H3K4 Monomethylation Research Articles

Methyl-Metabolite Depletion Elicits Coordinated Responses to Support Heterochromatin Stability and Epigenetic Persistence

S-adenosylmethionine (SAM) is the methyl-donor cofactor for the DNA and histone methyltransferases that regulate cellular epigenetic states; however, the adaptive mechanisms that allow cells to actively respond to – and recover their functional epigenomes from – perturbations in SAM availability are unknown. Here, we identify an evolutionarily conserved response to SAM depletion that is highlighted by preferential mono-methylation of H3 Lys 9 (H3K9me1) at the expense of global losses in histone di- and tri-methylation. These coordinated pathways drive de novo cytoplasmic and nuclear mono-methylation of H3K9 to preserve heterochromatin stability and support global epigenetic persistence upon metabolic recovery. Furthermore, the dynamic chromatin response at H3K9 to diet-induced SAM deficiency and subsequent metabolic recovery was robust in both young and old C57BL/6J mice, coinciding with whole animal changes in energy metabolism. Together, these studies are the first to reveal active mechanisms for epigenetic adaptation and persistence in response to metabolic stress.

High-Level Setd8 Expression Is Important for Establishment of Normal Patterns of Erythroid Gene Expression and Is Essential for Stress Erythropoiesis

Setd8 is the sole histone methyltransferase capable of mono-methylating histone H4, lysine 20. Setd8 is expressed at basal levels in most cell types and is important for many basic cellular functions, including cell cycle progression, transcriptional regulation, and mitotic chromatin condensation. Setd8 is expressed ~10-fold higher in erythroblasts than any other cell type and during erythroid maturation of human CD34+ HSPC, Setd8 protein levels increase in parallel with Gata1 levels, suggesting that Setd8 may have an erythroid-specific function(s). Consistent with this hypothesis, erythroid-specific deletion of Setd8 was embryonic lethal, resulting in profound anemia. Setd8-null erythroblasts had cell cycle abnormalities, failure of transcriptional repression, and defective terminal erythroid maturation. (Malik et al., Cell Reports, 2017). These studies provided important insights into the function of Setd8 in erythroid cells, but were not able to clearly delineate the “housekeeping” functions of Setd8 from its specific functions in erythropoiesis.To identify the erythroid-specific functions of Setd8, we sought to identify and disrupt the enhancer that drives high level Setd8 expression in erythroid cells. Using publically available ChIP-seq data sets, we identified a putative enhancer located in intron 1 of the SETD8 gene that was occupied by Gata1, Tal1, and H3K4me1 in human erythroblasts derived from culture of CD43+ HSPCs. This putative enhancer was able to drive luciferase expression in a reporter gene assay, and deletion of the Gata1:Tal1 site at the center of this region was sufficient to abrogate reporter gene activity. Based on these data, we hypothesized that this was the enhancer that drives high level expression of Setd8 in erythroid cells. To test this hypothesis, we used CRISPR/Cas9 genome editing to delete this region in HUDEP-2 cells. Briefly, Cas9 and guide RNA ribonucleoprotein complexes targeting the enhancer were delivered into the cells using electroporation (Gundry et al., Cell Reports, 2015). PCR and sequencing were used to confirm genome editing in monoclonal cell lines. Homozygous deletion of the enhancer (Δ/Δ) reduced SETD8 expression to 27.8% of WT (+/+) controls by RT-qPCR (n=3 for each genotype; p=0.0018). Decreased Setd8 protein levels and H4K20 mono-methylation was confirmed by Western blot. Further supporting an important function of Setd8 in erythropoiesis, deletion of the enhancer and exon 7 in CD34+ HSPCs resulted in a decreased efficiency of erythroid colony formation to 49.6% of control (n=5, p=0.0359).To gain insights into Setd8 gene regulation in erythroid cells, we performed RNA-seq, comparing the Δ/Δ and +/+ enhancer lines. In total, there were 603 genes differentially expressed (p<0.05; fold change >1.5), including SETD8, FAS, and CDKN1A (p21Cip1). Pathway analyses identified numerous genes associated with apoptosis and cell death to be up-regulated. Intriguingly, multiple genes in important for stress erythropoiesis were differentially expressed in the Setd8 Δ/Δ and +/+ enhancer lines and were also differentially expressed in Setd8-null murine erythroblasts (Malik et al., Cell Reports, 2017). Most notably, both the Δ/Δ enhancer lines and the Setd8-null erythroblasts had significantly higher levels of Fas death receptor transcript than control cells. Down-regulation of Fas is essential for stress erythropoiesis (Liu et al., Blood, 2006). We therefore hypothesized that Setd8 is important for the stress erythropoiesis response. To test this hypothesis, we subjected EpoR-Cre+/-;Setd8fl/+ (Setd8Δ/+) and EpoRCre+/-;Setd8+/+ (Setd8+/+) mice to anemic stress by retro-orbital bleeding. Setd8Δ/+ and Setd8+/+ mice had similar hematocrit after anemic stress (26.6 vs 29.4%; p=0.216), but the Setd8Δ/+ had an impaired ability to mount a stress response, with a lower MCV (43.0 vs 45.1 fL, p=0.003) and reticulocyte count (8.05 vs 2.14%, p=0.031) Consistent with the transcriptomic data, Setd8Δ/+ mice had higher levels of Fas transcript in splenic erythroblasts than Setd8+/+ controls. Together, these data suggest that high level Setd8 expression is important for normal erythroid maturation and gene expression, and for regulating the stress erythropoiesis response. DisclosuresNo relevant conflicts of interest to declare.

