scholarly journals Hypoxia induces rapid changes to histone methylation reprogramming chromatin for the cellular response

2019 ◽  
Author(s):  
Michael Batie ◽  
Julianty Frost ◽  
Mark Frost ◽  
James W. Wilson ◽  
Pieta Schofield ◽  
...  
Keyword(s):  
Histone Methylation ◽  
Cellular Response ◽  
Oxygen Sensing ◽  
Gene Signature ◽  
Oxygen Sensors ◽  
Histone Demethylases ◽  
Rapid Changes ◽  
Transcriptional Changes ◽  
Genomic Locations ◽  
In Cells

AbstractMolecular dioxygenases include JmjC-containing histone demethylases and PHD enzymes, but only PHDs are considered to be molecular oxygen sensors in cells. Although, it is known that hypoxia can alter chromatin, whether this is a direct effect on histone demethylases or due to hypoxia induced HIF-dependent transcriptional changes is not known. Here, we report that hypoxia induces a rapid and HIF-independent alteration to a variety of histone methylation marks. Genomic locations of H3K4me3 and H3K36me3 following short hypoxia predict the hypoxia gene signature observed several hours later in cells. We show that KDM5A inactivation mimics hypoxic changes to H3K4me3 in its targets and is required for the cellular response to hypoxia. Our results demonstrate a direct link between oxygen sensing and chromatin changes via KDM inhibition.One Sentence SummaryRapid oxygen sensing by chromatin

scholarly journals Hypoxia induces rapid changes to histone methylation and reprograms chromatin

Science ◽  
2019 ◽  
Vol 363 (6432) ◽  
pp. 1222-1226 ◽  
Author(s):  
Michael Batie ◽  
Julianty Frost ◽  
Mark Frost ◽  
James W. Wilson ◽  
Pieta Schofield ◽  
...  
Keyword(s):  
Histone Methylation ◽  
Cultured Cells ◽  
Hypoxia Inducible Factor ◽  
Transcriptional Response ◽  
Histone Demethylase ◽  
Histone Demethylases ◽  
Jmjc Domain ◽  
Genomic Locations ◽  
Multicellular Organisms ◽  
Lysine Demethylase

Oxygen is essential for the life of most multicellular organisms. Cells possess enzymes called molecular dioxygenases that depend on oxygen for activity. A subclass of molecular dioxygenases is the histone demethylase enzymes, which are characterized by the presence of a Jumanji-C (JmjC) domain. Hypoxia can alter chromatin, but whether this is a direct effect on JmjC-histone demethylases or due to other mechanisms is unknown. Here, we report that hypoxia induces a rapid and hypoxia-inducible factor–independent induction of histone methylation in a range of human cultured cells. Genomic locations of histone-3 lysine-4 trimethylation (H3K4me3) and H3K36me3 after a brief exposure of cultured cells to hypoxia predict the cell’s transcriptional response several hours later. We show that inactivation of one of the JmjC-containing enzymes, lysine demethylase 5A (KDM5A), mimics hypoxia-induced cellular responses. These results demonstrate that oxygen sensing by chromatin occurs via JmjC-histone demethylase inhibition.

scholarly journals Inhibition of Histone Demethylases LSD1 and UTX Regulates ERα Signaling in Breast Cancer

Cancers ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 2027 ◽  
Author(s):  
Rosaria Benedetti ◽  
Carmela Dell’Aversana ◽  
Tommaso De Marchi ◽  
Dante Rotili ◽  
Ning Qing Liu ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Histone Methylation ◽  
Ex Vivo ◽  
Acquired Resistance ◽  
Chemical Properties ◽  
Breast Cancers ◽  
Histone Demethylases ◽  
Lysine Specific Demethylase ◽  
Breast Cancer Model

