Dimethylation Of Histone H3 Lysine Research Articles

Biologic activity of LSD1 inhibition by novel tranylcypromine structural analogues in prostate cancer cells.

82 Background: Hormonal strategies to inhibit androgen receptor (AR) signalling remain inadequate and so novel approaches are urgently required. Lysine (K)-specific demethylase 1A (LSD1), is an epigenetic AR co-activator which modifies chromatin structure through de-methylation of histone H3 lysine 9 at androgen response elements to activate transcriptional expression of AR target genes. LSD1 is over-expressed and a poor prognostic factor in prostate cancer. We have synthesised novel analogues of the monoamine oxidase (MAO) inhibitor tranylcypromine as LSD1 inhibitors to exploit MAO and LSD1 sequence homology. Methods: We utilised prostate cancer cell line models to investigate the biological effect of LSD1 inhibition using tranylcypromine analogues. Results: Chemical inhibition of LSD1 was effective in inhibiting cell proliferation in prostate cancer models with around 1000 fold greater potency for synthesised analogues over tranylcypromine in LNCaP prostate cancer cells. Chemical inhibition of LSD1 induced the predicted histone methylation changes consequent on LSD1 inhibition of mono- and di-methylation of histone H3 lysine 9. In addition LSD1 depletion, AR depletion and reduced expression of the AR target gene prostate-specific antigen was demonstrated. Fractional effect assays demonstrated synergistic interactions in cell proliferation assays for tranylcypromine analogues with the androgen receptor antagonists bicalutamide and MDV3100. Conclusions: Our data demonstrate biological activity of LSD1 inhibition in prostate cancer cells with depletion of AR signalling using optimised structural analogues of established drugs for non-cancer indications. Therapeutic targeting of LSD1 for prostate cancer would represent a novel therapeutic paradigm for this disease.

Lysine methyltransferase G9a methylates the transcription factor MyoD and regulates skeletal muscle differentiation

Skeletal muscle cells have served as a paradigm for understanding mechanisms leading to cellular differentiation. The proliferation and differentiation of muscle precursor cells require the concerted activity of myogenic regulatory factors including MyoD. In addition, chromatin modifiers mediate dynamic modifications of histone tails that are vital to reprogramming cells toward terminal differentiation. Here, we provide evidence for a unique dimension to epigenetic regulation of skeletal myogenesis. We demonstrate that the lysine methyltransferase G9a is dynamically expressed in myoblasts and impedes differentiation in a methyltransferase activity-dependent manner. In addition to mediating histone H3 lysine-9 di-methylation (H3K9me2) on MyoD target promoters, endogenous G9a interacts with MyoD in precursor cells and directly methylates it at lysine 104 (K104) to constrain its transcriptional activity. Mutation of K104 renders MyoD refractory to inhibition by G9a and enhances its myogenic activity. Interestingly, MyoD methylation is critical for G9a-mediated inhibition of myogenesis. These findings provide evidence of an unanticipated role for methyltransferases in cellular differentiation states by direct posttranslational modification of a transcription factor.

Cryptotanshinone down‐regulates androgen receptor signaling by modulating lysine‐specific demethylase 1 function

Development and progression of prostate cancer are intimately associated with androgen receptor (AR) signaling. The emergence of hormone-refractory prostate cancer and consequent failure of conventional androgen deprivation therapies make it necessary to bypass hormonal resistance by targeting the same signaling pathway at new intervention points. In our study, we showed that cryptotanshinone inhibited the growth of AR-positive prostate cancer cells, suggesting that cryptotanshinone affected AR function. Cryptotanshinone also profoundly inhibited the transcriptional activity of AR and suppressed the expression of several AR-target genes at the mRNA and the protein levels. At the molecular level, cryptotanshinone disrupted the interaction between AR and lysine-specific demethylase 1 (LSD1), and inhibited the complex of AR and LSD1 to the promoter of AR target genes without affecting the protein degradation and translocation of AR. Cryptotanshinone increased the mono-methyl and di-methylation of Histone H3 lysine 9 (H3K9), a repressive histone marker which is demethylated and activated by LSD1. These data suggest that cryptotanshinone functions via inhibition of LSD1, a protein that promotes AR-dependent transcriptional activity via derepression of H3K9. In summary, we describe a novel mechanism whereby cryptotanshinone down-regulates AR signaling via functional inhibition of LSD1-mediated demethylation of H3K9 and represses the transcriptional activity of AR. Our data suggest that cryptotanshinone can be developed as a potential therapeutic agent for prostate cancer.