Mutant p53 regulates enhancer-associated H3K4 monomethylation through interactions with the methyltransferase MLL4

Monomethylation of histone H3 lysine 4 (H3K4me1) is enriched at enhancers that are primed for activation and the levels of this histone mark are frequently altered in various human cancers. Yet, how alterations in H3K4me1 are established and the consequences of these epigenetic changes in tumorigenesis are not well understood. Using ChIP-Seq in human colon cancer cells, we demonstrate that mutant p53 depletion results in decreased H3K4me1 levels at active enhancers that reveal a striking colocalization of mutant p53 and the H3K4 monomethyltransferase MLL4 following chronic tumor necrosis factor alpha (TNFα) signaling. We further reveal that mutant p53 forms physiological associations and direct interactions with MLL4 and promotes the enhancer binding of MLL4, which is required for TNFα-inducible H3K4me1 and histone H3 lysine 27 acetylation (H3K27ac) levels, enhancer-derived transcript (eRNA) synthesis, and mutant p53-dependent target gene activation. Complementary in vitro studies with recombinant chromatin and purified proteins demonstrate that binding of the MLL3/4 complex and H3K4me1 deposition is enhanced by mutant p53 and p300-mediated acetylation, which in turn reflects a MLL3/4-dependent enhancement of mutant p53 and p300-dependent transcriptional activation. Collectively, our findings establish a mechanism in which mutant p53 cooperates with MLL4 to regulate aberrant enhancer activity and tumor-promoting gene expression in response to chronic immune signaling.

