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

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.

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The UTX Tumor Suppressor Directly Senses Oxygen to Control Chromatin and Cell Fate

10.1101/510479 ◽

2019 ◽

Author(s):

Abhishek A. Chakraborty ◽

Tuomas Laukka ◽

Matti Myllykoski ◽

Alison E. Ringel ◽

Matthew A. Booker ◽

...

Keyword(s):

Cell Fate ◽

Indirect Effects ◽

Mammalian Cells ◽

Control Cell ◽

Histone Demethylase ◽

Hypoxic Induction ◽

Hypoxic Conditions ◽

Chromatin Regulators ◽

Oxygen Sensitive ◽

Demethylase Activity

AbstractMammalian cells express multiple 2-oxoglutarate (OG)-dependent dioxygenases, including many chromatin regulators. The oxygen affinities, and hence oxygen sensing capabilities, of the 2-oxoglutarate (OG)-dependent dioxygenases reported to date vary widely. Hypoxia can affect chromatin, but whether this reflects a direct effect on chromatin-modifying dioxygenases, or indirect effects caused by the hypoxic-induction of the HIF transcription factor or the endogenous 2-OG competitor 2-hydroxyglutarate (2-HG), is unclear. Here we report that hypoxia induces a HIF- and 2-HG-independent histone modification signature consistent with KDM inactivation. We also show that the H3K27 histone demethylase KDM6A (also called UTX), but not its paralog KDM6B, is oxygen-sensitive. KDM6A loss, like hypoxia, prevented H3K27me3 erasure and blocked differentiation. Conversely, restoring H3K27me3 homeostasis in hypoxic cells reversed these effects. Therefore, oxygen directly affects chromatin regulators to control cell fate.One Sentence SummaryKDM6A demethylase activity is diminished under hypoxic conditions and causes changes in gene expression programs that govern cell fate.

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Hypoxia induces rapid changes to histone methylation and reprograms chromatin

Science ◽

10.1126/science.aau5870 ◽

2019 ◽

Vol 363 (6432) ◽

pp. 1222-1226 ◽

Cited By ~ 84

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.

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Pcgf1 regulates early neural tube development through histone methylation in zebrafish

10.21203/rs.3.rs-25978/v1 ◽

2020 ◽

Author(s):

Xinyue Li ◽

Guangyu Ji ◽

Juan Zhou ◽

Jingyi Du ◽

Xian Li ◽

...

Keyword(s):

Cell Fate ◽

Neural Tube ◽

Histone Methylation ◽

Control Cell ◽

Neural Induction ◽

Induction Phase ◽

Zebrafish Embryos ◽

Rna Seq ◽

Self Renewal ◽

Neural Tube Development

Abstract Objective Early neural tube development in the embryo includes neural induction and self-renewal of neural stem cells (NSCs). The abnormal of neural tube development could lead to neural tube defects. The research on the mechanism of neural induction is the key to reveal the pathogenesis of the abnormal of neural tube. Though studies have confirmed a genetic component, the responsible mechanisms for the abnormal of neural tube are still largely unknown. Polycomb repressive complex 1 (PRC1) plays an important role in regulating early embryonic development, and has been sub-classified into six major complexes based on the presence of a Pcgf subunit. Pcgf1, as one of six Pcgf paralogs, is an important requirement in early embryonic brain development. Here, we intended to investigate the role and mechanism of Pcgf1 in early neural tube development of zebrafish embryos. Material and methods Morpholino (MO) antisense oligonucleotides were used to construct a Pcgf1 loss-of function zebrafish model. We analyzed the phenotype of zebrafish embryos and the expression of related genes in the process of neural induction by in situ hybridization, immunolabelling and RNA-sEq. The regulation of histone modifications on gene was detected by western blot and chromatin immunoprecipitation. Results In this study, we found that zebrafish embryos exhibited small head and reduced or even absence of telencephalon after inhibiting the expression of Pcgf1. Moreover, the neural induction process of zebrafish embryos was abnormal, and the subsequent NSCs self-renewal was inhibited under the inhibition of Pcgf1. RNA-seq and gene ontology (GO) analysis identified that the differentially expressed genes were enriched in many functional categories which related to the development phenotype. Finally, our results showed that Pcgf1 regulated the trimethylation of histone H3K27 in the Ngn1 and Otx2 promoter regions, and the levels of H3K4me3 at the promoters of Pou5f3 and Nanog. Conclusion Together, our data for the first time demonstrate that Pcgf1 plays an essential role in early neural induction phase through histone methylation in neural tube development. Our findings reveal a critical context-specific function for Pcgf1 in directing PRC1 to control cell fate.