Genome-wide Profiling of Chromatin Signatures Reveals Epigenetic Regulation of MicroRNA Genes in Colorectal Cancer

Altered expression of microRNAs (miRNA) occurs commonly in human cancer, but the mechanisms are generally poorly understood. In this study, we examined the contribution of epigenetic mechanisms to miRNA dysregulation in colorectal cancer by carrying out high-resolution ChIP-seq. Specifically, we conducted genome-wide profiling of trimethylated histone H3 lysine 4 (H3K4me3), trimethylated histone H3 lysine 27 (H3K27me3), and dimethylated histone H3 lysine 79 (H3K79me2) in colorectal cancer cell lines. Combining miRNA expression profiles with chromatin signatures enabled us to predict the active promoters of 233 miRNAs encoded in 174 putative primary transcription units. By then comparing miRNA expression and histone modification before and after DNA demethylation, we identified 47 miRNAs encoded in 37 primary transcription units as potential targets of epigenetic silencing. The promoters of 22 transcription units were associated with CpG islands (CGI), all of which were hypermethylated in colorectal cancer cells. DNA demethylation led to increased H3K4me3 marking at silenced miRNA genes, whereas no restoration of H3K79me2 was detected in CGI-methylated miRNA genes. DNA demethylation also led to upregulation of H3K4me3 and H3K27me3 in a number of CGI-methylated miRNA genes. Among the miRNAs we found to be dysregulated, many of which are implicated in human cancer, miR-1-1 was methylated frequently in early and advanced colorectal cancer in which it may act as a tumor suppressor. Our findings offer insight into the association between chromatin signatures and miRNA dysregulation in cancer, and they also suggest that miRNA reexpression may contribute to the effects of epigenetic therapy.

Inhibition of Osteogenic Differentiation of Human Adipose‐Derived Stromal Cells by Retinoblastoma Binding Protein 2 Repression of RUNX2‐Activated Transcription

Histone methylation is regarded as an important type of histone modification defining the epigenetic program during the lineage differentiation of stem cells. A better understanding of this epigenetic mechanism that governs osteogenic differentiation of human adipose-derived stromal cells (hASCs) can improve bone tissue engineering and provide new insights into the modulation of hASC-based cell therapy. Retinoblastoma binding protein 2 (RBP2) is a histone demethylase that specifically catalyzes demethylation of dimethyl or trimethyl histone H3 lysine 4 (H3K4me2 or H3K4me3), which is normally associated with transcriptionally active genes. In this study, the roles of RBP2 in osteogenic differentiation of hASCs were investigated. We found that RBP2 knockdown by lentiviruses expressing small interfering RNA promoted osteogenic differentiation of hASCs in vitro and in vivo. In addition, we demonstrated that knockdown of RBP2 resulted in marked increases of mRNA expression of osteogenesis-associated genes such as alkaline phosphatase (ALP), osteocalcin (OC), and osterix (OSX). RBP2 was shown to occupy the promoters of OSX and OC to maintain the level of the H3K4me3 mark by chromatin immunoprecipitation assays. Furthermore, coimmunoprecipitation and luciferase reporter experiments suggested that RBP2 was physically and functionally associated with RUNX2, an essential transcription factor that governed osteoblastic differentiation. Significantly, RUNX2 knockdown impaired the repressive activity of RBP2 in osteogenic differentiation of hASCs. Altogether, our study is the first to demonstrate the functional and biological roles of H3K4 demethylase RBP2 in osteogenic differentiation of hASCs and to link RBP2 to the transcriptional regulation of RUNX2.

