Specific Histone Demethylase Research Articles

Abstract 2887: Epigenetic silencing of the DNA repair genes, BRCA1 and MLH1, induced by hypoxic stress in a pathway dependent on the histone demethylase, LSD1

Abstract Hypoxia is a key microenviromental stress in solid tumors that is associated with poor prognosis. It has been indicated that hypoxia induces genetic instability through multiple mechanisms. Previously, we have shown that BRCA1 and RAD51, in the homology dependent repair (HDR) pathway, and MLH1 and MSH2, key components of MMR, are down-regulated at the transcriptional level in response to hypoxia. Here we show that hypoxia also drives epigenetic modification of the BRCA1 and MLH1 promoters, with decreased H3K4 methylation as a key repressive modification produced by the lysine specific histone demethylase, LSD1. In cells containing the BRCA1 promoter driving a selectable HPRT gene, long-term silencing of the promoter was observed following exposure to hypoxic stress. The silenced clones showed decreased H3K4 methylation and decreased H3K9 acetylation in the BRCA1 promoters, consistent with the acute effects of hypoxic stress. Similarly, we also found that hypoxia causes durable long-term silencing of the MLH1 promoter in a pathway that requires LSD1. Knockdown of LSD1 or its co-repressor, CoREST, also prevents the re-silencing (and associated cytosine DNA methylation) of the endogenous MLH1 promoter in RKO colon cancer cells following transient reactivation by treatment with the DNA methyltransferase inhibitor 5-aza-2′-deoxycytidine (5-aza-dC). These results suggest that hypoxia is a driving force for long-term silencing of DNA repair genes, including BRCA1 and MLH1, thereby promoting genome instability and tumor progression. Citation Format: Yuhong Lu, Adrian Chu, Narendra Wajapeyee, Mitchell S. Turker, Peter M. Glazer. Epigenetic silencing of the DNA repair genes, BRCA1 and MLH1, induced by hypoxic stress in a pathway dependent on the histone demethylase, LSD1. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2887. doi:10.1158/1538-7445.AM2015-2887

The histone demethylase KDM4B interacts with MyoD to regulate myogenic differentiation in C2C12 myoblast cells

Enzymes that mediate posttranslational modifications of histone and nonhistone proteins have been implicated in regulation of skeletal muscle differentiation. However, functions of histone demethylases that could counter the actions of H3-K9 specific histone methyltransferases remain still obscure. Here we present evidences that KDM4B histone demethylase regulates expression of myogenic regulators such as MyoD and thereby controls myogenic differentiation of C2C12 myoblast cells. We demonstrate that expression of KDM4B gradually increases during myogenic differentiation and depletion of KDM4B using shRNA results in inhibition of differentiation in C2C12 myoblast cells, which is correlated with decreased expression of MyoD and myogenin. In addition, we find that KDM4B shRNA represses expression of MyoD promoter-driven luciferase reporter and exogenous expression of MyoD rescues myogenic potential in KDM4B-depleted myoblast cells. We further show that KDM4B interacts with MyoD, binds to MyoD and myogenin promoters in vivo, and finally, is involved in demethylation of tri-methylated H3-K9 on promoters of MyoD and myogenin. Taken together, our data suggest that KDM4B plays key roles in myogenic differentiation of C2C12 cells, presumably by its function as a H3-K9 specific histone demethylase.

Abstract 5143: KDM3A promotes cell growth and cisplatin-resistance in ovarian cancer cells

