K56 Acetylation Research Articles

Reactive Oxygen species dependent increase in H3K27 acetylation by intermittent hypoxia is regulated by H3S28 phosphorylation.

Histones play a crucial role in regulating gene expression through post -translational modifications (PTMS) which include acetylation, methylation and phosphorylation. We have previously identified histone 3 acetylation (H3Kac) and methylation (H3Kme) as an early epigenetic mechanism associated with intermittent hypoxia (IH), a hallmark feature of sleep apnea. The goal of the present study was to determine the molecular mechanisms underlying IH increased H3 acetylation. IH-induced H3 acetylation was blocked by an antioxidant. Conversely, reactive oxygen species (ROS) mimetics, increased H3 acetylated protein expression similar to IH, suggesting a role for ROS. Trichostatin A (TSA), an HDAC (histone deacetylase) inhibitor mimicked IH-induced H3 acetylation under normoxic conditions, while pharmacological blockade of p300/CBP (HAT, histone acetylase) with CTK7A abolished IH-induced H3 acetylation. These results suggest that interplay between HATs and HDACs regulate ROS-dependent H3 acetylation by IH. Lysine 27 (H3K27) on H3 was one of the lysines specifically acetylated by IH and this acetylation was associated with dephsophorylation of H3 at serine 28 (H3S28). Inhibition of S28 dephosphorylation by protein phosphatase inhibitors (PIC or Calyculin A), prevented H3K27 acetylation by IH. Conversely, inhibiting K27 acetylation with CTK7A, increased S28 phosphorylation in IH-exposed cells. These findings highlight the intricate balance between H3 acetylation and phosphorylation in response to IH, shedding light on epigenetic mechanism regulating gene expression. (Supported by NIH-PO1-HL90554).

Abstract LB028: Discovery and characterization of selective heterobifunctional degraders of EP300 in hematopoietic malignancies

Abstract The paralogous histone acetyltransferases EP300 and CREBBP are two of the master regulators of transcription by controlling both enhancer and promoter activity through histone and non-histone acetylation. EP300 and CREBBP activity is primarily driven by their acetylation of K27 and K18 on histone H3 leading to open and active chromatin state. Targeting the EP300/CREBBP axis of chromatin regulation may be a way to disrupt the signaling pathways downstream of key oncogenic signaling networks like MYC/IRF4 in hematopoietic cancers. Successful development of dual EP300/CREBBP BRDi and HATi has led to promising pre-clinical efficacy, but due to observed tolerability issues may potentially limit their utility in the clinic. We hypothesized, based upon published mouse KO phenotypes, that a selective EP300 compound may improve tolerability. Due to the high sequence homology between EP300 and CREBBP in both the BRD and HAT domains, developing selective inhibitors has proven to be challenging. To combat this, we have utilized heterobifunctional protein degrader technology (ProDegs, also known as PROTACS) to develop EP300 selective ProDegs with greater than 100-fold selectivity over CREBBP. We observe rapid targeted degradation of EP300 with maximal degradation occurring within the first 2-4 hours after treatment. Concomitant with the loss of EP300, we see modulation of the associated H3K27ac and H3K18ac biomarkers as well as alterations in key oncogenic transcription networks. In both in vitro and in vivo assays looking at impact to platelet maturation, we observed that selective loss of EP300 largely abrogated observed thrombocytopenia compared to dual EP300/CREBBP inhibitors. Upon treatment, MM and NHL models show strong downregulation of MYC/IRF4 oncogenic signaling pathways, both of which culminate in a loss of cellular viability and cell death. Additionally, we observe in vivo dose responsive tumor growth inhibition in OPM2 and Pfeiffer xenograft models. Together, the data demonstrate the potential utility of EP300 selective ProDegs for the treatment of hematopoietic malignancies. Citation Format: Frederick A. Derheimer, Ninvita Givarkes, Natalie Miller, Rita Grantner, Casey Quinlan, Sonja Brun, Thomas Paul, Astrid Ruefli-Brasse, Stefan Steyn, Derek Bartlett, Matthew Hayward, Matthew Brown, Daniel Uccello, Benjamin J. Burke, Kris Borzilleri, Adam Gilbert, Michelle Hemkens. Discovery and characterization of selective heterobifunctional degraders of EP300 in hematopoietic malignancies [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr LB028.

