Dimethylation Of Lysine Research Articles

Reductive methylation and mutation of an anthrax toxin fusion protein modulates its stability and cytotoxicity.

We characterized an anti-cancer fusion protein consisting of anthrax lethal factor (LF) and the catalytic domain of Pseudomonas exotoxin A by (i) mutating the N-terminal amino acids and by (ii) reductive methylation to dimethylate all lysines. Dimethylation of lysines was achieved quantitatively and specifically without affecting binding of the fusion protein to PA or decreasing the enzymatic activity of the catalytic moiety. Ubiquitination in vitro was drastically decreased for both the N-terminally mutated and dimethylated variants, and both appeared to be slightly more stable in the cytosol of treated cells. The dimethylated variant showed greatly reduced neutralization by antibodies to LF. The two described modifications offer unique advantages such as increased cytotoxic activity and diminished antibody recognition, and thus may be applicable to other therapeutic proteins that act in the cytosol of cells.

Highly effective combination of LSD1 (KDM1A) antagonist and pan-histone deacetylase inhibitor against human AML cells

The histone demethylase LSD1 (KDM1A) demethylates mono- and di-methylated (Me2) lysine (K) 4 on histone H3. High LSD1 expression blocks differentiation and confers a poor prognosis in AML. Here, treatment with the novel LSD1 antagonist SP2509 attenuated the binding of LSD1 with the co-repressor CoREST, increased the permissive H3K4Me3 mark on the target gene promoters, and increased the levels of p21, p27 and C/EBPα in cultured AML cells. Additionally, SP2509 treatment or LSD1 shRNA inhibited the colony growth of AML cells. SP2509 also induced morphologic features of differentiation in the cultured and primary AML blasts. SP2509 induced more apoptosis of AML cells expressing mutant NPM1 than MLL fusion oncoproteins. Treatment with SP2509 alone significantly improved the survival of immune-depleted mice following tail-vein infusion and engraftment of cultured or primary human AML cells. Co-treatment with pan-HDAC inhibitor (HDI) panobinostat (PS) and SP2509 was synergistically lethal against cultured and primary AML blasts. Compared to each agent alone, co-treatment with SP2509 and PS significantly improved the survival of the mice engrafted with the human AML cells, without exhibiting any toxicity. Collectively, these findings show that the combination of LSD1 antagonist and pan-HDI is a promising therapy warranting further testing against AML.

Dynamic remodeling of histone modifications in response to osmotic stress in Saccharomyces cerevisiae

BackgroundSpecific histone modifications play important roles in chromatin functions; i.e., activation or repression of gene transcription. This participation must occur as a dynamic process. Nevertheless, most of the histone modification maps reported to date provide only static pictures that link certain modifications with active or silenced states. This study, however, focuses on the global histone modification variation that occurs in response to the transcriptional reprogramming produced by a physiological perturbation in yeast.ResultsWe did a genome-wide chromatin immunoprecipitation analysis for eight specific histone modifications before and after saline stress. The most striking change was rapid acetylation loss in lysines 9 and 14 of H3 and in lysine 8 of H4, associated with gene repression. The genes activated by saline stress increased the acetylation levels at these same sites, but this acetylation process was quantitatively minor if compared to that of the deacetylation of repressed genes. The changes in the tri-methylation of lysines 4, 36 and 79 of H3 and the di-methylation of lysine 79 of H3 were slighter than those of acetylation. Furthermore, we produced new genome-wide maps for seven histone modifications, and we analyzed, for the first time in S. cerevisiae, the genome-wide profile of acetylation of lysine 8 of H4.ConclusionsThis research reveals that the short-term changes observed in the post-stress methylation of histones are much more moderate than those of acetylation, and that the dynamics of the acetylation state of histones during activation or repression of transcription is a much quicker process than methylation.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-247) contains supplementary material, which is available to authorized users.