In breast cancer, Lysine-specific demethylase-1 (LSD1) and other lysine demethylases (KDMs), such as Lysine-specific demethylase 6A also known as Ubiquitously transcribed tetratricopeptide repeat, X chromosome (UTX), are co-expressed and co-localize with estrogen receptors (ERs), suggesting the potential use of hybrid (epi)molecules to target histone methylation and therefore regulate/redirect hormone receptor signaling. Here, we report on the biological activity of a dual-KDM inhibitor (MC3324), obtained by coupling the chemical properties of tranylcypromine, a known LSD1 inhibitor, with the 2OG competitive moiety developed for JmjC inhibition. MC3324 displays unique features not exhibited by the single moieties and well-characterized mono-pharmacological inhibitors. Inhibiting LSD1 and UTX, MC3324 induces significant growth arrest and apoptosis in hormone-responsive breast cancer model accompanied by a robust increase in H3K4me2 and H3K27me3. MC3324 down-regulates ERα in breast cancer at both transcriptional and non-transcriptional levels, mimicking the action of a selective endocrine receptor disruptor. MC3324 alters the histone methylation of ERα-regulated promoters, thereby affecting the transcription of genes involved in cell surveillance, hormone response, and death. MC3324 reduces cell proliferation in ex vivo breast cancers, as well as in breast models with acquired resistance to endocrine therapies. Similarly, MC3324 displays tumor-selective potential in vivo, in both xenograft mice and chicken embryo models, with no toxicity and good oral efficacy. This epigenetic multi-target approach is effective and may overcome potential mechanism(s) of resistance in breast cancer.

scholarly journals Histone demethylase KDM6A directly senses oxygen to control chromatin and cell fate

Science ◽  
2019 ◽  
Vol 363 (6432) ◽  
pp. 1217-1222 ◽  
Author(s):  
Abhishek A. Chakraborty ◽  
Tuomas Laukka ◽  
Matti Myllykoski ◽  
Alison E. Ringel ◽  
Matthew A. Booker ◽  
...  
Keyword(s):  
Cell Fate ◽  
Histone Methylation ◽  
Mammalian Cells ◽  
Control Cell ◽  
Hypoxia Inducible Factor ◽  
Histone Demethylase ◽  
Histone Demethylases ◽  
Independent Manner ◽  
H3k27 Methylation ◽  
Oxygen Sensitive

Oxygen sensing is central to metazoan biology and has implications for human disease. Mammalian cells express multiple oxygen-dependent enzymes called 2-oxoglutarate (OG)-dependent dioxygenases (2-OGDDs), but they vary in their oxygen affinities and hence their ability to sense oxygen. The 2-OGDD histone demethylases control histone methylation. Hypoxia increases histone methylation, but whether this reflects direct effects on histone demethylases or indirect effects caused by the hypoxic induction of the HIF (hypoxia-inducible factor) transcription factor or the 2-OG antagonist 2-hydroxyglutarate (2-HG) is unclear. Here, we report that hypoxia promotes histone methylation in a HIF- and 2-HG–independent manner. We found that the H3K27 histone demethylase KDM6A/UTX, but not its paralog KDM6B, is oxygen sensitive. KDM6A loss, like hypoxia, prevented H3K27 demethylation and blocked cellular differentiation. Restoring H3K27 methylation homeostasis in hypoxic cells reversed these effects. Thus, oxygen directly affects chromatin regulators to control cell fate.

scholarly journals Induction of protein aggregation and starvation response by tRNA modification defects

2020 ◽  
Vol 66 (6) ◽  
pp. 1053-1057
Author(s):  
Roland Klassen ◽  
Alexander Bruch ◽  
Raffael Schaffrath
Keyword(s):  
Cellular Response ◽  
Anticodon Loop ◽  
Protein Aggregate ◽  
Starvation Response ◽  
Codon Recognition ◽  
Growth Defects ◽  
Yeast Strains ◽  
Transcriptional Changes ◽  
Decoding Efficiency ◽  
Synthetic Growth