Inhibition of the H3K4 methyltransferase SET7/9 ameliorates peritoneal fibrosis

Transforming growth factor-β1 (TGF-β1) is a major mediator of peritoneal fibrosis and reportedly affects expression of the H3K4 methyltransferase, SET7/9. SET7/9-induced H3K4 mono-methylation (H3K4me1) critically activates transcription of fibrosis-related genes. In this study, we examined the effect of SET7/9 inhibition on peritoneal fibrosis in mice and in human peritoneal mesothelial cells (HPMCs). We also examined SET7/9 expression in nonadherent cells isolated from the effluent of peritoneal dialysis (PD) patients. Murine peritoneal fibrosis was induced by intraperitoneal injection of methylglyoxal (MGO) into male C57/BL6 mice over 21 days. Sinefungin, a SET7/9 inhibitor, was administered subcutaneously just before MGO injection (10 mg/kg). SET7/9 expression was elevated in both MGO-injected mice and nonadherent cells isolated from the effluent of PD patients. SET7/9 expression was positively correlated with dialysate/plasma ratio of creatinine in PD patients. Sinefungin was shown immunohistochemically to suppress expression of mesenchymal cells and collagen deposition, accompanied by decreased H3K4me1 levels. Peritoneal equilibration tests showed that sinefungin attenuated the urea nitrogen transport rate from plasma and the glucose absorption rate from the dialysate. In vitro, sinefungin suppressed TGF-β1-induced expression of fibrotic markers and inhibited H3K4me1. These findings suggest that inhibiting the H3K4 methyltransferase SET7/9 ameliorates peritoneal fibrosis.

Widespread transcriptional pausing and elongation control at enhancers.

Regulation by gene-distal enhancers is critical for cell type-specific and condition-specific patterns of gene expression. Thus, to understand the basis of gene activity in a given cell type or tissue, we must identify the precise locations of enhancers and functionally characterize their behaviors. Here, we demonstrate that transcription is a nearly universal feature of enhancers in Drosophila and mammalian cells and that nascent RNA sequencing strategies are optimal for identification of both enhancers and superenhancers. We dissect the mechanisms governing enhancer transcription and discover remarkable similarities to transcription at protein-coding genes. We show that RNA polymerase II (RNAPII) undergoes regulated pausing and release at enhancers. However, as compared with mRNA genes, RNAPII at enhancers is less stable and more prone to early termination. Furthermore, we found that the level of histone H3 Lys4 (H3K4) methylation at enhancers corresponds to transcriptional activity such that highly active enhancers display H3K4 trimethylation rather than the H3K4 monomethylation considered a hallmark of enhancers. Finally, our work provides insights into the unique characteristics of superenhancers, which stimulate high-level gene expression through rapid pause release; interestingly, this property renders associated genes resistant to the loss of factors that stabilize paused RNAPII.

HOXA9 Recruitment of Methyltransferase Complexes Alters Enhancer Landscape during Leukemic Transformation

HOXA9 is a homeodomain-containing transcription factor that regulates hematopoietic stem cell renewal and differentiation and is commonly over expressed in acute leukemia, including acute myeloid leukemia (AML), and T- and B-precursor acute lymphoblastic leukemia (B-ALL and T-ALL). Together with its co-binding factor MEIS1, HOXA9 has been shown to play a causal role in leukemic transformation; however, the mechanism through which HOXA9 promotes leukemogenesis is poorly understood.Previously, we showed that HOXA9 primarily binds to promoter-distal regions of the genome that show histone H3 lysine 4 (H3K4) monomethylation and histone H3 and H4 acetylation, epigenetic signatures indicative of active enhancers. HOXA9 cobinds with other lineage specific transcription factors such as C/EBPα, which we previously showed to be essential for leukemic transformation. This suggests that HOXA9 functions in a multi-subunit complex including lineage-specific transcription factors as well as chromatin modulators, but the role of HOXA9 in promoting the formation of these “enhanceosomes” and how HOXA9 alters the enhancer landscape remains unknown.In these studies, we found that in both myeloid and lymphoid murine leukemia models, HOXA9 alters the enhancer landscape through creation of de novo enhancers, many of which are active in other cell lineages in early embryogenesis. RNA expression analysis revealed that these de novo enhancers drive a leukemia-specific transcription program, whose up regulation is significantly impaired upon either HOXA9 inactivation or CRISPR-mediated deletion of specific HOXA9-bound enhancer sequences. Protein and chromatin immunoprecipitation studies showed that HOXA9 physically interacts with the MLL3/MLL4 histone methyltransferase complex and colocalizes with MLL3/MLL4 at many sites in vivo . HOXA9 is required for the recruitment of C/EBPα, the MLL3/MLL4 complex and histone H3 lysine 4 monomethylation at de novo enhancers. This activity of HOXA9 is essential for the activation of genes regulated by de novo enhancers and is associated with increased interaction of these enhancers with promoters as assessed by chromosome conformation capture (4C). In contrast, HOXA9 is dispensable for both C/EBPα and MLL3/MLL4 binding and H3K4 monomethylation at enhancers active in normal hematopoietic cells. Genetic disruption of components of the MLL3/MLL4 complex abrogates the active epigenetic profile of de novo enhancer regions, and significantly delays leukemia progression driven by HOXA9/MEIS1 in vivo . Together these findings show that HOXA9 reprograms the enhancer landscape of hematopoietic progenitors in leukemic cells, including formation of many de novo enhancers active during early embryonic development. This mechanism involves HOXA9-dependent recruitment of MLL3/MLL4 methyltransferase complexes, suggesting that targeting this methyltransferase complex could be an effective strategy for malignancies associated with HOX deregulation. DisclosuresNo relevant conflicts of interest to declare.