Coregulation of Genetic Programs by the Transcription Factors NFIB and STAT5

Mammary-specific genetic programs are activated during pregnancy by the common transcription factor signal transducer and activator of transcription (STAT) 5. More than one third of these genes carry nuclear factor I/B (NFIB) binding motifs that coincide with STAT5 in vivo binding, suggesting functional synergy between these two transcription factors. The role of NFIB in this governance was investigated in mice from which Nfib had been inactivated in mammary stem cells or in differentiating alveolar epithelium. Although NFIB was not required for alveolar expansion, the combined absence of NFIB and STAT5 prevented the formation of functional alveoli. NFIB controlled the expression of mammary-specific and STAT5-regulated genes and chromatin immunoprecipitation-sequencing established STAT5 and NFIB binding at composite regulatory elements containing histone H3 lysine dimethylation enhancer marks and progesterone receptor binding. By integrating previously published chromatin immunoprecipitation-sequencing data sets, the presence of NFIB-STAT5 modules in other cell types was investigated. Notably, genomic sites bound by NFIB in hair follicle stem cells were also occupied by STAT5 in mammary epithelium and coincided with enhancer marks. Many of these genes were under NFIB control in both hair follicle stem cells and mammary alveolar epithelium. We propose that NFIB-STAT5 modules, possibly in conjunction with other transcription factors, control cell-specific genetic programs.

SHOOT GROWTH1 Maintains Arabidopsis Epigenomes by Regulating IBM1

Maintaining correct DNA and histone methylation patterns is essential for the development of all eukaryotes. In Arabidopsis, we identified SHOOT GROWTH1 (SG1), a novel protein involved in the control of gene methylation. SG1 contains both a Bromo-Adjacent Homology (BAH) domain found in several chromatin regulators and an RNA-Recognition Motif (RRM). The sg1 mutations are associated with drastic pleiotropic phenotypes. The mutants degenerate after few generations and are similar to mutants of the histone demethylase INCREASE IN BONSAI METHYLATION1 (IBM1). A methylome analysis of sg1 mutants revealed a large number of gene bodies hypermethylated in the cytosine CHG context, associated with an increase in di-methylation of lysine 9 on histone H3 tail (H3K9me2), an epigenetic mark normally found in silenced transposons. The sg1 phenotype is suppressed by mutations in genes encoding the DNA methyltransferase CHROMOMETHYLASE3 (CMT3) or the histone methyltransferase KRYPTONITE (KYP), indicating that SG1 functions antagonistically to CMT3 or KYP. We further show that the IBM1 transcript is not correctly processed in sg1, and that the functional IBM1 transcript complements sg1. Altogether, our results suggest a function for SG1 in the maintenance of genome integrity by regulating IBM1.