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Histone H3K4 demethylases are essential in development and differentiationThis paper is one of a selection of papers published in this Special Issue, entitled 28th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.

Biochemistry and Cell Biology ◽

10.1139/o07-057 ◽

2007 ◽

Vol 85 (4) ◽

pp. 435-443 ◽

Cited By ~ 55

Author(s):

Elizaveta V. Benevolenskaya

Keyword(s):

Cell Fate ◽

Histone Methylation ◽

Peer Review Process ◽

Active Regions ◽

Model Organisms ◽

Global Changes ◽

Histone Demethylases ◽

Trithorax Group ◽

Demethylase Activity ◽

Jmjc Domain

Lysine histone methylation is one of the most robust epigenetic marks and is essential for the regulation of multiple cellular processes. The methylation of Lys4 of histone H3 seems to be of particular significance. It is associated with active regions of the genome, and in Drosophila it is catalyzed by trithorax-group proteins that have become paradigms of developmental regulators at the level of chromatin. Like other histone methylation events, H3K4 methylation was considered irreversible until the identification of a large number of histone demethylases indicated that demethylation events play an important role in histone modification dynamics. However, the described demethylases had no strictly assigned biological functions and the identity of the histone demethylases that would contribute to the epigenetic changes specifying certain biological processes was unknown. Recently, several groups presented evidence that a family of 4 JmjC domain proteins results in the global changes of histone demethylation, and in elegant studies using model organisms, they demonstrated the importance of this family of histone demethylases in cell fate determination. All 4 proteins possess the demethylase activity specific to H3K4 and belong to the poorly described JARID1 protein family.

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Glutathione in Cerebral Microvascular Endothelial Biology and Pathobiology: Implications for Brain Homeostasis

International Journal of Cell Biology ◽

10.1155/2012/434971 ◽

2012 ◽

Vol 2012 ◽

pp. 1-14 ◽

Cited By ~ 16

Author(s):

Wei Li ◽

Carmina Busu ◽

Magdalena L. Circu ◽

Tak Yee Aw

Keyword(s):

Cell Proliferation ◽

Endothelial Cell ◽

Cell Fate ◽

Mammalian Cells ◽

Redox Regulation ◽

Cell Injury ◽

Control Cell ◽

Endothelial Cell Proliferation ◽

Special Focus ◽

Vascular Integrity

The integrity of the vascular endothelium of the blood-brain barrier (BBB) is central to cerebrovascular homeostasis. Given the function of the BBB as a physical and metabolic barrier that buffers the systemic environment, oxidative damage to the endothelial monolayer will have significant deleterious impact on the metabolic, immunological, and neurological functions of the brain. Glutathione (GSH) is a ubiquitous major thiol within mammalian cells that plays important roles in antioxidant defense, oxidation-reduction reactions in metabolic pathways, and redox signaling. The existence of distinct GSH pools within the subcellular organelles supports an elegant mode for independent redox regulation of metabolic processes, including those that control cell fate. GSH-dependent homeostatic control of neurovascular function is relatively unexplored. Significantly, GSH regulation of two aspects of endothelial function is paramount to barrier preservation, namely, GSH protection against oxidative endothelial cell injury and GSH control of postdamage cell proliferation in endothelial repair and/or wound healing. This paper highlights our current insights and hypotheses into the role of GSH in cerebral microvascular biology and pathobiology with special focus on endothelial GSH and vascular integrity, oxidative disruption of endothelial barrier function, GSH regulation of endothelial cell proliferation, and the pathological implications of GSH disruption in oxidative stress-associated neurovascular disorders, such as diabetes and stroke.

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Histone demethylase KDM6B regulates human podocyte differentiation in vitro

Biochemical Journal ◽

10.1042/bcj20180968 ◽

2019 ◽

Vol 476 (12) ◽

pp. 1741-1751

Author(s):

Yanyan Guo ◽

Zuying Xiong ◽

Xiaoqiang Guo

Keyword(s):