Diminished NAD+ levels and activation of retrotransposons promote postovulatory aged oocyte (POAO) death

Death is the fate of postovulatory aged or unfertilized oocytes (POAO) in many animals. However, precise molecular mechanisms are yet to be discovered. Here, we demonstrate that increased amounts of reactive oxygen species (ROS), calcium ion (Ca+2) channels, and retrotransposon activity induce apoptosis, which in turn causes POAO death. Notably, suppression of ROS, Ca+2 channels, and retrotransposons delayed POAO death. Further, we found that the histone H4K12 and K16 acetylation increased via downregulation of NAD+ and NAD+ -dependent histone deacetylase SIRT3. Furthermore, adding NMN, sodium pyruvate, or CD38 inhibition delayed the death of postovulatory aged oocytes. Finally, we demonstrate the conservation of retrotransposon-induced DNA damage-dependent POAO death in higher-order vertebrates. Our findings suggest that POAO mortality is caused by cyclic cascade metabolic interactions in which low NAD+ levels increase histone acetylation by inhibiting histone deacetylases, resulting in an increase in retrotransposons, ROS, and Ca+2 channel activity and thus contributing to DNA damage-induced apoptosis.

KAT8 is upregulated and recruited to the promoter of Atg8 by FOXO to induce H4 acetylation for autophagy under 20-hydroxyecdysone regulation

Selective gene expression in cells in physiological or pathological conditions is important for the growth and development of organisms. Acetylation of K16 (H4K16ac) catalyzed by histone acetyltransferase 8 (KAT8) is known to promote gene transcription; however, the regulation of KAT8 transcription and the mechanism by which KAT8 acetylates H4K16ac to promote specific gene expression are unclear. Here, using the lepidopteran insect Helicoverpa armigera as a model, we reveal that the transcription factor FOXO promotes KAT8 expression and recruits KAT8 to the promoter region of autophagy-related gene 8 (Atg8) to increase H4 acetylation at that location, enabling Atg8 transcription under the steroid hormone 20-hydroxyecdysone (20E) regulation. H4K16ac levels are increased in the midgut during metamorphosis, which is consistent with the expression profiles of KAT8 and ATG8. Knockdown of Kat8 using RNA interference results in delayed pupation and repression of midgut autophagy and decreases H4K16ac levels. Overexpression of KAT8-GFP promotes autophagy and increases H4K16ac levels. FOXO, KAT8 and H4K16ac colocalized at the FOXO binding region to promote Atg8 transcription under 20E regulation. Acetylated FOXO at K180 and K183 catalyzed by KAT8 promotes gene transcription for autophagy. 20E via FOXO promotes Kat8 transcription. Knockdown or overexpression of FOXO appeared to give similar results as knockdown or overexpression KAT8. Therefore, FOXO upregulates KAT8 expression and recruits KAT8 to the promoter region of Atg8, where the KAT8 induces H4 acetylation to promote Atg8 transcription for autophagy under 20E regulation. This study reveals the mechanism that KAT8 to promote transcription of a specific gene.

3D chromatin structure and massively parallel reporter assays in hiPSC‐derived microglia and human macrophages identifies novel putative Alzheimer’s Disease risk genes