Histone H3K4 monomethylation catalyzed by Trr and mammalian COMPASS-like proteins at enhancers is dispensable for development and viability

Histone H3 lysine 4 monomethylation (H3K4me1) is an evolutionarily conserved feature of enhancer chromatin catalyzed by the COMPASS-like methyltransferase family, which includes Trr in Drosophila melanogaster and MLL3 (encoded by KMT2C) and MLL4 (encoded by KMT2D) in mammals. Here we demonstrate that Drosophila embryos expressing catalytically deficient Trr eclose and develop to productive adulthood. Parallel experiments with a trr allele that augments enzyme product specificity show that conversion of H3K4me1 at enhancers to H3K4me2 and H3K4me3 is also compatible with life and results in minimal changes in gene expression. Similarly, loss of the catalytic SET domains of MLL3 and MLL4 in mouse embryonic stem cells (mESCs) does not disrupt self-renewal. Drosophila embryos with trr alleles encoding catalytic mutants manifest subtle developmental abnormalities when subjected to temperature stress or altered cohesin levels. Collectively, our findings suggest that animal development can occur in the context of Trr or mammalian COMPASS-like proteins deficient in H3K4 monomethylation activity and point to a possible role for H3K4me1 on cis-regulatory elements in specific settings to fine-tune transcriptional regulation in response to environmental stress.

Abstract 5372: Alterations in the chromatin accessibility in nonalcoholic steatohepatitis-associated hepatocellular carcinoma

Abstract Hepatocellular carcinoma (HCC) is one of the leading causes of cancer-related deaths worldwide. Accumulated evidence in the past decade has stablished that NASH, in addition to other well-identified risk factors, is becoming a major cause of HCC in United States. In the present study, we investigated cancer-associated chromatin alterations in the Stelic Animal Model (STAM) of NASH-related HCC. Using Assay for Transposase-Accessible Chromatin with high throughput sequencing (ATAC-seq), we identified 1666 differentially opened chromatin regions in HCC tumor tissue as compared to normal livers. Annotation of these regions showed that they were associated with 1773 differentially expressed genes, which were enriched in lipid and steroid metabolism, obesity, and cancer. Among the differentially opened chromatin regions, 10% resided within 5 kb from the transcription start site (TSS), while the remaining 90% were located distal to the TSS (&amp;gt; 5 kb). By combining ATAC-seq and transcriptomic profiles, we demonstrated that 182 of the up-regulated genes were associated with open chromatin regions in tumor tissue. Furthermore, 24 of these up-regulated genes, including Apoa4, Nupr1, Anxa2, and Igfbp1, had accessible chromatin regions located proximal to the TSS. Importantly, analysis of histone modifications at the open chromatin regions of the over-expressed cancer-related Apoa4 and Anxa2 genes demonstrated enrichment by H3K4 mono-methylation (H3H4me1) and H3K27 acetylation (H3K27ac), histone marks that associated with the active gene promoters (H3K27ac) and enhancers (H3Kme1 and H3K27ac). In conclusion, these data provide evidence for alterations in the chromatin accessibility in tumor tissue and potential role of open chromatin regions in the over-expression of critical cancer-related genes in HCC. Citation Format: Mekonnen Lemma Dechassa. Alterations in the chromatin accessibility in nonalcoholic steatohepatitis-associated hepatocellular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5372. doi:10.1158/1538-7445.AM2017-5372