Histone Methylation ◽

Chromatin Immunoprecipitation ◽

Kidney Development ◽

Histone Demethylase ◽

Differentiation Markers ◽

Chromatin Immunoprecipitation Assay ◽

H3k27 Methylation ◽

Filtration Barrier ◽

Histone H3k27

Abstract Podocytes are terminally differentiated and highly specialized glomerular cells, which have an essential role as a filtration barrier against proteinuria. Histone methylation has been shown to influence cell development, but its role in podocyte differentiation is less understood. In this study, we first examined the expression pattern of histone demethylase KDM6B at different times of cultured human podocytes in vitro. We found that the expression of KDM6B and podocyte differentiation markers WT1 and Nephrin are increased in the podocyte differentiation process. In cultured podocytes, KDM6B knockdown with siRNA impaired podocyte differentiation and led to expression down-regulation of WT1 and Nephrin. The treatment of podocytes with GSK-J4, a specific KDM6B inhibitor, can also obtain similar results. Overexpression of WT1 can rescue differentiated phenotype impaired by disruption of KDM6B. ChIP (chromatin immunoprecipitation) assay further indicated that KDM6B can bind the promoter region of WT1 and reduce the histone H3K27 methylation. Podocytes in glomeruli from nephrotic patients exhibited increased KDM6B contents and reduced H3K27me3 levels. These data suggest a role for KDM6B as a regulator of podocyte differentiation, which is important for the understanding of podocyte function in kidney development and related diseases.

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Regulation of Jumonji-domain-containing histone demethylases by hypoxia-inducible factor (HIF)-1α

Biochemical Journal ◽

10.1042/bj20081238 ◽

2008 ◽

Vol 416 (3) ◽

pp. 387-394 ◽

Cited By ~ 209

Author(s):

Patrick J. Pollard ◽

Christoph Loenarz ◽

David R. Mole ◽

Michael A. McDonough ◽

Jonathan M. Gleadle ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Cell Lines ◽

Epigenetic Regulation ◽

Histone Methylation ◽

Chromatin Immunoprecipitation ◽

Methylation Status ◽

Hypoxia Inducible Factor ◽

Transcriptional Response ◽

Histone Demethylases

The transcription factor HIF (hypoxia-inducible factor) mediates a highly pleiotrophic response to hypoxia. Many recent studies have focused on defining the extent of this transcriptional response. In the present study we have analysed regulation by hypoxia among transcripts encoding human Fe(II)- and 2-oxoglutarate-dependent oxygenases. Our results show that many of these genes are regulated by hypoxia and define two groups of histone demethylases as new classes of hypoxia-regulated genes. Patterns of induction were consistent across a range of cell lines with JMJD1A (where JMJD is Jumonji-domain containing) and JMJD2B demonstrating robust, and JMJD2C more modest, up-regulation by hypoxia. Functional genetic and chromatin immunoprecipitation studies demonstrated the importance of HIF-1α in mediating these responses. Given the importance of histone methylation status in defining patterns of gene expression under different physiological and pathophysiological conditions, these findings predict a role for the HIF system in epigenetic regulation.

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The murine Sim-2 gene product inhibits transcription by active repression and functional interference.

Molecular and Cellular Biology ◽

10.1128/mcb.17.9.4933 ◽

1997 ◽

Vol 17 (9) ◽

pp. 4933-4947 ◽

Cited By ~ 61

Author(s):

P Moffett ◽

M Reece ◽

J Pelletier

Keyword(s):

Gene Product ◽

Cell Fate ◽

Transcriptional Activation ◽

Mammalian Cells ◽

Regulatory Protein ◽

Hypoxia Inducible Factor ◽

Structure Mapping ◽

Helix Loop Helix ◽

Aryl Hydrocarbon ◽

Transcription Complexes

The Drosophila single-minded (Dsim) gene encodes a master regulatory protein involved in cell fate determination during midline development. This protein is a member of a rapidly expanding family of gene products possessing basic helix-loop-helix (bHLH) and hydrophobic PAS (designated a conserved region among PER, ARNT [aryl hydrocarbon receptor nuclear translocator] and SIM) protein association domains. Members of this family function as central transcriptional regulators in cellular differentiation and in the response to environmental stimuli such as xenobiotics and hypoxia. We have previously identified a murine member of this family, called mSim-2, showing sequence homology to the bHLH and PAS domains of Dsim. Immunoprecipitation experiments with recombinant proteins indicate that mSIM-2 associates with the arnt gene product. In the present work, by using fine-structure mapping we found that the HLH and PAS motifs of both proteins are required for optimal association. Forced expression of GAL4/mSIM-2 fusion constructs in mammalian cells demonstrated the presence of two separable repression domains within the carboxy terminus of mSIM-2. We found that mSIM-2 is capable of repressing ARNT-mediated transcriptional activation in a mammalian two-hybrid system. This effect (i) is dependent on the ability of mSIM-2 and ARNT to heterodimerize, (ii) is dependent on the presence of the mSIM-2 carboxy-terminal repression domain, and (iii) is not specific to the ARNT activation domain. These results suggest that mSIM-2 repression activity can dominantly override the activation potential of adjacent transcription factors. We also demonstrated that mSIM-2 can functionally interfere with hypoxia-inducible factor 1alpha (HIF-1alpha)/ARNT transcription complexes, providing a second mechanism by which mSIM-2 may inhibit transcription.