Abstract Posttranscriptional modifications of anticodon loops contribute to the decoding efficiency of tRNAs by supporting codon recognition and loop stability. Consistently, strong synthetic growth defects are observed in yeast strains simultaneously lacking distinct anticodon loop modifications. These phenotypes are accompanied by translational inefficiency of certain mRNAs and disturbed protein homeostasis resulting in accumulation of protein aggregates. Different combinations of anticodon loop modification defects were shown to affect distinct tRNAs but provoke common transcriptional changes that are reminiscent of the cellular response to nutrient starvation. Multiple mechanisms may be involved in mediating inadequate starvation response upon loss of critical tRNA modifications. Recent evidence suggests protein aggregate induction to represent one such trigger.

scholarly journals Manganese Suppresses the Haploinsufficiency of Heterozygous trpy1Δ/TRPY1 Saccharomyces cerevisiae Cells and Stimulates the TRPY1-Dependent Release of Vacuolar Ca2+ under H2O2 Stress

Cells ◽  
2019 ◽  
Vol 8 (2) ◽  
pp. 79 ◽  
Author(s):  
Lavinia Ruta ◽  
Ioana Nicolau ◽  
Claudia Popa ◽  
Ileana Farcasanu
Keyword(s):  
Oxidative Stress ◽  
Saccharomyces Cerevisiae ◽  
Cellular Response ◽  
Trp Channels ◽  
Homozygous Deletion ◽  
Growth Defect ◽  
Mechanical Stimuli ◽  
Hyperosmotic Shock ◽  
Diploid Cells ◽  
In Cells

Transient potential receptor (TRP) channels are conserved cation channels found in most eukaryotes, known to sense a variety of chemical, thermal or mechanical stimuli. The Saccharomyces cerevisiae TRPY1 is a TRP channel with vacuolar localization involved in the cellular response to hyperosmotic shock and oxidative stress. In this study, we found that S. cerevisiae diploid cells with heterozygous deletion in TRPY1 gene are haploinsufficient when grown in synthetic media deficient in essential metal ions and that this growth defect is alleviated by non-toxic Mn2+ surplus. Using cells expressing the Ca2+-sensitive photoprotein aequorin we found that Mn2+ augmented the Ca2+ flux into the cytosol under oxidative stress, but not under hyperosmotic shock, a trait that was absent in the diploid cells with homozygous deletion of TRPY1 gene. TRPY1 activation under oxidative stress was diminished in cells devoid of Smf1 (the Mn2+-high-affinity plasma membrane transporter) but it was clearly augmented in cells lacking Pmr1 (the endoplasmic reticulum (ER)/Golgi located ATPase responsible for Mn2+ detoxification via excretory pathway). Taken together, these observations lead to the conclusion that increased levels of intracytosolic Mn2+ activate TRPY1 in the response to oxidative stress.

Analysis of Changes in Endothelial Cell Protein Expression and Phosphorylation Induced by Cleaved High Molecular Weight Kininogen

Blood ◽  
2012 ◽  
Vol 120 (21) ◽  
pp. 5195-5195
Author(s):  
Venkaiah Betapudi ◽  
Keith R. McCrae
Keyword(s):  
Molecular Weight ◽  
Endothelial Cells ◽  
Protein Expression ◽  
Signaling Pathways ◽  
High Molecular Weight ◽  
Tissue Remodeling ◽  
High Molecular Weight Kininogen ◽  
Time Points ◽  
Rapid Changes ◽  
In Cells