AbstractBackgroundAlzheimer’s disease (AD) genome‐wide association studies (GWAS) identified 75 disease‐associated loci; however, interpretation of these results has proven difficult for two primary reasons. First, linkage disequilibrium between nearby variants makes it difficult to identify the causal variant(s) at each locus. Second, because the vast majority of OA risk variants are non‐coding and can regulate genes from distances of greater than one million base pairs, the genes impacted by AD risk variants are largely unknown. Recently developed genomic approaches can address these hurdles but must be applied to the correct cell types and biological contexts.MethodWe quantified the impact of 3,576 AD‐associated genetic variants on enhancer activity by performing massively parallel reporter assays (MPRAs) in resting and activated human macrophages. To map these variants to the genes they regulate we built regulatory networks by mapping 3D chromatin structure (Hi‐C), chromatin accessibility (ATAC), histone K27 acetylation (CUT&RUN), and gene expression (RNA‐seq) in both resting and activated iPSC‐derived microglia.ResultIn total we identified 20,992 chromatin loops across resting and activated iPSC‐derived microglia. Among these, 9,544 loops linked 14,576 enhancers to 11,487 genes. 58 loops connected 414 AD‐risk variants queried by our MPRA assays to 85 genes. 212, 19,256, and 2,790 of these loops, enhancers, and genes (respectively) changed in response to activation, providing further insight into their regulatory mechanisms and highlighting the need to study these events in the correct biological context.ConclusionOngoing analyses and data integration should reveal further mechanistic details and provide novel AD risk genes for further research and therapeutic development. By intersecting our MPRA results and dynamic regulatory networks with AD GWAS, we were able to identify novel putative genes regulated by non‐coding AD risk variants in a cell‐type and condition‐specific manner.

Abstract PR008: The SLC1A1/EAAT3 dicarboxylic amino acid transporter: An actionable, HIF-independent, hub that links epigenetic dysregulation to nucleotide metabolism in kidney cancer

Abstract Significance: The clear cell renal cell carcinomas (ccRCCs), which harbor the hallmark inactivation of the von Hippel Lindau tumor suppressor protein (pVHL), represent the majority of adult kidney cancers. Although, early stage/localized ccRCC is effectively managed by surgery and surveillance, therapeutic options for advanced stage disease are limited, highlighting the unmet need for novel therapies. Chromatin dysregulation is routinely observed in ccRCC and our previous work identified a distinct histone modification signature associated with pVHL-deficient ccRCCs, versus the pVHL-proficient chromophobe and papillary sub-types, which included elevated levels of bulk Histone H3 K27 acetylation (H3K27ac). H3K27ac marks transcriptionally activated regions in the genome. We hypothesized that, as in other biological contexts, H3K27ac accumulation in pVHL-deficient ccRCCs drives the expression of key oncogenes. Here, we functionally probed this dysregulated epigenetic program to identify actionable targets in kidney cancer. Experimental Approach and Results: We identified genes marked by elevated H3K27ac (ChIP-Seq) and higher expression (RNA-Seq), specifically in pVHL-deficient cells and prioritized the top 100 genes that encoded druggable products. Using a library representing these ORFs, we did an in vivo ‘sufficiency’ screen, to identify candidates whose expression promoted tumor growth in otherwise poorly tumorigenic pVHL-proficient cells. Our screen (and downstream validation studies) identified SLC1A1, which encodes an Asp/Glu transporter named EAAT3, as an oncogenic driver in ccRCC. Results: SLC1A1 expression was elevated in pVHL-deficient cells – but in a HIF-independent manner. Inactivation of SLC1A1 (using CRISPR/Cas9) led to fitness defects in a panel of ccRCC cell lines, along with a notable depletion of nucleotide biosynthesis precursors, likely because of the importance of the Asp carbon skeleton in this pathway. Consistent with this, esterified-Asp rescued the fitness defects associated with SLC1A1 loss. Moreover, SLC1A1 upregulation (high Asp/Glu) diminished dependency on Glutaminase; whereas, SLC1A1 loss (low Asp/Glu) increased Glutaminase dependency and promoted sensitivity to Glutaminase blockade. Finally, using clinical cohorts and cell-based studies, we found that SLC1A1 can impact its own transcriptional expression, but also the expression of certain other metabolic transporters involved in Asp/Glu metabolism (e.g. SLC22A11) and nucleotide metabolism (e.g SLC28A1). We speculate, these transcriptional alterations are driven by the conversion of Glu into a-ketoglutarate, a key cofactor for KDMs. Our ongoing studies are addressing the mechanistic basis of this transcriptional regulation and exploring the feasibility of pharmacologically targeting SLC1A1 in ccRCC. Altogether, we show that ccRCCs hijack nutrient reabsorption mechanisms (e.g. SLC1A1) to drive oncogenic programs. SLC1A1 thus links epigenetic dysregulation to a HIF-independent metabolic program regulating nucleotide biosynthesis/uptake. Citation Format: Abhishek A. Chakraborty. The SLC1A1/EAAT3 dicarboxylic amino acid transporter: An actionable, HIF-independent, hub that links epigenetic dysregulation to nucleotide metabolism in kidney cancer [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr PR008.