68 EPIGENETIC REMODELING OF HISTONE 3 MARKS DURING BOVINE PRE-IMPLANTATION DEVELOPMENT

During pre-implantation development, substantial epigenetic changes occur that are thought to play key roles in achieving embryonic genome activation and totipotency. Embryonic genome activation occurs at the 8- to 16-cell stage in cattle and, although it is a crucial step of development, the specific mechanisms involved are still poorly understood. The aim of this study was to determine whether 4 histone 3 marks associated with active genes are remodelled during oocyte and early embryo development in cattle. The dynamics of acetylation of lysine 27 (H3K27ac), di-methylation of lysine 79 (H3K79me2), and mono- and tri-methylation of lysine 4 (H3K4me1, H3K4me3) were assessed by immunofluorescence and confocal microscopy. Ovaries were obtained from an abattoir. Immature germinal vesicle stage oocytes were aspirated from small antral follicles and matured for 24 h to the metaphase II stage (MII). Embryos were produced by in vitro fertilization and collected at different stages of development: pronuclear [PN; 18 h post-fertilization (hpf)], 2-cell (30 hpf), 4-cell (44 hpf), 8-cell (56 hpf), 16-cell (72 hpf), morula (120 hpf), and blastocyst (180 hpf). Three to 4 biological replicates were done per antibody and a total of 197 oocytes per embryo were imaged (8 to 16 per stage/antibody). The images were analysed using Fiji (Schindelin et al. 2012 Nat. Methods 9, 676–682). The average nuclear intensity per oocyte per embryo was adjusted by the average of 2 cytoplasmic areas (background). An ANOVA mixed model was used for statistical analysis using SAS (SAS Institute Inc., Cary, NC, USA). The least squares means of the different stages were compared (within each antibody group) using a Tukey-Kramer adjustment and were considered to be significantly different at P < 0.05. The H3K79me2 marks showed a significant increase from germinal vesicle to MII, a change opposite that of H3K27ac, which experienced a significant decrease between these two stages. The H3K4me1/me3 marks showed no significant changes during oocyte maturation. All 3 methylation marks presented a significant reduction in nuclear intensity from MII to PN, indicating that these marks are actively removed right after fertilization. The opposite effect was observed for the acetylation mark, in which the levels increased significantly from MII to PN. The H3K4me1/me3 marks showed a gradual decrease in intensity levels from the 2-cell stage onward, reaching a minimum at the 16-cell per morula stages. The H3K79me2 levels were low from PN to 16-cell stage, at which point its intensity levels began to increase, reaching statistical significance at the blastocyst stage. The H3K27ac marks showed a slow decrease in intensity levels from the PN stage, achieving statistical significance as it dropped to a minimum at the 16-cell stage. These results show that the global levels of the assayed epigenetic marks undergo dynamic changes during oocyte maturation and embryo development, suggesting that their remodelling may be important for early development. The authors thank Alta Genetics for providing the semen.

Proteome-wide enrichment of proteins modified by lysine methylation

We present a protocol for using the triple malignant brain tumor domains of L3MBTL1 (3xMBT), which bind to mono- and di-methylated lysine with minimal sequence specificity, in order to enrich for such methylated lysine from cell lysates. Cells in culture are grown with amino acids containing light or heavy stable isotopic labels. Methylated proteins are enriched by incubating cell lysates with 3xMBT, or with the binding-null D355N mutant as a negative control. Quantitative liquid chromatography and tandem mass spectrometry (LC-MS/MS) are then used to identify proteins that are specifically enriched by 3xMBT pull-down. The addition of a third isotopic label allows the comparison of protein lysine methylation between different biological conditions. Unlike most approaches, our strategy does not require a prior hypothesis of candidate methylated proteins, and it recognizes a wider range of methylated proteins than any available method using antibodies. Cells are prepared by growing in isotopic labeling medium for about 7 d; the process of enriching methylated proteins takes 3 d and analysis by LC-MS/MS takes another 1-2 d.

Fluoxetine Epigenetically Alters the CaMKIIα Promoter in Nucleus Accumbens to Regulate ΔFosB Binding and Antidepressant Effects

Chronic social defeat stress in mice produces a susceptible phenotype characterized by several behavioral abnormalities consistent with human depression that are reversed by chronic but not acute exposure to antidepressant medications. Recent work in addiction models demonstrates that the transcription factor ΔFosB and protein kinase calmodulin-dependent protein kinase II (CaMKII) are co-regulated in nucleus accumbens (NAc), a brain reward region implicated in both addiction and depression models including social defeat. Previous work has also demonstrated that ΔFosB is induced in NAc after chronic social defeat stress or after chronic antidepressant treatment, wherein it mediates a pro-resilience or antidepressant-like phenotype. Here, using chromatin immunoprecipitation assays, we found that ΔFosB binds the CaMKIIα gene promoter in NAc and that this binding increases after mice are exposed to chronic social defeat stress. Paradoxically, chronic exposure to the antidepressant fluoxetine reduces binding of ΔFosB to the CaMKIIα promoter and reduces CaMKII expression in NAc, despite the fact that ΔFosB is induced under these conditions. These data suggest a novel epigenetic mechanism of antidepressant action, whereby fluoxetine induces some chromatin change at the CaMKIIα promoter, which blocks the ΔFosB binding. Indeed, chronic fluoxetine reduces acetylation and increases lysine-9 dimethylation of histone H3 at the CaMKIIα promoter in NAc, effects also seen in depressed humans exposed to antidepressants. Overexpression of CaMKII in NAc blocks fluoxetine's antidepressant effects in the chronic social defeat paradigm, whereas inhibition of CaMKII activity in NAc mimics fluoxetine exposure. These findings suggest that epigenetic suppression of CaMKIIα expression in NAc is behaviorally relevant and offer a novel pathway for possible therapeutic intervention in depression and related syndromes.

