SWI/SNF activity is needed for survival only during G1 phase of the cell cycle. The authors reveal that in several cancer settings, dependency on SWI/SNF arises from the need to reactivate factors involved in G1-S transition. Because of this role, authors find that SWI/SNF inhibition potentiates cell-cycle exit by retinoic acid.
- MeSH
- buněčný cyklus MeSH
- chromatin genetika MeSH
- DNA MeSH
- G1 fáze * MeSH
- lidé MeSH
- nádory * MeSH
- regulační oblasti nukleových kyselin MeSH
- restrukturace chromatinu MeSH
- transkripční faktory * metabolismus MeSH
- zesilovače transkripce MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- chromatin MeSH
- DNA MeSH
- SWI-SNF-B chromatin-remodeling complex MeSH Prohlížeč
- transkripční faktory * MeSH
Chromatin remodeling complexes are required for many distinct nuclear processes such as transcription, DNA replication, and DNA repair. However, the contribution of these complexes to the development of complex tissues within an organism is poorly characterized. Imitation switch (ISWI) proteins are among the most evolutionarily conserved ATP-dependent chromatin remodeling factors and are represented by yeast Isw1/Isw2, and their vertebrate counterparts Snf2h (Smarca5) and Snf2l (Smarca1). In this study, we focused on the role of the Snf2h gene during the development of the mammalian retina. We show that Snf2h is expressed in both retinal progenitors and post-mitotic retinal cells. Using Snf2h conditional knockout mice (Snf2h cKO), we found that when Snf2h is deleted, the laminar structure of the adult retina is not retained, the overall thickness of the retina is significantly reduced compared with controls, and the outer nuclear layer (ONL) is completely missing. The depletion of Snf2h did not influence the ability of retinal progenitors to generate all the differentiated retinal cell types. Instead, the Snf2h function is critical for the proliferation of retinal progenitor cells. Cells lacking Snf2h have a defective S-phase, leading to the entire cell division process impairments. Although all retinal cell types appear to be specified in the absence of the Snf2h function, cell-cycle defects and concomitantly increased apoptosis in Snf2h cKO result in abnormal retina lamination, complete destruction of the photoreceptor layer, and consequently, a physiologically non-functional retina.
- Klíčová slova
- Smarca5, Snf2h, apoptosis, cell cycle, photoreceptors, retina,
- MeSH
- adenosintrifosfatasy * metabolismus MeSH
- buněčné jádro metabolismus MeSH
- chromatin * metabolismus MeSH
- chromozomální proteiny, nehistonové * metabolismus MeSH
- myši knockoutované MeSH
- myši MeSH
- proliferace buněk MeSH
- restrukturace chromatinu * MeSH
- retina MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Názvy látek
- adenosintrifosfatasy * MeSH
- chromatin * MeSH
- chromozomální proteiny, nehistonové * MeSH
- Smarca5 protein, mouse MeSH Prohlížeč
Previous studies have demonstrated an involvement of chromatin-remodelling SWI/SNF complexes in the development of prostate cancer, suggesting both tumor suppressor and oncogenic activities. SMARCD1/BAF60A, SMARCD2/BAF60B, and SMARCD3/BAF60C are mutually exclusive accessory subunits that confer functional specificity and are components of all known SWI/SNF subtypes. To assess the role of SWI/SNF in prostate tumorigenesis, we studied the functions and functional relations of the SMARCD family members. Performing RNA-seq in LnCAP cells grown in the presence or absence of dihydrotestosterone, we found that the SMARCD proteins are involved in the regulation of numerous hormone-dependent AR-driven genes. Moreover, we demonstrated that all SMARCD proteins can regulate AR-downstream targets in androgen-depleted cells, suggesting an involvement in the progression to castration-resistance. However, our approach also revealed a regulatory role for SMARCD proteins through antagonization of AR-signalling. We further demonstrated that the SMARCD proteins are involved in several important cellular processes such as the maintenance of cellular morphology and cytokinesis. Taken together, our findings suggest that the SMARCD proteins play an important, yet paradoxical, role in prostate carcinogenesis. Our approach also unmasked the complex interplay of paralogue SWI/SNF proteins that must be considered for the development of safe and efficient therapies targeting SWI/SNF.
- Klíčová slova
- SMARCD1/BAF60A, SMARCD2/BAF60B, SMARCD3/BAF60C, SWI/SNF complex, chromatin-remodeling, prostate cancer,
- MeSH
- androgenní receptory * genetika metabolismus MeSH
- chromozomální proteiny, nehistonové genetika metabolismus MeSH
- lidé MeSH
- nádory prostaty * genetika MeSH
- regulace genové exprese MeSH
- restrukturace chromatinu genetika MeSH
- signální transdukce MeSH
- transkripční faktory metabolismus MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- androgenní receptory * MeSH
- chromozomální proteiny, nehistonové MeSH
- SMARCD1 protein, human MeSH Prohlížeč
- transkripční faktory 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
This Special Issue highlights the advantages of using combined approaches to explore chromatin molecular complexes [...].
