Chromatin remodelling complexes evict, slide, insert or replace nucleosomes, which represent an intrinsic barrier for access to DNA. These remodellers function in most aspects of genome utilization ...including transcription-factor binding, DNA replication and repair
. Although they are frequently mutated in cancer
, it remains largely unclear how the four mammalian remodeller families (SWI/SNF, ISWI, CHD and INO80) orchestrate the global organization of nucleosomes. Here we generated viable embryonic stem cells that lack SNF2H, the ATPase of ISWI complexes, enabling study of SNF2H cellular function, and contrast it to BRG1, the ATPase of SWI/SNF. Loss of SNF2H decreases nucleosomal phasing and increases linker lengths, providing in vivo evidence for an ISWI function in ruling nucleosomal spacing in mammals. Systematic analysis of transcription-factor binding reveals that these remodelling activities have specific effects on binding of different transcription factors. One group critically depends on BRG1 and contains the transcriptional repressor REST, whereas a non-overlapping set of transcription factors, including the insulator protein CTCF, relies on SNF2H. This selectivity readily explains why chromosomal folding and insulation of topologically associated domains requires SNF2H, but not BRG1. Collectively, this study shows that mammalian ISWI is critical for nucleosomal periodicity and nuclear organization and that transcription factors rely on specific remodelling pathways for correct genomic binding.
Abstract Spaceflight induces an immune response in astronauts. To better characterize this effect, we generated single-cell, multi-ome, cell-free RNA (cfRNA), biochemical, and hematology data for the ...SpaceX Inspiration4 (I4) mission crew. We found that 18 cytokines/chemokines related to inflammation, aging, and muscle homeostasis changed after spaceflight. In I4 single-cell multi-omics data, we identified a “spaceflight signature” of gene expression characterized by enrichment in oxidative phosphorylation, UV response, immune function, and TCF21 pathways. We confirmed the presence of this signature in independent datasets, including the NASA Twins Study, the I4 skin spatial transcriptomics, and 817 NASA GeneLab mouse transcriptomes. Finally, we observed that (1) T cells showed an up-regulation of FOXP3, (2) MHC class I genes exhibited long-term suppression, and (3) infection-related immune pathways were associated with microbiome shifts. In summary, this study reveals conserved and distinct immune disruptions occurring and details a roadmap for potential countermeasures to preserve astronaut health.
Around 2200 copies of genes encoding ribosomal RNA (rRNA) in pedunculate oak, Quercus robur, are organized into two rDNA loci, the major (NOR-1) and the minor (NOR-2) locus. We present the first ...cytogenetic evidence indicating that the NOR-1 represents the active nucleolar organizer responsible for rRNA synthesis, while the NOR-2 probably stays transcriptionally silent and does not participate in the formation of the nucleolus in Q. robur, which is a situation resembling the well-known phenomenon of nucleolar dominance. rDNA chromatin topology analyses in cycling root tip cells by light and electron microscopy revealed the minor locus to be highly condensed and located away from the nucleolus, while the major locus was consistently associated with the nucleolus and often exhibited different levels of condensation. In addition, silver precipitation was confined exclusively to the NOR-1 locus. Also, NOR-2 was highly methylated at cytosines and rDNA chromatin was marked with histone modifications characteristic for repressive state. After treatment of the root cells with the methylation inhibitor 5-aza-2'-deoxycytidine, we observed an increase in the total level of rRNA transcripts and a decrease in DNA methylation level at the NOR-2 locus. Also, NOR-2 sites relocalized with respect to the nuclear periphery/nucleolus, however, the relocation did not affect the contribution of this locus to nucleolar formation, nor did it affect rDNA chromatin decondensation, strongly suggesting that NOR-2 has lost the function of rRNA synthesis and nucleolar organization.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Glycans are essential regulators of protein function and are now in the focus of research in many physiological and pathophysiological processes. There are numerous modes of regulating their ...biosynthesis, including epigenetic mechanisms implicated in the expression of glyco-genes. Since N-glycans located at the cell membrane define intercellular communication as well as a cellular response to a given environment, we developed a method to preferentially analyze this fraction of glycans. The method is based on incorporation of living cells into polyacrylamide gels, partial denaturation of membrane proteins with 3 M urea and subsequent release of N-glycans with PNGase F followed by HPLC analysis. Using this newly developed method, we revealed multiple effects of epigenetic inhibitors Trichostatin A, sodium butyrate and zebularine on the composition of N-glycans in human cells. The induced changes were found to be reversible after inhibitor removal. Given that many epigenetic inhibitors are currently explored as a therapeutic strategy in treatment of cancer, wherein surface glycans play an important role, the presented work contributes to our understanding of their efficiency in altering the N-glycan profile of cancer cells in culture.