A UTX-MLL4-p300 Transcriptional Regulatory Network Coordinately Shapes Active Enhancer Landscapes for Eliciting Transcription

Enhancer activation is a critical step for gene activation. Here we report an epigenetic crosstalk at enhancers between the UTX (H3K27 demethylase)-MLL4 (H3K4 methyltransferase) complex and the histone acetyltransferase p300. We demonstrate that UTX, in a demethylase activity-independent manner, facilitates conversion of inactive enhancers in embryonic stem cells to an active (H3K4me1+/H3K27ac+) state by recruiting and coupling the enzymatic functions of MLL4 and p300. Loss of UTX leads to attenuated enhancer activity, characterized by reduced levels of H3K4me1 and H3K27ac as well as impaired transcription. The UTX-MLL4 complex enhances p300-dependent H3K27 acetylation through UTX-dependent stimulation of p300 recruitment, while MLL4-mediated H3K4 monomethylation, reciprocally, requires p300 function. Importantly, MLL4-generated H3K4me1 further enhances p300-dependent transcription. This work reveals a previously unrecognized cooperativity among enhancer-associated chromatin modulators, including a unique function for UTX, in establishing an "active enhancer landscape" and defines a detailed mechanism for the joint deposition of H3K4me1 and H3K27ac.

Mll3 and Mll4 Facilitate Enhancer RNA Synthesis and Transcription from Promoters Independently of H3K4 Monomethylation

Monomethylation of histone H3 at lysine 4 (H3K4me1) and acetylation of histone H3 at lysine 27 (H3K27ac) are correlated with transcriptionally engaged enhancer elements, but the functional impact of these modifications on enhancer activity isnot well understood. Here we used CRISPR/Cas9genome editing to separate catalytic activity-dependent and independent functions of Mll3 (Kmt2c) and Mll4 (Kmt2d, Mll2), the major enhancer H3K4 monomethyltransferases. Loss of H3K4me1 from enhancers in Mll3/4 catalytically deficient cells causes partial reduction of H3K27ac, but has surprisingly minor effects on transcription from either enhancers or promoters. In contrast, loss of Mll3/4 proteins leads to strong depletion of enhancer PolII occupancy and eRNA synthesis, concomitant with downregulation of target genes. Interestingly, downregulated genes exhibit reduced polymerase levels in gene bodies, but not at promoters, suggestive of pause-release defects. Altogether, our results suggest that enhancer H3K4me1 provides only a minor contribution to the long-range coactivator function of Mll3/4.

Cytosine modifications modulate the chromatin architecture of transcriptional enhancers.