Comprehensive Cell-specific Protein Analysis in Early and Late Pollen Development from Diploid Microsporocytes to Pollen Tube Growth

Pollen development in angiosperms is one of the most important processes controlling plant reproduction and thus productivity. At the same time, pollen development is highly sensitive to environmental fluctuations, including temperature, drought, and nutrition. Therefore, pollen biology is a major focus in applied studies and breeding approaches for improving plant productivity in a globally changing climate. The most accessible developmental stages of pollen are the mature pollen and the pollen tubes, and these are thus most frequently analyzed. To reveal a complete quantitative proteome map, we additionally addressed the very early stages, analyzing eight stages of tobacco pollen development: diploid microsporocytes, meiosis, tetrads, microspores, polarized microspores, bipolar pollen, desiccated pollen, and pollen tubes. A protocol for the isolation of the early stages was established. Proteins were extracted and analyzed by means of a new gel LC-MS fractionation protocol. In total, 3817 protein groups were identified. Quantitative analysis was performed based on peptide count. Exceedingly stage-specific differential protein regulation was observed during the conversion from the sporophytic to the gametophytic proteome. A map of highly specialized functionality for the different stages could be revealed from the metabolic activity and pronounced differentiation of proteasomal and ribosomal protein complex composition up to protective mechanisms such as high levels of heat shock proteins in the very early stages of development.

Identification and functional implication of nuclear localization signals in the N-terminal domain of JMJD5

JMJD5 has recently been reported to participate in circadian rhythm regulation, embryological development, osteoclastogenesis and tumorigenesis. Although JMJD5 has been found mainly localized in the nucleus of cells, how it enters the nucleus remains unclear. Here we report that JMJD5 contains a functional bipartite nuclear localization signal (NLS) and a chromosome region maintenance 1 (CRM1)-dependent nuclear export signal (NES). Importin α/β and transportin-1 were further identified as JMJD5-associated transport proteins, and different binding regions were determined for the two nuclear import receptors. Additionally, we demonstrate that both the active NLS and the JmjC domain of JMJD5 are necessary for cyclin A1 transcription. Chromatin immunoprecipitation (ChIP) analysis confirmed the alterations of di-methylated lysine 36 of histone H3 (H3K36me2) in the coding region of cyclin A1. These results reveal that the N-terminal domain is essential for the nuclear localization of JMJD5 and its normal enzymatic function towards substrates in the nucleus.

Folate Polyglutamylation Is Involved in Chromatin Silencing by Maintaining Global DNA Methylation and Histone H3K9 Dimethylation in Arabidopsis