Abstract Background: Ovarian cancer is the most lethal gynecological cancer affecting the women worldwide. One of the main challenging hurdles in ovarian cancer treatment is the high recurrence rate due to therapeutic resistance. Recent evidences showed that JmjC-domain (JMJD) containing histone demethylases plays a critical role in controlling gene expression during normal development and cancer progression. Aims: To determine whether histone demethylase plays a role in ovarian cancer progression and therapeutic resistance. Methods: We developed cisplatin-resistance ovarian cancer cell lines SKOV-3 and OVCAR-5 and isolated total RNA to screen the expression pattern of JMJD family genes by real-time RT-PCR. We performed stable knock-down of KDM3A by lentiviral mediated ShRNA transfection and studied its effects on cell proliferation and apoptosis by MTT assay and western blot analysis (PARP, caspase-3), respectively. We also determined the effect of KDM3A knock-down on cell cycle and apoptosis regulators by western blot. Results: Our observations indicated the differential expression of various JMJD family proteins between cisplatin-resistance and sensitive cell lines. To further evaluate our results, we also tested the expression of those differentially expressed JMJD proteins in a widely used cisplatin-resistance and sensitive A2780 cell lines. We observed that KDM3A/JMJD1A is consistently overexpressed in all the cisplatin-resistance cell lines studied. Next, we stably knock-down KDM3A in cisplatin-resistance OVCAR-5 and A2780 cell lines. More interestingly, we found that KDM3A depletion inhibited cell proliferation, induced apoptosis and enhanced the sensitivity to cisplatin treatment. Further, we confirmed that the important regulators of cell cycle and apoptosis including p21 and Bcl-2 were modulated by KDM3A knock-down. Conclusions: Our results indicate that KDM3A is a critical epigenetic factor required for the ovarian cancer growth by promoting cell proliferation and cisplatin-resistance. Our findings might have important clinical implications in targeting ovarian cancer cells by using specific histone demethylase inhibitors. Grant support: This work was supported by Carl and Roberta Deutsch, and Kelly Day Foundations. Citation Format: Sivakumar Ramadoss, Suvajit Sen, Gautam Chaudhuri, Robin Farias-Eisner. KDM3A promotes cell growth and cisplatin-resistance in ovarian cancer cells. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5143. doi:10.1158/1538-7445.AM2014-5143

Substrate- and cofactor-independent inhibition of histone demethylase KDM4C.

Inhibition of histone demethylases has within recent years advanced into a new strategy for treating cancer and other diseases. Targeting specific histone demethylases can be challenging, as the active sites of KDM1A-B and KDM4A-D histone demethylases are highly conserved. Most inhibitors developed up-to-date target either the cofactor- or substrate-binding sites of these enzymes, resulting in a lack of selectivity and off-target effects. This study describes the discovery of the first peptide-based inhibitors of KDM4 histone demethylases that do not share the histone peptide sequence or inhibit through substrate competition. Through screening of DNA-encoded peptide libraries against KDM1 and -4 histone demethylases by phage display, two cyclic peptides targeting the histone demethylase KDM4C were identified and developed as inhibitors by amino acid replacement, truncation, and chemical modifications. Hydrogen/deuterium exchange mass spectrometry revealed that the peptide-based inhibitors target KDM4C through substrate-independent interactions located on the surface remote from the active site within less conserved regions of KDM4C. The sites discovered in this study provide a new approach of targeting KDM4C through substrate- and cofactor-independent interactions and may be further explored to develop potent selective inhibitors and biological probes for the KDM4 family.

Cell-type-specific Jumonji histone demethylase gene expression in the healthy rat CNS: detection by a novel flow cytometry method.

Our understanding of how histone demethylation contributes to the regulation of basal gene expression in the brain is largely unknown in any injury model, and especially in the healthy adult brain. Although Jumonji genes are often regulated transcriptionally, cell-specific gene expression of Jumonji histone demethylases in the brain remains poorly understood. Thus, in the present study we profiled the mRNA levels of 26 Jumonji genes in microglia (CD11b+), neurons (NeuN+) and astrocytes (GFAP+) from the healthy adult rat brain. We optimized a method combining a mZBF (modified zinc-based fixative) and FCM (flow cytometry) to simultaneously sort cells from non-transgenic animals. We evaluated cell-surface, intracellular and nuclear proteins, including histones, as well as messenger- and micro-RNAs in different cell types simultaneously from a single-sorted sample. We found that 12 Jumonji genes were differentially expressed between adult microglia, neurons and astrocytes. While JMJD2D was neuron-restricted, PHF8 and JMJD1C were expressed in all three cell types although the expression was highest in neurons. JMJD3 and JMJD5 were expressed in all cell types, but were highly enriched in microglia; astrocytes had the lowest expression of UTX and JHDM1D. Levels of global H3K27 (H3 lysine 27) methylation varied among cell types and appeared to be lowest in microglia, indicating that differences in basal gene expression of specific Jumonji histone demethylases may contribute to cell-specific gene expression in the CNS (central nervous system). This multiparametric technique will be valuable for simultaneously assaying chromatin modifications and gene regulation in the adult CNS.