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Regulation of the Histone Demethylase JMJD1A by Hypoxia-Inducible Factor 1α Enhances Hypoxic Gene Expression and Tumor Growth

Molecular and Cellular Biology ◽

10.1128/mcb.00444-09 ◽

2009 ◽

Vol 30 (1) ◽

pp. 344-353 ◽

Cited By ~ 225

Author(s):

Adam J. Krieg ◽

Erinn B. Rankin ◽

Denise Chan ◽

Olga Razorenova ◽

Sully Fernandez ◽

...

Keyword(s):

Gene Expression ◽

Tumor Growth ◽

Histone Methylation ◽

Hypoxia Inducible Factor ◽

Histone Demethylase ◽

Carcinoma Cell Lines ◽

Signal Amplifier ◽

Reduce Tumor Growth ◽

Inducible Genes

ABSTRACT The hypoxia-inducible transcription factors (HIFs) directly and indirectly mediate cellular adaptation to reduced oxygen tensions. Recent studies have shown that the histone demethylase genes JMJD1A, JMJD2B, and JARID1B are HIF targets, suggesting that HIFs indirectly influence gene expression at the level of histone methylation under hypoxia. In this study, we identify a subset of hypoxia-inducible genes that are dependent on JMJD1A in both renal cell and colon carcinoma cell lines. JMJD1A regulates the expression of adrenomedullin (ADM) and growth and differentiation factor 15 (GDF15) under hypoxia by decreasing promoter histone methylation. In addition, we demonstrate that loss of JMJD1A is sufficient to reduce tumor growth in vivo, demonstrating that histone demethylation plays a significant role in modulating growth within the tumor microenvironment. Thus, hypoxic regulation of JMJD1A acts as a signal amplifier to facilitate hypoxic gene expression, ultimately enhancing tumor growth.

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Fanconi Anemia FANCM/FNCM-1 and FANCD2/FCD-2 are required for maintaining histone methylation levels and interact with the histone demethylase LSD1/SPR-5 in C. elegans

10.1101/265876 ◽

2018 ◽

Author(s):

Hyun-Min Kim ◽

Sara E. Beese-Sims ◽

Monica P. Colaiácovo

Keyword(s):

Dna Damage ◽

Fanconi Anemia ◽

Histone Methylation ◽

Dna Damage Repair ◽

Replication Stress ◽

Histone Demethylase ◽

Histone Demethylases ◽

Checkpoint Activation ◽

C Elegans ◽

Damage Repair

ABSTRACTThe histone demethylase LSD1 was originally discovered as removing methyl groups from di- and monomethylated histone H3 lysine 4 (H3K4me2/1), and several studies suggest it plays roles in meiosis as well as epigenetic sterility given that in its absence there is evidence of a progressive accumulation of H3K4me2 through generations. In addition to transgenerational sterility, growing evidence for the importance of histone methylation in the regulation of DNA damage repair has attracted more attention to the field in recent years. However, we are still far from understanding the mechanisms by which histone methylation is involved in DNA damage repair and only a few studies have been focused on the roles of histone demethylases in germline maintenance. Here, we show that the histone demethylase LSD1/CeSPR-5 is interacting with the Fanconi Anemia (FA) protein FANCM/CeFNCM-1 based on biochemical, cytological and genetic analyses. LSD1/CeSPR-5 is required for replication stress-induced S-phase checkpoint activation and its absence suppresses the embryonic lethality and larval arrest observed in fncm-1 mutants. FANCM/CeFNCM-1 re-localizes upon hydroxyurea exposure and co-localizes with FANCD2/CeFCD-2 and LSD1/CeSPR-5 suggesting coordination between this histone demethylase and FA components to resolve replication stress. Surprisingly, the FA pathway is required for H3K4me2 maintenance regardless of the presence of replication stress. Our study reveals a connection between Fanconi Anemia and epigenetic maintenance, therefore providing new mechanistic insight into the regulation of histone methylation in DNA repair.

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