DNA methylation and repressive histone Histone3 Lysine9 (H3K9) dimethylation correlate with chromatin silencing in plants and mammals. To identify factors required for DNA methylation and H3K9 dimethylation, we screened for suppressors of the repressor of silencing1 (ros1) mutation, which causes silencing of the expression of the RD29A (RESPONSE TO DESSICATION 29A) promoter-driven luciferase transgene (RD29A-LUC) and the 35S promoter-driven NPTII (NEOMYCIN PHOSPHOTRANSFERASE II) transgene (35S-NPTII). We identified the folylpolyglutamate synthetase FPGS1 and the known factor DECREASED DNA METHYLATION1 (DDM1). The fpgs1 and ddm1 mutations release the silencing of both RD29A-LUC and 35S-NPTII. Genome-wide analysis indicated that the fpgs1 mutation reduces DNA methylation and releases chromatin silencing at a genome-wide scale. The effect of fpgs1 on chromatin silencing is correlated with reduced levels of DNA methylation and H3K9 dimethylation. Supplementation of fpgs1 mutants with 5-formyltetrahydrofolate, a stable form of folate, rescues the defects in DNA methylation, histone H3K9 dimethylation, and chromatin silencing. The competitive inhibitor of methyltransferases, S-adenosylhomocysteine, is markedly upregulated in fpgs1, by which fpgs1 reduces S-adenosylmethionine accessibility to methyltransferases and accordingly affects DNA and histone methylation. These results suggest that FPGS1-mediated folate polyglutamylation is required for DNA methylation and H3K9 dimethylation through its function in one-carbon metabolism. Our study makes an important contribution to understanding the complex interplay among metabolism, development, and epigenetic regulation.

Regulation of Matrix Metalloproteinase-9 by Epigenetic Modifications and the Development of Diabetic Retinopathy

Diabetes activates retinal matrix metalloproteinase-9 (MMP-9), and MMP-9 damages the mitochondria and augments capillary cell apoptosis. Our aim is to elucidate the mechanism responsible for MMP-9 activation. Histone modifications and recruitment of the nuclear transcriptional factor-κB (p65 subunit) at the MMP-9 promoter and the activity of lysine-specific demethylase 1 (LSD1) were measured in the retina from streptozotocin-induced diabetic rats. The role of LSD1 in MMP-9 activation was investigated in isolated retinal endothelial cells transfected with LSD1 small interfering RNA (siRNA). The results were confirmed in the retina from human donors with diabetic retinopathy. Diabetes decreased histone H3 dimethyl lysine 9 (H3K9me2) and increased acetyl H3K9 (Ac-H3K9) and p65 at the retinal MMP-9 promoter. LSD1 enzyme activity and its transcripts were elevated. LSD1 siRNA ameliorated the glucose-induced decrease in H3K9me2 and increase in p65 at the MMP-9 promoter, and prevented MMP-9 activation, mitochondrial damage, and cell apoptosis. Human donors with diabetic retinopathy had similar epigenetic changes at the MMP-9 promoter. Thus, activated LSD1 hypomethylates H3K9 at the MMP-9 promoter and this frees up that lysine 9 for acetylation. Increased Ac-H3K9 facilitates the recruitment of p65, resulting in MMP-9 activation and mitochondrial damage. Thus, the regulation of LSD1 by molecular or pharmacological means has the potential to retard the development of diabetic retinopathy.

Lysine dimethylation in the BH4 domain of Bcl-2 and functional significance (P1306)

Abstract Bcl-2 is an anti-apoptotic protein that can protect developing and mature T cells against a variety of apoptotic signals. The Bcl-2 family of proteins, compromised of anti-apoptotic as well as pro-apoptotic members, plays key roles in apoptosis; the balance of these members determines cell survival. Anti-apoptotic Bcl-2 contains four conserved Bcl-2 homology (BH) domains and the BH4 domain is indispensable for its ability to suppress cell death. Using mass spectroscopy to analyze a murine T cell line, we identified dimethylation of two lysine residues in the BH4 domain: K17 and K22. Mutation of K22 (but not K17) to alanine abrogated Bcl-2 binding to pro-apoptotic proteins Bax, Bak, Bad, Bim and Puma and greatly reduced Bcl-2 anti-apoptotic function in cytokine withdrawal. This assigns functional importance to K22 (which is conserved across species and other anti-apoptotic members) and suggests that dimethylation could affect its function. K22, based on structural models, appears to be involved in stabilizing peptide secondary structure, rather than directly interacting with pro-apoptotic proteins. We developed a monoclonal antibody that recognizes dimethylated K22 in the Bcl-2 sequence and detected expression in murine B cells (but not thymocytes). This suggests that Bcl-2 dimethylation may regulate B cell survival.