Drought-Stress-Related Reprogramming of Gene Expression in Barley Involves Differential Histone Modifications at ABA-Related Genes.

Plants respond to drought by the major reprogramming of gene expression, enabling the plant to survive this threatening environmental condition. The phytohormone abscisic acid (ABA) serves as a crucial upstream signal, inducing this multifaceted process. This report investigated the drought response in barley plants (Hordeum vulgare, cv. Morex) at both the epigenome and transcriptome levels. After a ten-day drought period, during which the soil water content was reduced by about 35%, the relative chlorophyll content, as well as the photosystem II efficiency of the barley leaves, decreased by about 10%. Furthermore, drought-related genes such as HvS40 and HvA1 were already induced compared to the well-watered controls. Global ChIP-Seq analysis was performed to identify genes in which histones H3 were modified with euchromatic K4 trimethylation or K9 acetylation during drought. By applying stringent exclusion criteria, 129 genes loaded with H3K4me3 and 2008 genes loaded with H3K9ac in response to drought were identified, indicating that H3K9 acetylation reacts to drought more sensitively than H3K4 trimethylation. A comparison with differentially expressed genes enabled the identification of specific genes loaded with the euchromatic marks and induced in response to drought treatment. The results revealed that a major proportion of these genes are involved in ABA signaling and related pathways. Intriguingly, two members of the protein phosphatase 2C family (PP2Cs), which play a crucial role in the central regulatory machinery of ABA signaling, were also identified through this approach.

DIPG-24. BRD4 INHIBITION AS A RADIOSENSITIZER THROUGH BLOCKING DNA REPAIR FOR THE TREATMENT OF DIFFUSE MIDLINE GLIOMA

Abstract Diffuse intrinsic pontine glioma (DIPG) is one of the devastating childhood cancers. Radiation therapy (RT) remains the only effective treatment yet provides a 5-year survival rate of only 1%. Several clinical trials have attempted to enhance RT efficacy by combining it with radiosensitizing agents, though none have been successful in doing so. Given this, there is a critical need to identify effective therapeutics to enhance the RT anti-tumor activity in DIPG. Here, we identified BRD4 inhibitors as candidate radiosensitizers from a high throughput drug screening. DIPG cells show increased H3 K27 acetylation (H3K27ac) levels, which bind to BET bromodomain protein 4 (BRD4) and are strongly associated with active transcription. We tested two BRD4 inhibitors (BRD4i: AZD5153 and JQ-1) as well as genetic BRD4 depletion, and observed enhancement of radiation-induced DNA damage, confirming BRD4i as potential radiosensitizers in the treatment of DIPG. We evaluated the effects of BRD4i on gene expression using RNAseq, and observed significant inhibition of DNA-repair proteins such as BRCA1 and RAD51. CUT-RUN qPCR showed decreased H3K27ac at BRCA1 and RAD51 promoters. Combination of BRD4i and RT inhibited cell viability significantly using clonogenic survival assay, apoptosis assay, and also showed cell cycle arrest. Radiation-induced DNA double-strand break (DSB) repair was prolonged with BRD4i with high levels of gH2AX and 53BP1 likely due to inhibition of DNA-repair. In vivo studies revealed increased survival of animals treated with combination therapy of RT and BRD4i in comparison to either monotherapy. Together, these results highlight BRD4i as a potential radiosensitizer and provide a rationale for developing combination therapy with radiation in the treatment of DIPG.