Abstract Abstract 5195 Background and objective: High molecular weight kininogen (HK) is an abundant plasma protein that functions as a critical cofactor in the kallikrein-kinin system. HK normally circulates in the single chain form, but is cleaved by plasma kallikrein to release the nonapeptide bradykinin and form cleaved high molecular weight kininogen (HKa) that consists of a heavy and light chain linked by a single disulfide bond. Conformational changes occurring in cleaved kininogen result in increased exposure of histidine and glycine-rich regions within kininogen domain 5 that impart HKa with unique properties, including the ability to inhibit angiogenesis by causing selective apoptosis of proliferating endothelial cells. However, neither the receptors that mediate the antiangiogenic activity of HKa nor the signaling pathways that lead to apoptosis have been rigorously defined. In this study we attempted to define specific signaling pathways activated following exposure of proliferating endothelial cells to HKa using a high-throughput, unbiased, microarray approach (Kinexus, Vancouver BC). Results: Endothelial cells were cultured at low density and stimulated to proliferate using 20 ng/ml bFGF in the absence or presence of HKa (15 nM). At various time points (20, 60 and 300 minutes) total cell extracts were prepared and analyzed using the Kinexus antibody microarray that includes 530 pan-specific and 270 phospho-site specific antibodies. In cells exposed to HKa, the analysis revealed increased expression of 109, 141 and 162 proteins, and decreased expression of 117, 68 and 59 proteins at the 20 min, 60 min, and 300 minute time points, respectively. In cells exposed to HKa, the number of newly-phosphorylated proteins increased from 30 at 20 minutes to 61 at 300 minutes after HKa treatment. Segregation of proteins whose expression level and/or phosphorylation state changed following exposure of cells to HKa into families demonstrated that HKa primarily targets protein kinases (61–70% of all proteins affected at the various time points), transcription factors (8–11%), and phosphatases (4–5%). Increased expression of several proteins involved in apoptosis, such as caspases 4, 6 and 7 and DNA fragmentation factors 35 and 45, and increased phosphorylation of stress regulated activating transcription factor 2 (ATF2) and apoptosis signal regulating protein kinase1 (ASK1) were evident within 20 minutes of exposure of cells to HKa. Metacore and Ingenuity pathway analysis of proteins that exhibited rapid changes in expression or phosphorylation revealed activation of several major signaling pathways including apoptosis, DNA damage response, angiogenesis, inflammation, and tissue remodeling and wound repair. Conclusion: Exposure of proliferating endothelial cells to HKa led to rapid changes in protein expression and phosphorylation. Most remarkable was the increased expression of several caspases within 20 minutes of addition of HKa to cells. Patterns of protein expression were consistent with activation of several pathways related to apoptosis, inflammation and tissue remodeling. These findings support suspected physiological functions of HK/HKa in vivo, and suggest specific proteins that may be targeted to further dissect effects of HKa on discrete cellular functions. Disclosures: No relevant conflicts of interest to declare.

The Role of Histone Demethylases in the Transcription Regulation of HOX Genes in PML-RARa+ AML Patients

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 876-876
Author(s):  
Katerina Rejlova ◽  
Karolina Kramarzova ◽  
Meritxell Alberich-Jorda ◽  
Karel Fiser ◽  
Marketa Zaliova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Histone Methylation ◽  
Hox Genes ◽  
Histone Demethylases ◽  
Atra Treatment ◽  
Hox Gene ◽  
Genes Expression ◽  
Methylation Mark