Abstract 4063: Histone methyltransferase G9a promotes the oral cancer cells recovery from drug-induced DNA damage.

Abstract Oral cancer is one of the serious life-threatening diseases in the world. In addition to surgery, the conventional treatment for oral cancer includes radiation and anti-cancer drugs, which usually act by induction of DNA damage. However, approximately one-third of treated patients will experience local or regional recurrence. G9a is a histone methyltransferase responsible for mono- or dimethylation of lysine 9 in histone H3. Our recent work has demonstrated that G9a level is highly correlated with aggressiveness and poor prognosis of lung, ovarian and colon cancer patients in Taiwanese population. Here, we report that knockdown of G9a resulted in decrease cell survival and cologenic capacity following DNA damage induced independently by etoposide and ionizing radiation. Depletion of G9a caused sustained phosphorylation of γ-H2AX after etoposide treatment. Together, our data suggest that a novel function of G9a may increase the DNA repair efficiency and promote the oral cancer cells recovery and survival from the DNA damage agents. We suggest that G9a may contribute to oral cancer proliferation by improvement of homologous recombination repair of DNA double break. Our study paves the way for exploring the blockade of G9a overexpression as a novel approach for the prevention and treatment of oral cancer. Citation Format: Chia-Wen Liu, Shih-Ting Cha, Ching-Ting Tan, Min-Liang Kuo. Histone methyltransferase G9a promotes the oral cancer cells recovery from drug-induced DNA damage. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4063. doi:10.1158/1538-7445.AM2013-4063

Abstract 1127: MMSET: Can we flip the switch.

Abstract Epigenetic regulation of gene expression involves covalent modifications of histones and DNA in a way that does not alter the underlying DNA sequence. Recently, misregulation of epigenetic mechanisms has been linked to a number of diseases, including cancer. These data signify the importance of understanding normal and aberrant epigenetic regulation and for development of tools that allow us to modulate various aspects of epigenetic machinery. One approach to do this is by targeting epigenetic enzymes with small molecule inhibitors. MMSET (Multiple Myeloma SET domain), is a histone methyltransferase overexpressed in many cancers, including a subset of multiple myelomas (MM) harboring the t(4;14) translocation. Overexpression of MMSET leads to a global increase in dimethylation of lysine 36 on histone H3 (H3K36me2). The ability of MMSET to methylate H3 depends on a functional SET (Suppressor of variegation, Enhancer of zeste and Trithorax) domain, found in most histone methyltransferases. Methylation of H3K36 by MMSET affects overall chromatin structure thereby affecting the expression of many genes, including genes that play a role in cellular proliferation and adhesion. Conversely, the loss of MMSET in t(4;14)+ cells suppresses cell growth and induces apoptosis thus supporting the idea that inhibition of MMSET activity is a viable approach to treatment of this particular type of myeloma. Currently there are not any known inhibitors of MMSET. Using the previously identified structure of the SET domain of NSD1, an MMSET homologue, we performed an in silico screen against a library of compounds to identify those that may fit in the substrate binding pocket of MMSET. We tested the in silico hits in a high throughput screen (HTS) that combines Self-Assembled Monolayers and matrix-assisted laser Desorption Ionization time-of-flight (SAMDI). This method allows us to test the ability of the compounds to inhibit MMSET's methylation activity in a label-free format. From this screen two potential hits have been identified. These compounds have IC50 values in the micromolar range and Differential Scanning Fluorimetry (DSF) confirmed the binding of the small molecule to MMSET. Future in vivo work will determine the potency and selectivity of these compounds towards MMSET. Identifying an effective inhibitor of MMSET could make way for new potential therapeutics in the treatment of t(4;14)+ multiple myeloma, as well as other cancers that overexpress this protein, and could also prove to be highly useful in our efforts to understand the various mechanisms of epigenetic regulation. Citation Format: Christine Will, Michael Scholle, Roodolph St. Pierre, Ji Hyun Shim, Zhong Jun Cheng, Relja Popovic, Dinshaw J. Patel, James E. Bradner, Alex D. MacKerell, Milan Mrksich, Jonathan D. Licht. MMSET: Can we flip the switch. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1127. doi:10.1158/1538-7445.AM2013-1127