Cross talk between histone 3 acetylation, methylation and phosphorylation by intermittent hypoxia.

We have previously identified histone 3 (H3) post translational modifications, specifically acetylation and methylation as an early epigenetic mechanism associated with sympathetic nerve activation and hypertension in rodent models of intermittent hypoxia (IH), a hallmark feature of sleep apnea (Nanduri et al, Physiol genomics 2021, Ning et al, Front Physiol 2021). Phosphorylation of H3 serine (S) residues that are adjacent to acetylation and methylation sites are also shown to regulate chromatin structure and gene expression. The aim of the present study is to assess whether IH affect H3 phosphorylation and whether phosphorylation influences H3 acetylation by IH. Studies were performed on rat pheochromocytoma (PC12) cells and adrenal chromaffin cells of rats treated with 10d IH as well as heme oxygenase (HO)-2 null mice, which exhibit spontaneous apneas. IH increased H3 lysine (K) 27 acetylation in PC12 cells, rat adrenal chromaffin cells and HO-2 null mice. These effects were associated with dephsophorylation of H3 at S28 and demethylation of K27. Inhibition of S28 dephosphorylation by protein phosphatase inhibitor (PIC) or Calyculin A, a specific inhibitor of protein phosphatase (PP)-1 and -2, inhibited H3K27 acetylation by IH. Conversely, inhibition of K27 acetylation with CTK7A a specific inhibitor of acetyl transferase p300/CBP increased S28 phosphorylation and K27 methylation in IH exposed cells. These results demonstrate that effects of IH on H3 lysine acetylation, methylation and phosphorylation are complex and a cross-talk between the three events regulate IH-induced transcriptional activity. This is the full abstract presented at the American Physiology Summit 2023 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

High levels of histone H3 K27 acetylation and tri-methylation are associated with shorter survival in oral squamous cell carcinoma patients.

Acetylation and trimethylation of histone H3 lysine 27 (H3K27ac and H3K27me3) generally activate and repress transcription, respectively. Concurrent activation of H3K27ac and H3K27me3 has been reported to correlate with poor prognosis in hepatocellular carcinoma. A high level of H3K27me3 has been shown to be associated with advanced oral squamous cell carcinoma (OSCC) tumour stage, but prognostic impact of H3K27ac level alone/or in combination with H3K27me3 in OSCC patients had not yet been reported. In this study, immunohistochemistry using specific antibodies against H3K27ac and H3K27me3 was performed on a series of 72 OSCC samples to investigate the association between H3K27ac and H3K27me3 levels and OSCC patient's survival. For each mark, the proportion of labelled cells (percentage) and the intensity of the labelling were measured, and a score of percentage x intensity was calculated. A high percentage of H3K27me3 positive cells was significantly associated with survival in univariate and multivariate analyses (logrank p-value < 0.05). Patients with high total scores of H3K27ac and H3K27me3 labelling also showed significantly shorter survival probabilities (logrank p-value < 0.05) compared to patients with low total scores of labelling for these histone posttranslational modifications (PTMs). Our findings suggest that the detection of both H3K27ac and H3k27me3 could help evaluating prognosis in OSCC patients.