Abstract 1458: Arid4b: A germline breast cancer progression modifier gene

Abstract Our laboratory's research focuses on the role of host genetics in breast cancer metastasis. The MMTV-PyMT transgenic mouse model exhibits varying metastatic efficiency to the lungs when transgenic mice in an FVB background are bred to other strains such as DBA and AKR. Combining quantitative measurement of metastasis with genetic mapping studies of the AKXD recombinant inbred panel of mice has allowed us to determine quantitative trait loci (QTLs) that affect metastatic efficiency. My work has focused on the potential role of Arid4b in breast cancer tumorigenesis and metastasis. Arid4b is a component of the mSin3a histone deacetylase complex, which has an established role in breast cancer progression, and Arid4b is a candidate gene underlying a metastasis QTL peak we have identified on mouse chromosome 13. Sequencing revealed a high density of non-synonymous SNPs between the AKR and DBA alleles in exon 22, which encodes a C-terminal region of the Arid4b protein that is known to mediate interaction with the mSin3a HDAC complex. We have recently discovered that Arid4b binds another protein that our laboratory has implicated in metastasis susceptibility, the transcriptional elongation regulator Bromodomain 4 (Brd4), and we are currently using co-IPs and proteomics strategies such as tandem affinity purification to identify other proteins that may bind differentially to the AKR or DBA Arid4b proteins. In orthotopic implantation assays, cells ectopically expressing the DBA allele of Arid4b formed larger primary tumors compared to cells expressing the AKR allele, and western blots using an Ab specific for dimethylated histone H3 lysine 27 suggest that the mechanism of Arid4b action may involve modification of chromatin structure. Arid4b is also alternately spliced, and a second isoform lacks part of a conserved Chromo domain that is predicted to bind methylated histone tails. We are currently investigating the consequences of ectopic expression of the multiple alleles and isoforms of Arid4b in vivo using orthotopic implantation assays. It is likely that both the alternate splicing of the Chromo domain and the allelic variation in the C-terminal domain modulate an epigenetic influence of Arid4b on tumorigenesis and metastasis. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 1458. doi:10.1158/1538-7445.AM2011-1458

Epigenetic modifications of the 35S promoter in cultured gentian cells

Our previous studies found strict gene silencing associated with CaMV-35S promoter-specific de novo methylation in transgenic gentian plants. To dissect the de novo methylation machinery, especially in association with histone modification, 35S-driven sGFP-expressing and -silenced gentian cultured cell lines that originated from a single transformation event were produced and used for epigenetic analyses. A sGFP-expressing primarily induced cell suspension culture (PS) was hypomethylated in the 35S promoter region, although a low level of de novo methylation at the 35S enhancer region (−148 to −85) was detected. In contrast, a sGFP-silenced re-induced cell suspension culture (RS), which originated from leaf tissues of a transgenic plant, was hypermethylated in the 35S promoter region. Chromatin immunoprecipitation analysis showed that in RS, histone H3 of the silenced 35S promoter region was deacetylated and also dimethylated on lysine 9. Interestingly, in the silenced 35S promoter 3′ region, dimethylation of histone H3 lysine 4 was also observed. When hypomethylation and histone H3 acetylation of the 35S region occurred in PS, de novo methylation at the 35S enhancer region had already taken place. The de novo methylation status was also resistant to 5-aza-2′-deoxycytidine treatment. These results suggest that de novo methylation of the enhancer region is a primitive process of 35S silencing that triggers histone H3 deacetylation.

Methylation of histone H3 lysine 36 enhances DNA repair by nonhomologous end-joining

Given its significant role in the maintenance of genomic stability, histone methylation has been postulated to regulate DNA repair. Histone methylation mediates localization of 53BP1 to a DNA double-strand break (DSB) during homologous recombination repair, but a role in DSB repair by nonhomologous end-joining (NHEJ) has not been defined. By screening for histone methylation after DSB induction by ionizing radiation we found that generation of dimethyl histone H3 lysine 36 (H3K36me2) was the major event. Using a novel human cell system that rapidly generates a single defined DSB in the vast majority of cells, we found that the DNA repair protein Metnase (also SETMAR), which has a SET histone methylase domain, localized to an induced DSB and directly mediated the formation of H3K36me2 near the induced DSB. This dimethylation of H3K36 improved the association of early DNA repair components, including NBS1 and Ku70, with the induced DSB, and enhanced DSB repair. In addition, expression of JHDM1a (an H3K36me2 demethylase) or histone H3 in which K36 was mutated to A36 or R36 to prevent H3K36me2 formation decreased the association of early NHEJ repair components with an induced DSB and decreased DSB repair. Thus, these experiments define a histone methylation event that enhances DNA DSB repair by NHEJ.