Epigenetic mechanisms are believed to play key roles in the establishment of cell-specific transcription programs. Accordingly, the modified bases 5-methylcytosine (5mC) and 5-hydroxymethylcytosine (5hmC) have been observed in DNA of genomic regulatory regions such as enhancers, and oxidation of 5mC into 5hmC by Ten-eleven translocation (TET) proteins correlates with enhancer activation. However, the functional relationship between cytosine modifications and the chromatin architecture of enhancers remains elusive. To gain insights into their function, 5mC and 5hmC levels were perturbed by inhibiting DNA methyltransferases and TETs during differentiation of mouse embryonal carcinoma cells into neural progenitors, and chromatin characteristics of enhancers bound by the pioneer transcription factors FOXA1, MEIS1, and PBX1 were interrogated. In a large fraction of the tested enhancers, inhibition of DNA methylation was associated with a significant increase in monomethylation of H3K4, a characteristic mark of enhancer priming. In addition, at some specific enhancers, 5mC oxidation by TETs facilitated chromatin opening, a process that may stabilize MEIS1 binding to these genomic regions.

Multiple Roles for the MLL/COMPASS Family in the Epigenetic Regulation of Gene Expression and in Cancer

The mixed lineage leukemia (MLL) gene is involved in numerous chromosomal translocations that result in acute myeloid and acute lymphoid leukemias. The MLL protein belongs to a family of six methyltransferases in mammals that can methylate histone H3 on lysine 4 (H3K4). The methyltransferase activities of MLL and the other family members, SETD1A, SETD1B, MLL2, MLL3 and MLL4, depend on their participation within macromolecular complexes called COMPASS (complex of proteins associated with Set1). Functional diversity within the COMPASS family includes the propensity to mono-, di-, or trimethylate H3K4 and to regulate promoters or enhancers. Recent cancer genome sequencing and animal studies have identified MLL3 and MLL4 as cancer drivers in a wide variety of hematologic and solid tumors. MLL3 and MLL4 implement monomethylation of H3K4 at enhancer regions, whereas another enzyme in MLL3 and MLL4 COMPASS, UTX, which is also frequently mutated in multiple types of cancer, demethylates H3K27me3, a modification associated with transcription repression by the Polycomb group of proteins. Here, we review the different roles for the COMPASS family in cancer and suggest directions for future research toward elucidating the cellular pathways disregulated due to altered COMPASS functions.

Cancer-specific changes in DNA methylation reveal aberrant silencing and activation of enhancers in leukemia

AbstractAcute myeloid leukemia (AML) is characterized by an impaired differentiation process leading to an accumulation of immature blasts in the blood. One feature of cytogenetically normal AML is alterations to the DNA methylome. We analyzed 57 AML patients with normal karyotype by using Illumina's 450k array and showed that aberrant DNA methylation is significantly altered at enhancer regions and that the methylation levels at specific enhancers predict overall survival of AML patients. The majority of sites that become differentially methylated in AML occur in regulatory elements of the human genome. Hypermethylation associates with enhancer silencing. In addition, chromatin immunoprecipitation sequencing analyses showed that a subset of hypomethylated sites correlate with enhancer activation, indicated by increased H3K27 acetylation. DNA hypomethylation is therefore not sufficient for enhancer activation. Some sites of hypomethylation occur at weak/poised enhancers marked with H3K4 monomethylation in hematopoietic progenitor cells. Other hypomethylated regions occur at sites inactive in progenitors and reflect the de novo acquisition of AML-specific enhancers. Altered enhancer dynamics are reflected in the gene expression of enhancer target genes, including genes involved in oncogenesis and blood cell development. This study demonstrates that histone variants and different histone modifications interact with aberrant DNA methylation and cause perturbed enhancer activity in cytogenetically normal AML that contributes to a leukemic transcriptome.

The SUV39H1 Protein Lysine Methyltransferase Methylates Chromatin Proteins Involved in Heterochromatin Formation and VDJ Recombination.