Correction: Corrigendum: Drosophila Kdm4 demethylases in histone H3 lysine 9 demethylation and ecdysteroid signalling

The dynamic regulation of chromatin structure by histone post-translational modification is an essential regulatory mechanism that controls global gene transcription. The Kdm4 family of H3K9me2,3 and H3K36me2,3 dual specific histone demethylases has been implicated in development and tumorigenesis. Here we show that Drosophila Kdm4A and Kdm4B are together essential for mediating ecdysteroid hormone signaling during larval development. Loss of Kdm4 genes leads to globally elevated levels of the heterochromatin marker H3K9me2,3 and impedes transcriptional activation of ecdysone response genes, resulting in developmental arrest. We further show that Kdm4A interacts with the Ecdysone Receptor (EcR) and colocalizes with EcR at its target gene promoter. Our studies suggest that Kdm4A may function as a transcriptional co-activator by removing the repressive histone mark H3K9me2,3 from cognate promoters.

HIF-1-dependent induction of Jumonji domain-containing protein (JMJD) 3 under hypoxic conditions.

Jumonji domain-containing proteins (JMJD) catalyze the oxidative demethylation of a methylated lysine residue of histones by using O2, α-ketoglutarate, vitamin C, and Fe(II). Several JMJDs are induced by hypoxic stress to compensate their presumed reduction in catalytic activity under hypoxia. In this study, we showed that an H3K27me3 specific histone demethylase, JMJD3 was induced by hypoxia-inducible factor (HIF)-1α/β under hypoxia and that treatment with Clioquinol, a HIF-1α activator, increased JMJD3 expression even under normoxia. Chromatin immunoprecipitation (ChIP) analyses showed that both HIF-1α and its dimerization partner HIF-1β/Arnt occupied the first intron region of the mouse JMJD3 gene, whereas the HIF-1α/β heterodimer bound to the upstream region of the human JMJD3, indicating that human and mouse JMJD3 have hypoxia-responsive regulatory regions in different locations. This study shows that both mouse and human JMJD3 are induced by HIF-1.

Drosophila Kdm4 demethylases in histone H3 lysine 9 demethylation and ecdysteroid signaling

The dynamic regulation of chromatin structure by histone post-translational modification is an essential regulatory mechanism that controls global gene transcription. The Kdm4 family of H3K9me2,3 and H3K36me2,3 dual specific histone demethylases has been implicated in development and tumorigenesis. Here we show that Drosophila Kdm4A and Kdm4B are together essential for mediating ecdysteroid hormone signaling during larval development. Loss of Kdm4 genes leads to globally elevated levels of the heterochromatin marker H3K9me2,3 and impedes transcriptional activation of ecdysone response genes, resulting in developmental arrest. We further show that Kdm4A interacts with the Ecdysone Receptor (EcR) and colocalizes with EcR at its target gene promoter. Our studies suggest that Kdm4A may function as a transcriptional co-activator by removing the repressive histone mark H3K9me2,3 from cognate promoters.

Structural and evolutionary basis for the dual substrate selectivity of human KDM4 histone demethylase family.

N(ε)-Methylations of histone lysine residues play critical roles in cell biology by "marking" chromatin for transcriptional activation or repression. Lysine demethylases reverse N(ε)-methylation in a sequence- and methylation-selective manner. The determinants of sequence selectivity for histone demethylases have been unclear. The human JMJD2 (KDM4) H3K9 and H3K36 demethylases can be divided into members that act on both H3K9 and H3K36 and H3K9 alone. Kinetic, crystallographic, and mutagenetic studies in vitro and in cells on KDM4A-E reveal that selectivity is determined by multiple interactions within the catalytic domain but outside the active site. Structurally informed phylogenetic analyses reveal that KDM4A-C orthologues exist in all genome-sequenced vertebrates with earlier animals containing only a single KDM4 enzyme. KDM4D orthologues only exist in eutherians (placental mammals) where they are conserved, including proposed substrate sequence-determining residues. The results will be useful for the identification of inhibitors for specific histone demethylases.

PKA-dependent regulation of the histone lysine demethylase complex PHF2–ARID5B

Reversible histone methylation and demethylation are highly regulated processes that are crucial for chromatin reorganization and regulation of gene transcription in response to extracellular conditions. However, the mechanisms that regulate histone-modifying enzymes are largely unknown. Here, we characterized a protein kinase A (PKA)-dependent histone lysine demethylase complex, PHF2-ARID5B. PHF2, a jmjC demethylase, is enzymatically inactive by itself, but becomes an active H3K9Me2 demethylase through PKA-mediated phosphorylation. We found that phosphorylated PHF2 then associates with ARID5B, a DNA-binding protein, and induce demethylation of methylated ARID5B. This modification leads to targeting of the PHF2-ARID5B complex to its target promoters, where it removes the repressive H3K9Me2 mark. These findings suggest that the PHF2-ARID5B complex is a signal-sensing modulator of histone methylation and gene transcription, in which phosphorylation of PHF2 enables subsequent formation of a competent and specific histone demethylase complex.