In vivo evidence of enhanced di-methylation of histone H3 K4 on upregulated genes in adipose tissue of diabetic db/db mice

Di-methylation of histone H3 lysine (K) 4, a component of the epigenetic memory, is associated with gene transactivation. In this study, we examined whether the development of diabetes induces di-methylation of histone H3 K4 on the upregulated genes. We searched for upregulated genes in mesenteric adipose tissue of insulin-resistant/diabetic db/db mice compared with non-diabetic db/m mice using microarray analysis. We also performed chromatin immunoprecipitation assays for di-methylation of histone H3 K4 in the upregulated genes in mesenteric adipose tissue of db/m and db/db mice. Di-methylation of histone H3 K4 was enhanced at the upstream and/or transcribed regions of upregulated genes including Atp6v0d2, Mmp12, Trem2 and Clec4d genes in mesenteric adipose tissue of db/db mice, as compared with db/m mice. These results suggest that di-methylation of histone H3 K4 is involved in the induction of Atp6v0d2, Mmp12, Trem2 and Clec4d in mesenteric adipose tissue in db/db mice.

Butyrate, an HDAC inhibitor, stimulates interplay between different posttranslational modifications of histone H3 and differently alters G1-specific cell cycle proteins in vascular smooth muscle cells

HDACs and HATs regulate histone acetylation, an epigenetic modification that controls chromatin structure and through it, gene expression. Butyrate, a dietary HDAC inhibitor, inhibits VSMC proliferation, a crucial factor in atherogenesis, and the principle mechanism in arterial and in-stent restenosis. Here, the link between antiproliferation action of butyrate and the portraits of global covalent modifications of histone H3 that it induces are characterized to understand the mechanics of butyrate-arrested VSMC proliferation. Analysis of histone H3 modifications specific to butyrate arrested VSMC proliferation display induction of histone H3-Lysine9 acetylation, inhibition of histone H3-Serine10 phosphorylation, reduction of histone H3-Lysine9 dimethylation and stimulation of histone H3-Lysine4 di-methylation, which is linked to transcriptional activation, cell cycle/mitosis, transcriptional suppression and activation, respectively. Conversely, untreated VSMCs exhibit inhibition of H3-Lysine9 acetylation, induction of H3-Serine10 phosphorylation, stimulation of H3-Lysine9 di-methylation and reduction in H3-Lysine4 di-methylation. Butyrate's cooperative effects on H3-Lysine9 acetylation and H3-Serine10 phosphorylation, and contrasting effects on di-methylation of H3-Lysine9 and H3-Lysine4 suggests that the interplay between these site-specific modifications cause distinct chromatin alterations that allow cyclin D1 and D3 induction, G1-specific cdk4, cdk6 and cdk2 downregulation, and upregulation of cdk inhibitors, p15INK4b and p21Cip1. Regardless of butyrate's effect on D-type cyclins, downregulation of G1-specific cdks and upregulation of cdk inhibitors by butyrate prevents cell cycle progression by failing to inactivate Rb. Overall, through chromatin remodeling, butyrate appears to differentially alter G1-specific cell cycle proteins to ensure proliferation arrest of VSMCs, a crucial cellular component of blood vessel wall.