- MeSH
- chromatin * genetika MeSH
- genom * MeSH
- restrukturace chromatinu MeSH
- Publikační typ
- úvodníky MeSH
- Názvy látek
- chromatin * MeSH
Smarca5, an ATPase of the ISWI class of chromatin remodelers, is a key regulator of chromatin structure, cell cycle and DNA repair. Smarca5 is deregulated in leukemia and breast, lung and gastric cancers. However, its role in oncogenesis is not well understood. Chromatin remodelers often play dosage-dependent roles in cancer. We therefore investigated the epigenomic and phenotypic impact of controlled stepwise attenuation of Smarca5 function in the context of primary cell transformation, a process relevant to tumor formation. Upon conditional single- or double-allele Smarca5 deletion, the cells underwent both accelerated growth arrest and senescence entry and displayed gradually increased sensitivity to genotoxic insults. These phenotypic characteristics were explained by specific remodeling of the chromatin structure and the transcriptome in primary cells prior to the immortalization onset. These molecular programs implicated Smarca5 requirement in DNA damage repair, telomere maintenance, cell cycle progression and in restricting apoptosis and cellular senescence. Consistent with the molecular programs, we demonstrate for the first time that Smarca5-deficient primary cells exhibit dramatically decreased capacity to bypass senescence and immortalize, an indispensable step during cell transformation and cancer development. Thus, Smarca5 plays a crucial role in key homeostatic processes and sustains cancer-promoting molecular programs and cellular phenotypes.
- Klíčová slova
- ATAC-seq, MEF, RNA-seq, Smarca5, Snf2h, cell cycle, cell immortalization, homologous recombination, non-homologous end-joining, senescence,
- MeSH
- adenosintrifosfatasy metabolismus MeSH
- chromatin * MeSH
- nádory * MeSH
- oprava DNA MeSH
- poškození DNA MeSH
- restrukturace chromatinu MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- adenosintrifosfatasy MeSH
- chromatin * MeSH
Nuclear deubiquitinase BAP1 (BRCA1-associated protein 1) is a core component of multiprotein complexes that promote transcription by reversing the ubiquitination of histone 2A (H2A). BAP1 is a tumor suppressor whose germline loss-of-function variants predispose to cancer. To our knowledge, there are very rare examples of different germline variants in the same gene causing either a neurodevelopmental disorder (NDD) or a tumor predisposition syndrome. Here, we report a series of 11 de novo germline heterozygous missense BAP1 variants associated with a rare syndromic NDD. Functional analysis showed that most of the variants cannot rescue the consequences of BAP1 inactivation, suggesting a loss-of-function mechanism. In T cells isolated from two affected children, H2A deubiquitination was impaired. In matching peripheral blood mononuclear cells, histone H3 K27 acetylation ChIP-seq indicated that these BAP1 variants induced genome-wide chromatin state alterations, with enrichment for regulatory regions surrounding genes of the ubiquitin-proteasome system (UPS). Altogether, these results define a clinical syndrome caused by rare germline missense BAP1 variants that alter chromatin remodeling through abnormal histone ubiquitination and lead to transcriptional dysregulation of developmental genes.
- Klíčová slova
- BAP1, BRCA1, UPS, cancer, chromatin remodeling, deubiquitination, histone 2A, intellectual disability, neurodevelopment, tumor, ubiquitin, ubiquitin-proteasome system,
- MeSH
- chromatin chemie imunologie MeSH
- dítě MeSH
- faktor C1 hostitelské buňky genetika imunologie MeSH
- heterozygot MeSH
- histony genetika imunologie MeSH
- kojenec MeSH
- lidé MeSH
- missense mutace * MeSH
- mladiství MeSH
- mutace ztráty funkce * MeSH
- nádorové supresorové proteiny nedostatek genetika imunologie MeSH
- neurovývojové poruchy genetika imunologie patologie MeSH
- předškolní dítě MeSH
- proteasomový endopeptidasový komplex genetika imunologie MeSH
- protein BRCA1 genetika imunologie MeSH
- regulace genové exprese MeSH
- restrukturace chromatinu genetika imunologie MeSH
- rodina MeSH
- T-lymfocyty imunologie patologie MeSH
- thiolesterasa ubikvitinu nedostatek genetika imunologie MeSH
- ubikvitin genetika imunologie MeSH
- ubikvitinace MeSH
- ubikvitinligasy genetika imunologie MeSH
- zárodečné mutace * MeSH
- Check Tag
- dítě MeSH
- kojenec MeSH
- lidé MeSH
- mladiství MeSH
- mužské pohlaví MeSH
- předškolní dítě MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Názvy látek
- BAP1 protein, human MeSH Prohlížeč
- BARD1 protein, human MeSH Prohlížeč
- BRCA1 protein, human MeSH Prohlížeč
- chromatin MeSH
- faktor C1 hostitelské buňky MeSH
- HCFC1 protein, human MeSH Prohlížeč
- histony MeSH
- nádorové supresorové proteiny MeSH
- proteasomový endopeptidasový komplex MeSH
- protein BRCA1 MeSH
- thiolesterasa ubikvitinu MeSH
- ubikvitin MeSH
- ubikvitinligasy 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