Epigenetic Dysregulation in Lymphoid Malignancies

AbstractAbstract SCI-29Greater understanding of the role of the epigenetic mechanisms and cancer cell epigenome in the pathogenesis of cancer in general and lymphoid malignancies in particular has emerged, which is yielding insights into how to therapeutically target these novel mechanisms. Epigenetic mechanisms include histone modifications, DNA methylation, nucleosome remodeling and small non-coding RNAs. In transformed cells, the methylome involves global DNA hypomethylation mostly targeting DNA repeats, and hypermethylation of CpG islands in the promoter regions of TSGs. For example, methylation and silencing of cell cycle dependent kinase inhibitors p16 and p15, and of DNA repair protein MGMT, is observed in lymphoma. A disequilibrium in the lysine (K) acetylation/deacetylation of the N-terminal tail of the core histone (H) proteins due to increased histone deacetylase (HDAC) activity leads to aberrant transcription repression of genes involved in regulation of proliferation and differentiation of lymphoid progenitors in lymphoid malignancies. Additionally, increased HDAC levels and activity may directly deacetylate and modify the transcriptional activity of transcription factors, or HDACs may be recruited along with co-repressors by transcriptional repressors such as Bcl-6 to the promoters of the repressed genes in lymphoma. Histone lysine methylation, regulated by the reciprocal activity of a specific histone methyl transferase (HMTs) and histone de-methylase, also modifies gene expression based on the lysine residue that is affected. For example, increased levels and activity of the polycomb repressive complex (PRC) 2 protein EZH (enhancer of zeste) 2, a histone methyl transferase induces the repressive chromatin mark H3K27 trimethylation (me3), which is erased by the demethylase, UTX. Mutations in EZH2 and UTX have been observed in transformed cells. Conversely, the methylation status of the permissive chromatin mark H3K4me3 and gene expression is reciprocally controlled by the HMTase, MLL, and the demethylases JARID1A and LSD1. PRC1 protein, BMI-1, is over-expressed and implicated in lymphoid malignancies. Genetic abnormalities of cell fate transcription factors (CFTFs), e.g., MYB, PAX5 and IKAROS, which recruit PRC1 and PRC2 complexes and their member proteins, e.g., BMI and EZH2, also deregulate the expression of developmentally regulated genes involved in stem cell behavior, related to self-renewal, proliferation and differentiation of transformed cells. PRC proteins EZH2 and BMI, in turn, can recruit DNMTs and promote de novo DNA methylation of TSGs. Levels and activity of the non-coding small (MiRs 101 and 26a for EZH2; MiR 29 for DNMT3a and DNMT3b; and MiR15a and 16 for BMI) may also be deregulated in transformed cells. Interestingly, the levels of MiRs are epigenetically regulated. Collectively, the complex interplay of the epigenetic mechanisms in the pathogenesis of lymphoid malignancies underscores the importance of targeting the deregulated mechanisms in a combinatorial fashion. Inhibitors of chromatin modifying enzymes including HDACs and DNMTs are approved for therapy by the FDA and, given alone or in combination, have shown efficacy in clinical trials in hematologic malignancies. Combined inhibition of EZH2 and HDACs also displays anti-lymphoma and anti-leukemia synergy. In the presentation, the emerging knowledge related to the role of epigenetic mechanisms in the pathogenesis of lymphoid malignancies, as well as the potential for combined therapeutic targeting of the deregulated mechanisms will be highlighted. Disclosures:Bhalla:Novartis: Honoraria, Research Funding; Merck: Honoraria.

Physiological Roles of Class I HDAC Complex and Histone Demethylase

Epigenetic gene silencing is one of the fundamental mechanisms for ensuring proper gene expression patterns during cellular differentiation and development. Histone deacetylases (HDACs) are evolutionally conserved enzymes that remove acetyl modifications from histones and play a central role in epigenetic gene silencing. In cells, HDAC forms a multiprotein complex (HDAC complex) in which the associated proteins are believed to help HDAC carry out its cellular functions. Though each HDAC complex contains distinct components, the presence of isoforms for some of the components expands the variety of complexes and the diversity of their cellular roles. Recent studies have also revealed a functional link between HDAC complexes and specific histone demethylases. In this paper, we summarize the distinct and cooperative roles of four class I HDAC complexes, Sin3, NuRD, CoREST, and NCoR/SMRT, with respect to their component diversity and their relationship with specific histone demethylases.