Abstract Homeobox genes (HOX) encode transcription factors that are frequently deregulated in leukemias. Our previous findings described that HOX gene expression differs among genetically characterized subtypes of pediatric AML with PML-RARa+ patients having the lowest overall HOX gene expression. We observed that HOX gene expression positively correlated with expression of histone 3 lysine 27 (H3K27) demethylases JMJD3 and UTX and negatively with DNA methyltransferase DNMT3b. Interestingly, it has been shown that JMJD3 is a direct target of PML-RARa protein (Martens, JH et al, 2010, Cancer Cell). These findings led us to postulate the hypothesis that reduced levels of HOX genes in PML-RARa+ AML can be caused by the suppressed expression of histone demethylases, such as JMJD3 and UTX, resulting in increased H3K27 methylation and transcription inhibition. We chose PML-RARa+ NB4 cell line to study the role of PML-RARa fusion gene in the regulation of HOX gene expression. To inhibit the effect of PML-RARa we used all-trans retinoic acid (ATRA; 1 uM, 10 uM) which was described to release the block caused by this fusion protein. Expression of particular HOX genes (e.g., HOXA1, HOXA3, HOXA5, HOXA7) together with that of JMJD3 and UTX assessed by qPCR was significantly elevated after ATRA treatment, while gene expression of DNMT3b was decreased. To test whether the reduction in HOX gene expression is directly related to the levels of JMJD3 and UTX, we cultured NB4 cells with a specific inhibitor of these histone demethylases, GSK-J4 (1 uM, 10 uM), in combination with ATRA. This co-treatment led to inhibition of JMJD3 and UTX proteins, followed by significant reduction of HOX genes expression (e.g., HOXA1, HOXA3, HOXA5, HOXA7). This result supports our hypothesis that HOX genes expression is directly related to JMJD3/UTX activity. To determine the effect of ATRA and GSK-J4 on histone marks we have isolated histones by acid extraction and detected the levels of histones by western blot in NB4 ATRA or GSK-J4/ATRA treated cells. We observed that the level of repressive histone methylation mark (trimethylated H3K27; H3K27me3) was decreased after ATRA treatment (activation of JMJD3/UTX) and increased after GSK-J4/ATRA co-treatment (inhibition of JMJD3/UTX). The opposite effect was observed in active histone methylation marks where di- and tri-methylated H3K4 (H3K4me2, H3K4me3) increased after ATRA treatment and decreased after GSK-J4/ATRA co-treatment. H3K9 dimethylated (another repressive histone methylation mark) levels did not change. Next, to investigate the histone code directly in particular HOX genes regions we performed chromatin immunoprecipitation (ChIP) assays. We studied the presence of H3K27me3 and H3K4me2 in 5´UTR genomic region of particular HOX genes (HOXA1, HOXA2, HOXA3, HOXA5, HOXA7) in cells treated with ATRA alone or in the combination with GSK-J4. Preliminary results showed reduction in repressive marks (H3K27me3) upon ATRA treatment, whereas addition of GSK-J4 prevented this decrease. Accordingly, we observed that ATRA/GSK-J4 co-treatment reduced active histone mark H3K4me2. To evaluate the role of DNA methylation in observed expression changes after ATRA treatment we performed bisulfite sequencing of particular promoter sites of HOX genes (e.g., HOXA7, HOXA5). Although we detected decreased DNMT3b gene expression after ATRA treatment there was no change in DNA methylation of CpGs in studied regions. Our results demonstrate that changes in chromatin activity correspond with changes in HOX gene expression. Moreover, ChIP data show direct binding of the modified histones and HOX 5´UTR sites. Our data implicate histone demethylases in regulation of HOX gene expression in PML-RARa+ leukemic blasts. DNA methylation in these particular HOX genes is not involved in the regulation. Elucidating the mechanism of regulation of HOX genes expression can help to understand their role in the leukemogenic process. Supported by GACR P304/12/2214 and GAUK 568213. Disclosures No relevant conflicts of interest to declare.

scholarly journals Robust optical oxygen sensors based on polymer-bound NIR-emitting platinum(ii)–benzoporphyrins

2014 ◽  
Vol 2 (36) ◽  
pp. 7589-7598 ◽  
Author(s):  
L. H. Hutter ◽  
B. J. Müller ◽  
K. Koren ◽  
S. M. Borisov ◽  
I. Klimant
Keyword(s):  
High Performance ◽  
Oxygen Sensing ◽  
Oxygen Sensors ◽  
Covalently Bound

New high performance optical oxygen sensing materials based on NIR-emitting indicators covalently bound to various polymers overcome main limitations of the conventional sensors.

scholarly journals Spectroscopic analysis of myoglobin and cytochrome c dynamics in isolated cardiomyocytes during hypoxia and reoxygenation