EXTH-29. RADIOSENSITIZATION BY BRD4 INHIBITION IN DIFFUSE INTRINSIC PONTINE GLIOMA

Abstract Diffuse intrinsic pontine glioma (DIPG), the most frequent brainstem tumor in pediatrics, is one of the devastating childhood cancers, and virtually all patients die within two years after diagnosis. Since these tumors occur in the brainstem which is vital area, there are no surgical options for providing relief to patients, and conventional chemotherapy. Radiation therapy (RT) remains the only effective treatment. Radiosensitization is a mean to improve the therapeutic balance between efficacy and toxicity of RT, but not used in clinically. Here, we found BRD4 inhibitor as a radiosensitizer from drug screening. DIPG shows increased H3 K27 acetylation (H3K27ac), which binds to BET bromodomain protein 4 (BRD4) and they are strongly associated with active transcription. We tested two BRD4 inhibiter (BRD4i : AZD5153 and JQ-1) and genetic BRD4 depletion enhances radiation-induced DNA damage, making it a potential radiosensitizer in the treatment of DIPG. We evaluated the effects of BRD4i on genes expression using RNA sequence, inhibited significantly DNA-repair proteins such as BRCA1 and RAD51. CUT-RUN qPCR showed decreased H3K27ac at BRCA1 and RAD51. Combination with BRD4i and RT inhibited cell viability significantly in clonogenic survival assay, apoptosis assay, and showed cell cycle arrest. Radiation-induced DNA double-strand break (DSB) repair was prolonged high level of rH2AHX and 53BP1 with BRD4i because of inhibited DNA-repair. In vivo studies revealed increased survival of animals treated with combination therapy of RT and BRD4i in compared to either monotherapy. Together, these results highlight BRD4i as a potential radiosensitizer and provide a rationale for developing combination therapy with radiation in the treatment of DIPG.

Impact of Nuclear De Novo NAD+ Synthesis via Histone Dynamics on DNA Repair during Cellular Senescence To Prevent Tumorigenesis.

NAD+ synthesis is a fundamental process in living cells. The effects of local metabolite production on chromatin influence the epigenetic status of chromatin in DNA metabolism. We have previously shown that K5 acetylation of H2AX by TIP60 is required for the ADP ribosylation activity of PARP-1, for histone H2AX exchange at DNA damage sites. However, the detailed molecular mechanism has remained unclear. Here, we identified de novo NAD synthetase 1 (NAD syn1) as a novel binding partner to H2AX. The enzymatic activity of NAD syn1 is crucial for the ADP ribosylation activity of PARP-1 for the H2AX dynamics at sites of DNA damage. Inhibition of the NAD synthetase activity in the cell nucleus decreased the overall cellular NAD+ concentration, leading to cellular senescence. Accordingly, the acetylation-dependent H2AX dynamics and homologous recombination repair were suppressed, leading to increased tumorigenesis. Our findings have revealed the importance of de novo NAD+ production in the cell nucleus for protection against the decreased DNA repair capacity caused by cellular senescence and thus against tumorigenesis.

Retinoic acid receptor gamma is required for proliferation of pancreatic cancer cells.

Despite the expectation that retinoic acid receptor could be the potential therapeutic targets for pancreatic cancers, there has been the lack of information about the role and the impact of retinoic acid receptor gamma (RARγ, RARG) on pancreatic cancer, unlike other two RARs. Herein, we applied TCGA and GEO database to show that the expression and prognosis of RARG is closely related to pancreatic cancer, which demonstrates that RARG is commonly overexpressed in human pancreatic cancer and is an independent diagnostic marker predicting the poor prognosis of pancreatic cancer patients. In addition, we demonstrated that the reduction in the expression of RARG in human pancreatic cancer cells dramatically suppress their proliferation and tumor growth in vivo, partially attributable to the downregulation of tumor-supporting biological processes such as cell proliferation, antiapoptosis and metabolism and the decreased expression of various oncogenes like MYC and STAT3. Mechanistically, RARG binds on the promoters of MYC, STAT3, and SLC2A1 which is distinguished from well-known conventionalRetinotic acid response elements (RAREs) and that the binding is likely to be responsible for the epigenetic activation in the level of chromatin, assessed by the measurement of deposition of the gene activation marker histone H3 K27 acetylation (H3K27ac) using ChIP-qPCR. In this study, we reveal that RARG plays important role in the tumorigenesis of pancreatic cancer and represents new therapeutic targets for human pancreatic cancer.