Abstract 3796: Inhibition of epigenetic chromatin-modification enzymes: histone deacetylases and DNA methyltransferases by silibinin in human NSCLC H1299 cells

Abstract Epigenetic modifications of histones (e.g. hypoacetylation) and DNA (e.g. hypermethylation) cause reversible alterations in chromatin structure leading to aberrant changes in gene expression, which eventually impact cellular processes like cell cycle, apoptosis, and invasion during malignant transformation of cells. Several tumor suppressor genes like CDH1, RARB, RASSF1A, MGMT etc are silenced by these interlinked mechanisms in human lung cancer; the leading diagnosed and lethal malignancy world wide. Hence, the impetus has been on developing novel agents that target ‘epigenome’ for both cancer therapy and chemoprevention. Silibinin, a flavanolignan isolated from the seeds of milk thistle exerts strong anti-cancer efficacy against many epithelial cancers including lung. Recently, we showed that silibinin inhibits p53 null-H1299 cell growth through G1 arrest by modulating the expression and function of associated key cell-cycle regulators. Herein, we assessed the effect of silibinin on major chromatin-modification enzymes to delineate their possible involvement in the observed silibinin effects. A time response study for histone deacetylase (HDAC) activity in total cell extract showed that silibinin treatment causes a dose-dependent decrease in enzyme activity from 6h [(100 µM; p<0.05)]-72h [(75-100 µM; p<0.001)]. Concomitantly, under similar treatment conditions, a sustained accumulation of acetylated histones (H3 and H4) in total cellular chromatin was observed between 6-24h time points. We also addressed the question whether silibinin directly inhibits HDAC activity in a cell free system. In both total and nuclear cell extracts, a decreasing trend in enzyme activity was observed by silibinin addition in incubation reactions, but the concentration for 50% inhibition (IC50) was ∼ 400 µM, suggesting an indirect effect of silibinin in regulating HDAC activity in cell free system. Consistent with these results, silibinin (75-100 µM) also caused a decrease in the protein levels of HDAC1, HDAC2, HDAC3, DNMT1 and DNMT3A in nuclear and total extracts after 24, 48 and 72h of treatment. Next, we evaluated the expression profile of 84 key genes encoding chromatin-modification enzymes in H1299 cells after silibinin treatment (100 µM; 72h). Real time RT-PCR array analysis identified a subset of fifteen genes, primarily including DNMT3A, HDAC1, HDAC6, SET domain proteins (SETD1A, D4, D6) and lysine specific demethylases (KDM 5B, 5C, 4A) which were significantly down-regulated (∼2-4 fold) in silibinin treated samples compared to vehicle controls. Collectively, these results show that silibinin inhibits specific histone deacetylases, histone demethylases and DNA methyltransferases, which might cooperatively contribute to the anti-cancer efficacy of this non-toxic phytochemical. (Supported by CA113876) Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3796.

Inflammation, HIF-1, and the Epigenetics That Follows

We summarize recent findings linking inflammatory hypoxia to chromatin modifications, in particular to repressive histone signatures. We focus on the role of Hypoxia-Induced Factor-1 in promoting the activity of specific histone demethylases thus deeply modifying chromatin configuration. The consequences of these changes are depicted in terms of gene expression and cellular phenotypes. We finally integrate available data to introduce novel speculations on the relationship between inflammation, histones, and DNA function and integrity.

500. THE MANIPULATION OF THE EPIGENETIC MARK HISTONE 3 LYSINE 9 TRIMETHYLATION IN DONOR CELLS AND ITS EFFECTS ON THE DEVELOPMENT OF CLONED MOUSE EMBRYOS