Celotno besedilo
Dostopno za:
DOBA, IZUM, KILJ, NUK, PILJ, PNG, SAZU, SIK, UILJ, UKNU, UL, UM, UPUK
Epigenetic changes play a role in all major events during tumorigenesis and changes in glycan structures are hallmarks of virtually every cancer. Also, proper N-glycosylation of membrane receptors is ...important in cell to cell and cell–environment communication. To study how modulation of epigenetic information can affect N-glycan expression we analyzed effects of epigenetic inhibitors on HeLa cell membrane N-glycome.
HeLa cells were treated with DNA methylation (zebularin and 5-aza-2-deoxycytidine) and histone deacetylation (trichostatin A and Na-butyrate) inhibitors. The effects on HeLa cell membrane N-glycome were analyzed by hydrophilic interaction high performance liquid chromatography (HILIC).
Each of the four epigenetic inhibitors induced changes in the expression of HeLa cell membrane N-glycans that were seen either as an increase or a decrease of individual glycans in the total N-glycome. Compared to DNA methylation inhibitors, histone deacetylation inhibitors showed more moderate changes, probably due to their higher gene target selectivity.
The results clearly show that composition of HeLa cell membrane N-glycome can be specifically altered by epigenetic inhibitors.
Glycans on the cell membrane are essential elements of tumor cell's metastatic potential and are also an entry point for nearly all pathogenic microorganisms. Since epigenetic inhibitors used in this work are registered drugs, our results provide a new line of research in the application of these drugs as anticancer and antimicrobial agents. This article is part of a Special Issue entitled Glycoproteomics.
► Aberrant epigenetic profiles and aberrant N-glycosylation are involved in tumorigenesis. ► HeLa cells were treated with DNA methylation and histone deacetylation inhibitors. ► Hydrophilic interaction high performance liquid chromatography revealed membrane N-glycome. ► Epigenetic inhibitors either up- or down-regulated individual N-glycan structures. ► Applied epigenetic inhibitors are efficient modulators of the cell membrane N-glycome.
Loss-of-function mutations in KMT2D are a striking feature of germinal center (GC) lymphomas, resulting in decreased histone 3 lysine 4 (H3K4) methylation and altered gene expression. We hypothesized ...that inhibition of the KDM5 family, which demethylates H3K4me3/me2, would reestablish H3K4 methylation and restore the expression of genes repressed on loss of KMT2D. KDM5 inhibition increased H3K4me3 levels and caused an antiproliferative response in vitro, which was markedly greater in both endogenous and gene-edited KMT2D mutant diffuse large B-cell lymphoma cell lines, whereas tumor growth was inhibited in KMT2D mutant xenografts in vivo. KDM5 inhibition reactivated both KMT2D-dependent and -independent genes, resulting in diminished B-cell signaling and altered expression of B-cell lymphoma 2 (BCL2) family members, including BCL2 itself. KDM5 inhibition may offer an effective therapeutic strategy for ameliorating KMT2D loss-of-function mutations in GC lymphomas.
•KDM5 inhibition reverts the effects of KMT2D mutations by increasing levels of H3K4me3 and restoring expression of KMT2D-regulated genes.
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Mutations in the SWI/SNF chromatin remodeling complex BAF are a recurring feature in many cancers, with a high prevalence in follicular lymphoma (FL; >19%) and diffuse large B-cell lymphoma (DLBCL; ...>34%). Despite this, the mechanism that links mutations in ARID1A, most frequently mutated BAF subunit, to the development of lymphoma is still not understood. To this aim, we crossed Arid1a-floxed mice with Cγ1-Cre mice to yield offspring with a conditional (cKO) Arid1a deletion in germinal center (GC) B cells, FL and DLBCL cell-of-origin. We immunized WT/WT ( Arid1a+/+; Cγ1Cre/+) and cKO/WT ( Arid1a+/-; Cγ1Cre/+) mice with sheep red blood cells and analyzed 10 days later at the peak of the GC reaction. Upon Arid1a deletion, we found a decrease in the total number of GC B cells relative to total B cells (WT/WT vs. cKO/WT; p<0.001). However, we observed skewing of GC polarity manifesting as increased proportions of proliferating centroblasts (CB) vs. centrocytes (CC) (WT/WT vs. cKO/WT; p=0.004). These observations imply a substantial dysfunction at the CC stage, which could account for the overall reduced number of GC B-cells. To investigate this, we performed a detailed molecular characterization of these cells. We performed the ATAC-seq assay on sorted CB and CC from our mouse model and observed an extensive loss of chromatin accessibility. Changes in chromatin accessibility are thought to be dependent on the recruitment of the BAF complex by specific transcription factors. We discovered strong enrichment for DNA motifs of PU.1 and NF-kB factors in closing chromatin (p-value <0.001), indicating their dependence on the BAF complex. Furthermore, we noted that this chromatin closing occurred in proximity to canonical GC exit programs, including genes induced by the CD40, NF-kB signaling, IRF4, STAT3, IL2, IL4, IL6 and Notch pathways (hypergeometric p-value <0.001), indicating GC-exit perturbation. Expanding upon our findings, we leveraged a combined single-cell RNA and