PHF8 is a histone H3K9me2 demethylase regulating rRNA synthesis

Dimethylation of histone H3 lysine 9 (H3K9me2) is an important epigenetic mark associated with transcription repression. Here, we identified PHF8, a JmjC-domain-containing protein, as a histone demethylase specific for this repressing mark. Recombinant full-length wild type protein could remove methylation from H3K9me2, but mutation of a conserved histidine to alanine H247A abolished the demethylase activity. Overexpressed exogenous PHF8 was colocalized with B23 staining. Endogenous PHF8 was also colocalized with B23 and fibrillarin, two well-established nucleolus proteins, suggesting that PHF8 is localized in the nucleolus and may regulate rRNA transcription. Indeed, PHF8 bound to the promoter region of the rDNA gene. Knockdown of PHF8 reduced the expression of rRNA, and overexpression of the gene resulted in upregulation of rRNA transcript. Concomitantly, H3K9me2 level was elevated in the promoter region of the rDNA gene in PHF8 knockdown cells and reduced significantly when the wild type but not the catalytically inactive H247A mutant PHF8 was overexpressed. Thus, our study identified a histone demethylase for H3K9me2 that regulates rRNA transcription.

The Arabidopsis Paf1c Complex Component CDC73 Participates in the Modification ofFLOWERING LOCUS CChromatin

FLOWERING LOCUS C (FLC) is a key repressor of flowering in Arabidopsis (Arabidopsis thaliana) and is regulated, both positively and negatively, by posttranslational histone modifications. For example, vernalization (the promotion of flowering by cold temperatures) epigenetically silences FLC expression through repressive histone modifications such as histone H3 lysine-9 dimethylation (H3K9me2) and H3K27me3. In contrast, an RNA polymerase II-associated complex (Paf1c) activates FLC expression through increased H3K4 and H3K36 methylation. As a result of this regulation, FLC has become a useful model for the study of chromatin structure in Arabidopsis. Here we show that At3g22590 is the Arabidopsis homolog of the yeast (Saccharomyces cerevisiae) Paf1c component CDC73 and is enriched at FLC chromatin. In contrast to other Paf1c component mutants that exhibit pleiotropic developmental phenotypes, the effects of cdc73 mutations are primarily limited to flowering time, suggesting that CDC73 may only be required for Paf1c function at a subset of target genes. In rapid-cycling strains, cdc73 mutants showed reduced FLC mRNA levels and decreased H3K4me3 at the FLC locus. Interestingly, in late-flowering autonomous-pathway mutants, which contain higher levels of FLC, cdc73 mutations only suppressed FLC in a subset of mutants. H3K4me3 was uniformly reduced in all autonomous-pathway cdc73 double mutants tested; however, those showing reduced FLC expression also showed an increase in H3K27me3. Thus, CDC73 is required for high levels of FLC expression in a subset of autonomous-pathway-mutant backgrounds and functions both to promote activating histone modifications (H3K4me3) as well as preventing repressive ones (e.g. H3K27me3).

Abstract 2371: Arid4b is a potential breast cancer progression modifier gene

Abstract Our laboratory's research focuses on the role of host genetics in breast cancer metastasis. The MMTV-PyMT mouse model exhibits varying metastatic efficiency to the lungs when transgenic mice in an FVB background are bred to other strains such as DBA and AKR. Combining quantitative measurement of metastasis with genetic mapping studies of the AKXD recombinant inbred panel of mice has allowed us to determine quantitative trait loci (QTLs) that affect metastatic efficiency. My work has focused on the potential role of Arid4b in breast cancer tumorigenesis and metastasis. Arid4b is a component of the mSin3a histone deacetylase complex that has a known role in breast cancer progression and is a candidate gene underlying a metastasis QTL peak we have identified on mouse chromosome 13. In two independent mouse breast cancer cell lines, Met-1 and PyMT-luc, stable expression of the AKR (high metastatic strain) allele caused significantly larger primary tumor growth than the DBA (low metastatic strain) allele following orthotopic implantation into the mammary fat pads of syngeneic hosts. In Met-1 cells we detected lung surface metastases in the AKR cohort but not in the DBA cohort. We are in the process of performing functional analyses to determine a mechanism of action whereby Arid4b polymorphisms influence tumorigenesis and metastasis. Sequencing has revealed a high density of non-synonymous SNPs between the AKR and DBA alleles in exon 22, which encodes a C-terminal region of the Arid4b protein that is known to mediate interaction with the mSin3a HDAC complex. We are currently using co-IPs and proteomics strategies, such as tandem affinity purification, to identify proteins that bind differentially to the AKR or DBA Arid4b proteins. Arid4b is also alternately spliced and cells ectopically expressing the shorter isoform 2 formed significantly larger tumors in our orthotopic model compared to cells expressing the full-length isoform 1. Interestingly, the alternately spliced exon encodes part of a conserved Chromodomain, which is known to mediate binding of other Chromodomain containing proteins such as HP1 to modified histone tails. Western blots using an Ab specific for dimethylated histone H3 lysine 27 suggest a potential role of Arid4b in modifying chromatin structure. It is likely that both the alternate splicing of the Chromo domain and the allelic variation in the C-terminal domain modulate the epigenetic influence of Arid4b on tumorigenesis and metastasis. 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 2371.