SUV39H1 is an H3K9 methyltransferase involved in the formation of heterochromatin. We investigated its substrate specificity profile and show recognition of H3 residues between K4 and G12 with highly specific readout of R8. The specificity profile of SUV39H1 is distinct from its paralog SUV39H2, indicating that they can have different additional substrates. Using the specificity profile, several novel SUV39H1 candidate substrates were identified. We observed methylation of 19 novel substrates at the peptide level and for six of them at the protein level. Methylation of RAG2, SET8, and DOT1L was confirmed in cells, which all have important roles in chromatin regulation. Methylation of SET8 allosterically stimulates its H4K20 monomethylation activity connecting SUV39H1 to the generation of increased H4K20me3 levels, another heterochromatic modification. Methylation of RAG2 alters its subnuclear localization, indicating that SUV39H1 might regulate VDJ recombination. Taken together, our results indicate that beyond the generation of H3K9me3, SUV39H1 has additional roles in chromatin biology by direct stimulation of the establishment of H4K20me3 and the regulation of chromatin binding of RAG2.

Gene-body chromatin modification dynamicsmediate epigenome differentiation inArabidopsis.

Heterochromatin is marked by methylation of lysine 9 on histone H3 (H3K9me). A puzzling feature of H3K9me is that this modification localizes not only in promoters but also in internal regions (bodies) of silent transcription units. Despite its prevalence, the biological significance of gene-body H3K9me remains enigmatic. Here we show that H3K9me-associated removal of H3K4 monomethylation (H3K4me1) in gene bodies mediates transcriptional silencing. Mutations in an Arabidopsis H3K9 demethylase gene IBM1 induce ectopic H3K9me2 accumulation in gene bodies, with accompanying severe developmental defects. Through suppressor screening of the ibm1-induced developmental defects, we identified the LDL2 gene, which encodes a homolog of conserved H3K4 demethylases. The ldl2 mutation suppressed the developmental defects, without suppressing the ibm1-induced ectopic H3K9me2. The ectopic H3K9me2 mark directed removal of gene-body H3K4me1 and caused transcriptional repression in an LDL2-dependent manner. Furthermore, mutations of H3K9 methylases increased the level of H3K4me1 in the gene bodies of various transposable elements, and this H3K4me1 increase is a prerequisite for their transcriptional derepression. Our results uncover an unexpected role of gene-body H3K9me2/H3K4me1 dynamics as a mediator of heterochromatin silencing and epigenome differentiation.

Kinetic isotope effects reveal early transition state of protein lysine methyltransferase SET8

Protein lysine methyltransferases (PKMTs) catalyze the methylation of protein substrates, and their dysregulation has been linked to many diseases, including cancer. Accumulated evidence suggests that the reaction path of PKMT-catalyzed methylation consists of the formation of a cofactor(cosubstrate)-PKMT-substrate complex, lysine deprotonation through dynamic water channels, and a nucleophilic substitution (SN2) transition state for transmethylation. However, the molecular characters of the proposed process remain to be elucidated experimentally. Here we developed a matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF-MS) method and corresponding mathematic matrix to determine precisely the ratios of isotopically methylated peptides. This approach may be generally applicable for examining the kinetic isotope effects (KIEs) of posttranslational modifying enzymes. Protein lysine methyltransferase SET8 is the sole PKMT to monomethylate histone 4 lysine 20 (H4K20) and its function has been implicated in normal cell cycle progression and cancer metastasis. We therefore implemented the MS-based method to measure KIEs and binding isotope effects (BIEs) of the cofactor S-adenosyl-l-methionine (SAM) for SET8-catalyzed H4K20 monomethylation. A primary intrinsic 13C KIE of 1.04, an inverse intrinsic α-secondary CD3 KIE of 0.90, and a small but statistically significant inverse CD3 BIE of 0.96, in combination with computational modeling, revealed that SET8-catalyzed methylation proceeds through an early, asymmetrical SN2 transition state with the C-N and C-S distances of 2.35-2.40 Å and 2.00-2.05 Å, respectively. This transition state is further supported by the KIEs, BIEs, and steady-state kinetics with the SAM analog Se-adenosyl-l-selenomethionine (SeAM) as a cofactor surrogate. The distinct transition states between protein methyltransferases present the opportunity to design selective transition-state analog inhibitors.