γH2A-Binding Protein Brc1 Affects Centromere Function in Fission Yeast

The coordinated replication and transcription of pericentromeric repeats enable RNA interference (RNAi)-mediated transmission of pericentromeric heterochromatin in fission yeast, which is essential for the proper function of centromeres. Rad3/ATR kinase phosphorylates histone H2A on serine-128/-129 to create γH2A in pericentromeric heterochromatin during S phase, which recruits Brc1 through its breast cancer gene 1 protein (BRCA1) C-terminal (BRCT) domains. Brc1 prevents the collapse of stalled replication forks; however, it is unknown whether this activity influences centromere function. Here, we show that Brc1 localizes in pericentromeric heterochromatin during S phase, where it enhances Clr4/Suv39-mediated H3 lysine-9 dimethylation (H3K9me2) and gene silencing. Loss of Brc1 increases sensitivity to the microtubule-destabilizing drug thiabendazole (TBZ) and increases chromosome missegregation in the presence of TBZ. Brc1 retains significant function even when it cannot bind γH2A. However, elimination of the serine-121 site on histone H2A, a target of Bub1 spindle assembly checkpoint kinase, sensitizes γH2A-deficient and brc1Δ cells to replication stress and microtubule destabilization. Collective results suggest that Brc1-mediated stabilization of stalled replication forks is necessary for fully efficient transmission of pericentromeric heterochromatin, which is required for accurate chromosome segregation during mitosis.

Retinoic acid impairs estrogen signaling in breast cancer cells by interfering with activation of LSD1 via PKA

More than 70% of breast cancers in women require estrogens for cell proliferation and survival. 17β-estradiol (E2) effect on mammary target cells is almost exclusively mediated by its binding to the estrogen receptor-α (ERα) that joins chromatin where it assembles active transcription complexes. The proliferative and pro-survival action of estrogens is antagonized in most cases by retinoic acid (RA), even though the cognate retinoic acid receptor-α (RARα) cooperates with ERα on promoters of estrogen-responsive genes.We have examined at the molecular level the crosstalk between these nuclear receptors from the point of view of their control of cell growth and show here that RA reverts estrogen-stimulated transcription of the pivotal anti-apoptotic bcl-2 gene by preventing demethylation of dimethyl lysine 9 in histone H3 (HeK9me2). As we previously reported, this is obtained by means of E2-triggered activation of the lysine-specific demethylase 1 (LSD1), an enzyme that manages chromatin plasticity in order to allow specific movements of chromosomal regions within the nucleus. We find that E2 fuels LSD1 by inducing migration of the catalytic subunit of protein kinase A (PKA) into the nucleus, where it targets estrogen-responsive loci. RA rescues LSD1-dependent disappearance of H3K9me2 at bcl-2 regulatory regions upon the prevention of PKA assembly to the same sites.