ATAC assay (Multiome) to scrutinize subtle shifts within GC populations. Determining the chromatin accessibility within the pseudo-time trajectory of GC transitions, we found that PU.1 and NF-kB factors are chronologically dependent on ARID1A with PU.1 accessibility initially compromised, followed by a subsequent decrease at binding sites for NF-kB factors. This sequence reveals ARID1A's unrecognized function as a regulator of temporal dynamics of these key transcription factors. Strikingly, our Multiome data revealed expansion of the pre-memory B cells accompanied by a decrease in the proportion of pre-plasma cells upon Arid1a deletion (p-value <0.001), suggesting that Arid1a loss favors GC exit towards the memory cell fate. To validate our findings, we performed immunophenotyping and observed an increase in memory B cells in cKO/WT mice (p=0.019), and a decrease in long-lived plasma cells (p=0.012) upon NP-KLH immunization. Furthermore, we observed that the absence of ARID1A tilts GC cell-fate towards immature IgM+CD80-PDL2- memory B cells (p=0.0016), known for their potential to re-enter new GCs. Linking this critical role of ARID1A in chromatin regulation to lymphomagenesis, we observed a reduction in overall survival for mice carrying VavP-Bcl2; Arid1a+/- allele (compared to VavP-Bcl2; Arid1a+/+; p=0.0087). Remarkably, we further show that FL patients with ARID1A-inactivating mutations display an immature memory B-cell-like state with increased transformation risk to aggressive disease (p=0.0391). These observations offer mechanistic understanding into the emergence of both indolent and aggressive lymphomas in ARID1A-mutant patients through formation of immature memory-like clonal precursors.
ARID1A, a subunit of the canonical BAF nucleosome remodeling complex, is commonly mutated in lymphomas. We show that ARID1A orchestrates B cell fate during the germinal center (GC) response, ...facilitating cooperative and sequential binding of PU.1 and NF-kB at crucial genes for cytokine and CD40 signaling. The absence of ARID1A tilts GC cell fate toward immature IgM+CD80−PD-L2− memory B cells, known for their potential to re-enter new GCs. When combined with BCL2 oncogene, ARID1A haploinsufficiency hastens the progression of aggressive follicular lymphomas (FLs) in mice. Patients with FL with ARID1A-inactivating mutations preferentially display an immature memory B cell-like state with increased transformation risk to aggressive disease. These observations offer mechanistic understanding into the emergence of both indolent and aggressive ARID1A-mutant lymphomas through the formation of immature memory-like clonal precursors. Lastly, we demonstrate that ARID1A mutation induces synthetic lethality to SMARCA2/4 inhibition, paving the way for potential precision therapy for high-risk patients.
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•ARID1A enables stepwise and cooperative chromatin binding for PU.1 and NF-kB factors•Multiome analysis shows ARID1A loss drives cell fate toward memory B cell program•ARID1A loss links memory-like FLs to higher DLBCL transformation risk in patients•ARID1A-mutant lymphoma cells show enhanced vulnerability to BAF complex inhibition
Barisic et al. show a chromatin remodeling mechanism by which the BAF complex enables stepwise binding of PU.1 and NF-kB factors, thus restricting the memory B cell program and transformation to an aggressive form of lymphoma.
SMARCA4 encodes one of two mutually exclusive ATPase subunits in the BRG/BRM associated factor (BAF) complex that is recruited by transcription factors (TFs) to drive chromatin accessibility and ...transcriptional activation. SMARCA4 is among the most recurrently mutated genes in human cancer, including ∼30% of germinal center (GC)-derived Burkitt lymphomas. In mice, GC-specific Smarca4 haploinsufficiency cooperated with MYC over-expression to drive lymphomagenesis. Furthermore, monoallelic Smarca4 deletion drove GC hyperplasia with centroblast polarization via significantly increased rates of centrocyte recycling to the dark zone. Mechanistically, Smarca4 loss reduced the activity of TFs that are activated in centrocytes to drive GC-exit, including SPI1 (PU.1), IRF family, and NF-κB. Loss of activity for these factors phenocopied aberrant BCL6 activity within murine centrocytes and human Burkitt lymphoma cells. SMARCA4 therefore facilitates chromatin accessibility for TFs that shape centrocyte trajectories, and loss of fine-control of these programs biases toward centroblast cell-fate, GC hyperplasia and lymphoma.
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•Smarca4 is a haploinsufficient tumor suppressor in B cells•Partial, but not complete, loss of Smarca4 drives germinal center hyperplasia•Smarca4 loss biases centrocyte cell fate toward dark zone recycling•BCL6-antagonistic TFs SPI1, IRF4, and NF-κB have reduced activity following Smarca4 loss
Deng et al. identify a germinal center-specific role for SMARCA4 (BRG1) in regulating centrocyte cell fate decisions by facilitating chromatin accessibility in association with SPI1 (PU.1) and IRF transcription factors. Loss of Smarca4 partially phenocopies BCL6 activation and cooperates with MYC over-expression to drive lymphomagenesis.
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