β-Carotene enhances the expression of inflammation-related genes and histone H3 K9 acetylation, K4 dimethylation, and K36 trimethylation around these genes in juvenile macrophage-like THP-1 cells

β-Carotene is converted into vitamin A in the body and can remove reactive oxygen species. However, it is still unclear whether β-carotene alters the expression levels of inflammation-related genes in macrophages and how this is regulated. In the present study, we investigated whether the administration of β-carotene under hyperglycemic conditions altered the expression level of inflammation-related genes and whether any observed differences were associated with changes in histone modifications in juvenile macrophage-like THP-1 cells. THP-1 cells (from a human monocytic leukemia cell line) were cultured in low glucose (5 mM), high glucose (25 mM), or high glucose (25 mM) + β-carotene (5 μM) media for 1 day, and mRNA expression levels of genes related to oxidative stress and inflammation, and histone modifications were determined by mRNA microarray and qRT-PCR analyses, and chromatin immunoprecipitation assays, respectively. The expression of inflammation-related genes, such as IL31RA, CD38, and NCF1B, and inflammation-associated signaling pathway genes, such as ITGAL, PRAM1, and CSF3R, were upregulated by β-carotene under high-glucose conditions. Under these conditions, histone H3 lysine 4 (K4) demethylation, H3K36 trimethylation, and H3K9 acetylation around the CD38, NCF1B, and ITGAL genes were higher in β-carotene-treated cells than in untreated cells. Treatment of juvenile macrophage-like THP-1 cells with β-carotene under these high glucose conditions induced the expression of inflammation-related genes, K9 acetylation, and K4 di- and K36 trimethylation of histone H3 around these genes.

Acetylation stabilizes stathmin1 and promotes its activity contributing to gallbladder cancer metastasis

Gallbladder cancer is the most common biliary tract malignant tumor with highly metastatic characters and poor prognosis. However, the underlying mechanism remains unclear. Stathmin1 is ubiquitous phosphoprotein, regulating microtubule stabilization. We identified the acetylation of stahtmin1 at lysine 9 (K9) in gallbladder cancer. K9 acetylation of stathmin1 was reversely regulated by the acetyltransferase PCAF and the deacetylases sirt2. K9 acetylation of stathmin1 inhibited the combining of stathmin1 to E3 ubiquitin ligase RLIM, thereby inhibiting its ubiquitination degradation. Moreover, K9 acetylation also promoted the activity of stahtmin1 interacting and destabilizing microtubule through the inhibition of stathmin1 phosphorylation. K9 acetylated stathmin1 significantly promoted gallbladder cancer cell migration and invasion viability in vitro and lung metastasis in vivo, and indicated poor prognosis of nude mice. IHC assay suggested the positive correlation of high levels of K9 acetylation and stathmin1 expression in gallbladder cancer. Our study revealed that K9 acetylation up-regulated stathmin1 protein stability and microtubule-destabilizing activity to promoted gallbladder cancer metastasis, which provides a potential target for gallbladder cancer therapy.

Rare germline heterozygous missense variants in BRCA1-associated protein 1, BAP1, cause a syndromic neurodevelopmental disorder

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 Tcells 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.

Potential functions of histone H3.3 lysine 56 acetylation in mammals

ABSTRACT H3K56 acetylation (H3K56Ac) was first identified in yeast and has recently been reported to play important roles in maintaining genomic stability, chromatin assembly, DNA replication, cell cycle progression and DNA repair. Although H3.1K56Ac has been relatively well studied, the function of H3.3K56Ac remains mostly unknown in mammals. In this study, we used H3.3K56Q and H3.3K56R mutants to study the possible function of H3.3K56 acetylation. The K-to-Q substitution mimics a constitutively acetylated lysine, while the K-to-R replacement mimics a constitutively unmodified lysine. We report that cell lines harbouring mutation of H3.3K56R exhibit increased cell death and dramatic morphology changes. Using a Tet-Off inducible system, we found an increased population of polyploid/aneuploid cells and decreased cell viability in H3.3K56R mutant cells. Consistent with these results, the H3.3K56R mutant had compromised H3.3 incorporation into several pericentric and centric heterochromatin regions we tested. Moreover, mass spectrometry analysis coupled with label-free quantification revealed that biological processes regulated by the H3.3-associating proteins, whose interaction with H3.3 was markedly increased by H3.3K56Q mutation but decreased by H3.3K56R mutation, include sister chromatid cohesion, mitotic nuclear division, and mitotic nuclear envelope disassembly. These results suggest that H3.3K56 acetylation is crucial for chromosome segregation and cell division in mammals.