Structural basis for the recognition of Set1 family Win motifs by WDR5

The Mixed Lineage Leukemia protein‐1 (MLL1) associates with WDR5, RbBP5 and Ash2L to form the MLL1 core complex that catalyzes mono‐ and dimethylation of histone H3 Lysine 4 (H3K4). We have recently established that WDR5 interacts with MLL1 through a highly conserved WDR5 interaction (Win) motif in MLL1 and a peptide derived from the Win motif in MLL1 has been shown to disrupt this interaction and specifically inhibit the H3K4 dimethylation activity of the MLL1 core complex. The Win motif is highly conserved among the metazoan Set1 family members, however, little is known about how the different Set1 family Win motifs are recognized by WDR5. To understand the molecular details of these interactions, here we compare 3‐dimensional structures and thermodynamic binding properties of different human Set1 family Win motif based peptides bound to WDR5. We show that Win motif peptides derived from human Set1 family members (MLL2, MLL3, MLL4, SET1a and SET1b) interact with WDR5 with dissociation constants (Kd) ranging from 50–470 nM. These binding affinities are 4 to 30‐fold tighter than the interaction between MLL1 Win motif and WDR5. The crystal structure of WDR5 bound to the human SET1a Win motif peptide reveals more favorable interactions outside the Arginine binding pocket in WDR5 that contributes to the increased affinity as compared to that of MLL1 Win motif peptide. We also demonstrate that the human SET1a Win motif peptide is a four‐fold better inhibitor of the H3K4 dimethylation activity of the MLL1 core complex with an IC50 value of 70 μM. These studies establish the structural basis for the differential interaction affinities between WDR5 and Set1 family Win motifs and suggest a framework for the design of Win motif based peptide inhibitors of Set1 family complexes.

Association of Global Levels of Histone Modifications with Recurrence-Free Survival in Stage IIB and III Esophageal Squamous Cell Carcinomas

This study was aimed at understanding the effects of histone modifications on recurrence-free survival (RFS) after esophagectomy in esophageal squamous cell carcinoma (ESCC). The acetylation of histone H3 lysine (H3K9Ac), histone H3 lysine 18 (H3K18Ac), and histone H4 lysine 12 (H4K12Ac), and the dimethylation of histone H3 lysine 9 (H3K9diMe) and histone H4 arginine 3 (H4R3diMe) were analyzed by immunohistochemistry in 237 ESCCs. The K-means clustering algorithm was used to identify unique patterns of histone modifications. At a median follow-up of 5.1 years, 109 (46%) of 237 patients had developed recurrence of disease. Mean global levels of H3K9Ac, H3K18Ac, H3K9diMe, H4K12Ac, and H4R3diMe were 81.5%, 65.1%, 80.3%, 45.9%, and 27.4%, respectively. In the analysis of individual histones, a 1% increase in the global level of H3K18Ac in pathologic stage III worsened RFS at 1.009 times [95% confidence interval (CI), 1.001-1.016; P = 0.03], after adjusting for age, sex, and operative method. Cluster analysis also showed significant effects of histone modifications on RFS. For stage IIB cancers, Cox proportional hazards analysis showed that RFS of cluster 1, with high global levels of H3K18Ac and H4R3diMe, was 2.79 times poorer (95% CI, 1.14-6.27; P = 0.008) than that of cluster 2, with low levels. RFS for stage III cancers was also poorer in cluster 1 than cluster 2 (adjusted hazard ratio, 2.42; 95% CI, 1.10-5.34; P = 0.02). In conclusion, the present study suggests that global levels of histone modifications in ESCC may be an independent prognostic factor of RFS.