PELP1 oncogenic functions involve CARM1 regulation

Estrogen receptor alpha (ERα) is implicated in the initiation and progression of breast cancer and its transcription depends on the modulation of epigenetic changes at target gene promoters via coregulators. There is a critical need to understand the molecular mechanism(s) by which deregulation of epigenetic changes occurs during breast cancer progression. The ERα coregulator PELP1 plays an important role in ERα signaling and is a proto-oncogene with aberrant expression in breast cancer. PELP1 interacts with histones and may be a reader of chromatin modifications. We profiled PELP1's epigenetic interactome using a histone peptide array. Our results show that PELP1 recognizes histones modified by arginine and lysine dimethylation. PELP1 functionally interacts with the arginine methyltransferase CARM1 and their interaction is enhanced by ERα. PELP1-CARM1 interactions synergistically enhance ERα transactivation. Chromatin immunoprecipitation assays revealed that PELP1 alters histone H3 arginine methylation status at ERα target gene promoters. Pharmacological inhibition or small interfering RNA knockdown of CARM1 substantially reduced PELP1 oncogenic functions. The critical role of PELP1 status in modulating arginine methylation status was also observed through in vivo studies where PELP1 knockdown mediated decreased tumorigenesis correlated with decreased arginine dimethylation. Further, immunohistochemical analysis of human breast tumor tissues revealed co-overexpression of PELP1 and CARM1 in a subset of ERα-positive breast tumors. Our findings show PELP1 is a reader of histone arginine methyl modifications and deregulation promotes tumor proliferation via epigenetic alterations at ERα target promoters. Targeting these epigenetic alterations through inhibition of PELP1 and the arginine methyltransferases could be a promising cancer therapeutic.

Ligand-based and structure-based design of novel histone demethylase inhibitors

The genetic information in eukaryotic cells is organized in a specific structure called chromatin. The basic unit of chromatin is the nucleosome, which consist of four histone proteins and ~147 bp of DNA [1]. The N-terminal tails of these proteins contain sited for post-translational modifications directly linked to gene expression. The modifications include acetylation, methylation, phosphorylation, ubiquitinylation, sumoylation and ribosylation. Specific enzymes mediate each modification. LSD1 (Lysine Specific Demethylase I) is one of the histone demethylases, which removes one methyl group from mono- or di-methylated lysine residue. It has recently been demonstrated that androgen receptor (AR)-LSD1 complex demethylates a repressive histone mark (H3K9) promoting genes activation [2]. Experimental data show, also, that LSD1 is strongly expressed in prostate cancers [3]. For these reasons, specific modulation of LSD1 might be a promising therapeutic strategy in tissues where AR has a key physiological role. LSD1 is a flavin-dependent amine oxidase, which shares sequence identity with other flavin dependent amine oxidases like monoamine oxidase (MAO), and polyamine oxidase (PAO). After we analyzed structural differences and similarities among these enzymes several docking studies were evaluated using the available crystal structures of LSD1 and the related oxidases to discover novel LSD1 inhibitors. For the evaluation studies we selected different ligand data sets containing known inhibitors of MAO and PAO. The docking setup that showed the highest accuracy and enrichment factors was selected for virtual screening of LSD1 inhibitors. Preliminary biological data were obtained and will be discussed in the context of the target structure.

An Approach for Triplex-Isobaric Peptide Termini Labeling (Triplex-IPTL)

Isobaric peptide termini labeling (IPTL) is based on labeling of both peptide termini with complementary isotopic labels resulting in isobaric peptides. MS/MS analysis after IPTL derivatization produces peptide-specific fragment ions which are distributed throughout the MS/MS spectrum. Thus, several quantification points can be obtained per peptide. In this report, we present triplex-IPTL, a chemical labeling strategy for IPTL allowing the simultaneous quantification of three states within one MS run. For this purpose, dimethylation of the N-terminal amino group followed by dimethylation of lysines was used with different stable isotopes of formaldehyde and cyanoborohydride. Upon LC-MS/MS analysis, the combined samples revealed three corresponding isotopic fragment ion series reflecting quantitatively the peptide ratios. To support this multiplexing labeling strategy, we have further developed the data analysis tool IsobariQ and included multidimensional VSN normalization, statistical inference, and graphical visualization of triplex-IPTL data and clustering of protein profiling patterns. The power of the triplex-IPTL approach in combination with IsobariQ was demonstrated through temporal profiling of HeLa cells incubated with the kinesin Eg5 inhibitor S-Trityl-l-cysteine (STLC). As a result, clusters of quantified proteins were found by their ratio profiles which corresponded well to their gene ontology association in mitotic arrest and cell death, respectively.