Dynamics of SAS-I mediated H4 K16 acetylation during DNA replication in yeast.

The acetylation of H4 lysine 16 (H4 K16Ac) in Saccharomyces cerevisiae counteracts the binding of the heterochromatin complex SIR to chromatin and inhibits gene silencing. Contrary to other histone acetylation marks, the H4 K16Ac level is high on genes with low transcription, whereas highly transcribed genes show low H4 K16Ac. Approximately 60% of cellular H4 K16Ac in S. cerevisiae is provided by the SAS-I complex, which consists of the MYST-family acetyltransferase Sas2, Sas4 and Sas5. The absence of SAS-I causes inappropriate spreading of the SIR complex and gene silencing in subtelomeric regions. Here, we investigated the genome-wide dynamics of SAS-I dependent H4 K16Ac during DNA replication. Replication is highly disruptive to chromatin and histone marks, since histones are removed to allow progression of the replication fork, and chromatin is reformed with old and new histones after fork passage. We found that H4 K16Ac appears in chromatin immediately upon replication. Importantly, this increase depends on the presence of functional SAS-I complex. Moreover, the appearance of H4 K16Ac is delayed in genes that are strongly transcribed. This indicates that transcription counteracts SAS-I-mediated H4 K16 acetylation, thus "sculpting" histone modification marks at the time of replication. We furthermore investigated which acetyltransferase acts redundantly with SAS-I to acetylate H4 K16Ac. esa1Δ sds3Δ cells, which were also sas2Δ sir3Δ in order to maintain viability, contained no detectable H4 K16Ac, showing that Esa1 and Sas2 are redundant for cellular H4 K16 acetylation. Furthermore, esa1Δ sds3Δ sas2Δ sir3Δ showed a more pronounced growth defect compared to the already defective esa1Δ sds3Δ sir3Δ. This indicates that SAS-I has cellular functions beyond preventing the spreading of heterochromatin.

The Amazing Acrobat: Yeast's Histone H3K56 Juggles Several Important Roles While Maintaining Perfect Balance.

Acetylation on lysine 56 of histone H3 of the yeast Saccharomyces cerevisiae has been implicated in many cellular processes that affect genome stability. Despite being the object of much research, the complete scope of the roles played by K56 acetylation is not fully understood even today. The acetylation is put in place at the S-phase of the cell cycle, in order to flag newly synthesized histones that are incorporated during DNA replication. The signal is removed by two redundant deacetylases, Hst3 and Hst4, at the entry to G2/M phase. Its crucial location, at the entry and exit points of the DNA into and out of the nucleosome, makes this a central modification, and dictates that if acetylation and deacetylation are not well concerted and executed in a timely fashion, severe genomic instability arises. In this review, we explore the wealth of information available on the many roles played by H3K56 acetylation and the deacetylases Hst3 and Hst4 in DNA replication and repair.

Rtt109 slows replication speed by histone N-terminal acetylation.

The wrapping of DNA around histone octamers challenges processes that use DNA as their template. In vitro, DNA replication through chromatin depends on histone modifiers, raising the possibility that cells modify histones to optimize fork progression. Rtt109 is an acetyl transferase that acetylates histone H3 before its DNA incorporation on the K56 and N-terminal residues. We previously reported that, in budding yeast, a wave of histone H3 K9 acetylation progresses ∼3–5 kb ahead of the replication fork. Whether this wave contributes to replication dynamics remained unknown. Here, we show that the replication fork velocity increases following deletion of RTT109, the gene encoding the enzyme required for the prereplication H3 acetylation wave. By using histone H3 mutants, we find that Rtt109-dependent N-terminal acetylation regulates fork velocity, whereas K56 acetylation contributes to replication dynamics only when N-terminal acetylation is compromised. We propose that acetylation of newly synthesized histones slows replication by promoting replacement of nucleosomes evicted by the incoming fork, thereby protecting genome integrity.