Jmjd1a Demethylase-regulated Histone Modification Is Essential for cAMP-response Element Modulator-regulated Gene Expression and Spermatogenesis

Spermatogenesis, a fundamental process in the male reproductive system, requires a series of tightly controlled epigenetic and genetic events in germ cells ranging from spermatogonia to spermatozoa. Jmjd1a is a key epigenetic regulator expressed in the testis. It specifically demethylates mono- and di-methylated histone H3 lysine 9 (H3K9me1 and H3K9me2) but not tri-methylated H3K9 (H3K9me3). In this study, we generated a Jmjd1a antibody for immunohistochemistry and found Jmjd1a was specifically produced in pachytene and secondary spermatocytes. Disruption of the Jmjd1a gene in mice significantly increased H3K9me1 and H3K9me2 levels in pachytene spermatocytes and early elongating spermatids without affecting H3K9me3 levels. Concurrently, the levels of histone acetylation were decreased in Jmjd1a knock-out germ cells. This suggests Jmjd1a promotes transcriptional activation by lowering histone methylation and increasing histone acetylation. Interestingly, the altered histone modifications in Jmjd1a-deficient germ cells caused diminished cAMP-response element modulator (Crem) recruitment to chromatin and decreased expression of the Crem coactivator Act and their target genes Tnp1 (transition protein 1), Tnp2, Prm1 (protamine 1), and Prm2, all of which are essential for chromatin condensation in spermatids. In agreement with these findings, Jmjd1a deficiency caused extensive germ cell apoptosis and blocked spermatid elongation, resulting in severe oligozoospermia, small testes, and infertility in male mice. These results indicate that the Jmjd1a-controlled epigenetic histone modifications are crucial for Crem-regulated gene expression and spermatogenesis.

Transduction of RNA-directed DNA methylation signals to repressive histone marks in Arabidopsis thaliana

RNA-directed modification of histones is essential for the maintenance of heterochromatin in higher eukaryotes. In plants, cytosine methylation is an additional factor regulating inactive chromatin, but the mechanisms regulating the coexistence of cytosine methylation and repressive histone modification remain obscure. In this study, we analysed the mechanism of gene silencing mediated by MORPHEUS' MOLECULE1 (MOM1) of Arabidopsis thaliana. Transcript profiling revealed that the majority of up-regulated loci in mom1 carry sequences related to transposons and homologous to the 24-nt siRNAs accumulated in wild-type plants that are the hallmarks of RNA-directed DNA methylation (RdDM). Analysis of a single-copy gene, SUPPRESSOR OF drm1 drm2 cmt3 (SDC), revealed that mom1 activates SDC with concomitant reduction of di-methylated histone H3 lysine 9 (H3K9me2) at the tandem repeats in the promoter region without changes in siRNA accumulation and cytosine methylation. The reduction of H3K9me2 is not observed in regions flanking the tandem repeats. The results suggest that MOM1 transduces RdDM signals to repressive histone modification in the core region of RdDM.

Mass spectrometry analysis of the variants of histone H3 and H4 of soybean and their post-translational modifications