2015 ◽  
Vol 12 (105) ◽  
pp. 20141339 ◽  
Author(s):  
A. Almohammedi ◽  
S. M. Kapetanaki ◽  
B. R. Wood ◽  
E. L. Raven ◽  
N. M. Storey ◽  
...  
Keyword(s):  
Dissolved Oxygen ◽  
Cellular Response ◽  
Ex Vivo ◽  
Reductase Activity ◽  
Sodium Dithionite ◽  
Raman Microspectroscopy ◽  
Chemical Agent ◽  
Rat Cardiomyocytes ◽  
Hypoxic Conditions ◽  
In Cells

Raman microspectroscopy was applied to monitor the intracellular redox state of myoglobin and cytochrome c from isolated adult rat cardiomyocytes during hypoxia and reoxygenation. The nitrite reductase activity of myoglobin leads to the production of nitric oxide in cells under hypoxic conditions, which is linked to the inhibition of mitochondrial respiration. In this work, the subsequent reoxygenation of cells after hypoxia is shown to lead to increased levels of oxygen-bound myoglobin relative to the initial levels observed under normoxic conditions. Increased levels of reduced cytochrome c in ex vivo cells are also observed during hypoxia and reoxygenation by Raman microspectroscopy. The cellular response to reoxygenation differed dramatically depending on the method used in the preceding step to create hypoxic conditions in the cell suspension, where a chemical agent, sodium dithionite, leads to reduction of cytochromes in addition to removal of dissolved oxygen, and bubbling-N 2 gas leads to displacement of dissolved oxygen only. These results have an impact on the assessment of experimental simulations of hypoxia in cells. The spectroscopic technique employed in this work will be used in the future as an analytical method to monitor the effects of varying levels of oxygen and nutrients supplied to cardiomyocytes during either the preconditioning of cells or the reperfusion of ischaemic tissue.

scholarly journals Structural and functional interactions of the prostate cancer suppressor protein NKX3.1 with topoisomerase I

2013 ◽  
Vol 453 (1) ◽  
pp. 125-136 ◽  
Author(s):  
Liang-Nian Song ◽  
Cai Bowen ◽  
Edward P. Gelmann
Keyword(s):  
Dna Damage ◽  
Protein Interactions ◽  
Topoisomerase I ◽  
Cellular Response ◽  
Peptide Fragments ◽  
The Core ◽  
Tumour Suppressor Protein ◽  
Linker Domain ◽  
In Cells

NKX3.1 (NK3 homeobox 1) is a prostate tumour suppressor protein with a number of activities that are critical for its role in tumour suppression. NKX3.1 mediates the cellular response to DNA damage by interacting with ATM (ataxia telangiectasia mutated) and by activation of topoisomerase I. In the present study we characterized the interaction between NKX3.1 and topoisomerase I. The NKX3.1 homeodomain binds to a region of topoisomerase I spanning the junction between the core and linker domains. Loss of the topoisomerase I N-terminal domain, a region for frequent protein interactions, did not affect binding to NKX3.1 as was shown by the activation of Topo70 (N-terminal truncated topoisomerase I) in vitro. In contrast, NKX3.1 interacts with the enzyme reconstituted from peptide fragments of the core and linker active site domains, but inhibits the DNA-resolving activity of the reconstituted enzyme in vitro. The effect of NKX3.1 on both Topo70 and the reconstituted enzyme was seen in the presence and absence of camptothecin. Neither NKX3.1 nor CPT (camptothecin) had an effect on the interaction of the other with topoisomerase I. Therefore the interactions of NKX3.1 and CPT with the linker domain of topoisomerase I are mutually exclusive. However, in cells the effect of NKX3.1 on topoisomerase binding to DNA sensitized the cells to cellular toxicity and the induction of apoptosis by low doses of CPT. Lastly, topoisomerase I is important for the effect of NKX3.1 on cell survival after DNA damage as topoisomerase knockdown blocked the effect of NKX3.1 on clonogenicity after DNA damage. Therefore NKX3.1 and topoisomerase I interact in vitro and in cells to affect the CPT sensitivity and DNA-repair functions of NKX3.1.

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