To produce live cloned mammals from adult somatic cells the nuclei of these cells must be first reprogrammed from a very restricted, cell lineage-specific gene expression profile to an embryo-like expression pattern, compatible with embryonic development. Although this has been achieved in a number of species the efficiency of cloning remains very low. Inadequate reprogramming of epigenetic marks in the donor cells correlated with aberrant embryonic gene expression profiles has been identified as a key cause of this inefficiency. Some of the most common epigenetic marks are chemical modifications of histones, the main structural proteins of chromatin. A range of different histone modifications, including acetylation and methylation, exists and can be attributed to either repression or activation of genes. One epigenetic mark which is known to be very stable and difficult to remove during reprogramming is the trimethylation of lysine 9 in histone H3 (H3K9Me3). To test the hypothesis that H3K9Me3 marks are a major stumbling block for successful cloning we are attempting to remove these marks by overexpression of the H3K9Me3 specific histone demethylase, jmjd2b, in donor cells, prior to their use for nuclear transfer. We have engineered mouse embryonic stem (ES) cells for the tet inducible expression of a fusion protein with a functional jmjd2b or non-functional mutant jmjd2b histone demethylase. Approximately 94% and 88% of the cells can be induced for the expression of functional and mutant jmjd2b-EGFP in the respective ES cell lines. Immunofluorescence analyses have shown that induction of functional jmjd2b-EGFP results in an approximately 50% reduction of H3K9Me3 levels compared to non-induced cells and induced mutant jmjd2b-EGFP cells. The comparison of the in-vitro embryo development following nuclear transfer with induced and non-induced donor cells show significantly better overall development to blastocysts and morulae from induced donor cells with reduced H3K9Me3 levels.

Derepression in the Desert: The Third Workshop on Clinical Translation of Epigenetics in Cancer Therapeutics

In the past decade, the scientific and medical community has witnessed dramatic progress in epigenetics and has begun to understand some of the epigenetic mechanisms that contribute to human disease, particularly cancer. In January 2007, the third biannual workshop on Clinical Translation of

Histone Methylation-Dependent Mechanisms Impose Ligand Dependency for Gene Activation by Nuclear Receptors

Nuclear receptors undergo ligand-dependent conformational changes that are required for corepressor-coactivator exchange, but whether there is an actual requirement for specific epigenetic landmarks to impose ligand dependency for gene activation remains unknown. Here we report an unexpected and general strategy that is based on the requirement for specific cohorts of inhibitory histone methyltransferases (HMTs) to impose gene-specific gatekeeper functions that prevent unliganded nuclear receptors and other classes of regulated transcription factors from binding to their target gene promoters and causing constitutive gene activation in the absence of stimulating signals. This strategy, based at least in part on an HMT-dependent inhibitory histone code, imposes a requirement for specific histone demethylases, including LSD1, to permit ligand- and signal-dependent activation of regulated gene expression. These events link an inhibitory methylation component of the histone code to a broadly used strategy that circumvents pathological constitutive gene induction by physiologically regulated transcription factors.

8 Demethylation pathways for histone methyllysine residues

Histone lysine methylation is one of the posttranslational modifications involved in transcriptional regulation and chromatin remodeling. The first lysine specific histone demethylase (LSD1) has been recently discovered, whichrules out the hypothesis that histone methylation represents a permanent epigenetic mark. LSD1 (previously known as KIAA0601) has been typically found in association with CoREST (a corepressor protein) and histone deacetylases 1 and 2, forming a highly conserved core complex. These proteins have been shown to be part of several megadalton corepressor complexes, which are proposed to operate in the context of a stable and extended form of repression through silencing of entire chromatin domains. LSD1 is a FAD-dependent protein that specifically catalyzes the demethylation of Lys4 of histone H3 by an oxidative process. The amino acid sequence of the human enzyme (90 kDa) has a modular organization with an N-terminal SWIRM domain, which has been found to mediate protein-protein interactions, and a C-terminal domain similar to FAD-dependent amine oxidases. Three assays based on different events of the demethylation reaction can be used to study LSD1 biochemical properties. The strict substrate specificity of LSD1 suggests the existence of other putative histone lysine demethylases that may use alternative mechanisms for the regulation of this posttranslational modification.

Regulation of LSD1 Histone Demethylase Activity by Its Associated Factors

LSD1 is a recently identified human lysine (K)-specific histone demethylase. LSD1 is associated with HDAC1/2; CoREST, a SANT domain-containing corepressor; and BHC80, a PHD domain-containing protein, among others. We show that CoREST endows LSD1 with the ability to demethylate nucleosomal substrates and that it protects LSD1 from proteasomal degradation in vivo. We find hyperacetylated nucleosomes less susceptible to CoREST/LSD1-mediated demethylation, suggesting that hypoacetylated nucleosomes may be the preferred physiological substrates. This raises the possibility that histone deacetylases and LSD1 may collaborate to generate a repressive chromatin environment. Consistent with this model, TSA treatment results in derepression of LSD1 target genes. While CoREST positively regulates LSD1 function, BHC80 inhibits CoREST/LSD1-mediated demethylation in vitro and may therefore confer negative regulation. Taken together, these findings suggest that LSD1-mediated histone demethylation is regulated dynamically in vivo. This is expected to have profound effects on gene expression under both physiological and pathological conditions.