BackgroundHistone modifications and histone variants are of importance in many biological processes. To understand the biological functions of the global dynamics of histone modifications and histone variants in higher plants, we elucidated the variants and post-translational modifications of histones in soybean, a legume plant with a much bigger genome than that of Arabidopsis thaliana.ResultsIn soybean leaves, mono-, di- and tri-methylation at Lysine 4, Lysine 27 and Lysine 36, and acetylation at Lysine 14, 18 and 23 were detected in HISTONE H3. Lysine 27 was prone to being mono-methylated, while tri-methylation was predominant at Lysine 36. We also observed that Lysine 27 methylation and Lysine 36 methylation usually excluded each other in HISTONE H3. Although methylation at HISTONE H3 Lysine 79 was not reported in A. thaliana, mono- and di-methylated HISTONE H3 Lysine 79 were detected in soybean. Besides, acetylation at Lysine 8 and 12 of HISTONE H4 in soybean were identified. Using a combination of mass spectrometry and nano-liquid chromatography, two variants of HISTONE H3 were detected and their modifications were determined. They were different at positions of A31F41S87S90 (HISTONE variant H3.1) and T31Y41H87L90 (HISTONE variant H3.2), respectively. The methylation patterns in these two HISTONE H3 variants also exhibited differences. Lysine 4 and Lysine 36 methylation were only detected in HISTONE H3.2, suggesting that HISTONE variant H3.2 might be associated with actively transcribing genes. In addition, two variants of histone H4 (H4.1 and H4.2) were also detected, which were missing in other organisms. In the histone variant H4.1 and H4.2, the amino acid 60 was isoleucine and valine, respectively.ConclusionThis work revealed several distinct variants of soybean histone and their modifications that were different from A. thaliana, thus providing important biological information toward further understanding of the histone modifications and their functional significance in higher plants.

Changes in histone methylation during human oocyte maturation and IVF- or ICSI-derived embryo development

To characterize the histone methylation pattern during human oocyte maturation and embryo development after conventional IVF and ICSI. Experimental study. Reproductive center of hospital. Women underwent IVF or ICSI. Immature and mature oocytes were collected from patients undergoing ICSI. Tripronuclear and normally fertilized embryos were obtained from patients undergoing IVF or ICSI. The distribution patterns of dimethylated histone H3 lysine 9 (H3K9) and histone H4 arginine 3 (H4R3) in oocytes and embryos were observed by indirect immunofluorescent staining and scanning confocal microscopy. H3K9 and H4R3 were dimethylated throughout the meiotic maturation of human oocytes and the tripronuclear embryo development from two-cell to blastocyst stage. However, at the pronuclear stage, approximately half of the tripronuclear IVF zygotes displayed strong staining of MeH3K9 in one pronucleus, whereas MeH4R3 staining was always uniform in all three pronuclei. In the other half of the tripronuclear zygotes, all three pronuclei were strongly stained with MeH3K9 in some cases, and the remaining zygotes were completely unstained. Moreover, with progressively increasing fragmentation of blastomeres in ICSI-derived 2PN embryos with low morphological grade, H3K9 dimethylation decreased when compared with that of IVF embryos. Asymmetric distribution of the dimethylation form of H3K9 exists in human zygote pronuclei. The ICSI-derived embryos with low morphological grade are more likely to display H3K9 demethylation than their IVF counterparts.

Chromatin Modification Requirements for 15-Lipoxygenase-1 Transcriptional Reactivation in Colon Cancer Cells

15-Lipoxygenase-1 (15-LOX-1) contributes significantly to inflammation regulation and terminal cell differentiation. 15-LOX-1 is transcriptionally silenced in cancer cells, and its transcriptional reactivation (e.g. via histone deacetylase inhibitors (HDACIs)) is essential for restoring terminal cell differentiation to cancer cells. STAT-6 acetylation via the histone acetyltransferase KAT3B has been proposed to be necessary for 15-LOX-1 transcriptional activation. However, the exact mechanism underlying 15-LOX-1 transcriptional reactivation in cancer cells is still undefined, especially in regard to the contribution of 15-LOX-1 promoter histone modifications. We therefore examined the relative mechanistic contributions of 15-LOX-1 promoter histone modifications and STAT-6 to 15-LOX-1 transcriptional reactivation by HDACIs in colon cancer cells. We found that: 1) histone H3 and H4 acetylation in the 15-LOX-1 promoter through KAT3B was critical to 15-LOX-1 transcriptional activation; 2) 15-LOX-1 transcription was activated independently from STAT-6; and 3) dimethyl-histone H3 lysine 9 (H3K9me2) demethylation in the 15-LOX-1 promoter via the histone lysine demethylase KDM3A was an early and specific histone modification and was necessary for activation of transcription. These findings demonstrate that histone modification in the 15-LOX-1 promoter is important to 15-LOX-1 transcriptional silencing in colon cancer cells and that HDACIs can activate gene transcription via KDM3A demethylation of H3K9me2.