Functional Characterization of a Dnase I Hypersensitive Site Located 4Kbp Upstream of the Gγ-Globin Gene Using a Synthetic Zinc Finger DNA-Binding Domain

The human β-globin genes are expressed in a developmental stage-specific manner and regulated by many cis- and trans-regulatory components including a locus control region (LCR) and proximal promoter and enhancer elements. The two γ-globin genes, Gγ and Aγ, are expressed in the fetal period. Persistent expression of γ-globin in the adult ameliorates the symptoms associated with mutations of the adult β-globin gene, such as sickle cell disease or β-thalassemia. Thus, understanding the mechanisms by which the fetal globin genes are activated and silenced during development may lead to new avenues for the treatment of hemoglobinopathies. Using data from the human ENCODE project we identified a DNase I hypersensitive site located 4 Kbp upstream of the Gγ-globin gene (Gγ -4Kb DHS) in K562 cell line. Gγ -4Kb DHS is characterized by the presence of histone modifications typical for enhancer elements (H3K4 monomethylation and H3K27 acetylation) and binding of ubiquitous (USF, E2F, YY1, c-Myc, Egr1, and MafK) or tissue-restricted (NF-E2) transcription factors in K562 cells which express high levels of the γ-globin genes (Figure 1). The presence of USF and NF-E2 is interesting as both proteins have been implicated in the recruitment of transcription complexes to the β-globin gene locus (Crusselle-Davis et al., 2006, Mol. Cell. Biol.; Liang et al., 2009 Mol. Cell. Biol.; Zhou et al., 2010, J. Biol. Chem.; Stee & Hossain et al., 2015, Mol. Cell. Biol.).We generated and expressed in K562 cells a synthetic Zinc Finger DNA-Binding Domain (ZF-DBD) designed to specifically target the Gγ -4Kb DHS and interfere its activities (ZF@Gγ-4KbDHS). The target site for the ZF-DBD overlaps with a CCCAC Egr1 motif and is close to an E-box sequence, which is predicted to bind USF and c-Myc (Figure 1). Figure 2A and C shows the Western blot results for cells transfected with empty vector or cells expressing the ZF@Gγ-4KbDHS in cell pools or a single cell clone selected from the pool of transfected cells (Figure 2A and C, respectively). We analyzed the binding of ZF@Gγ-4KbDHS at the globin locus in K562 cells using Chromatin Immunoprecipitation (ChIP). The data demonstrate that the ZF@Gγ-4KbDHS efficiently interacted with the Gγ -4Kb DHS and less efficiently with the γ-globin promoters (Figure 2B). Expression of the ZF@Gγ-4KbDHS led to a significant reduction in expression of the γ-globin genes but had no effect on expression of the GATA-1 gene (Figure 2D).The data suggest that the Gγ -4Kb DHS contributes to high-level γ-globin gene expression in K562 cells. Additionally, a SNP (rs11036496, Figure 1) within the Gγ -4Kb DHS has been reported to be associated with a disorder of γ-globin gene expression in African Americans and Chromatin Conformation Capture (3C) experiments showed that the Gγ-globin upstream region participates in interactions with the LCR and γ-globin genes (Shriner et al., 2015, BMC Medical Genetics; Kiefer et al., 2011, Blood). Therefore, further characterization of the Gγ -4Kb DHS will enhance understanding molecular mechanism(s) regulating hemoglobin switching. [Display omitted] [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Lysine Methyltransferase Kmt5a Restricts Myeloid-Biased Output of Lymphoid-Primed Multipotent Progenitors

Distinct, lineage-biased subsets of multipotent progenitor cells (MPP) dynamically respond to the demands of the hematopoietic system to replenish mature hematopoietic cells as needed. It currently remains unclear as to whether distinct epigenetic mechanisms regulate lineage-specific expansion and differentiation from MPPs. Focusing on lymphoid-primed multipotent progenitor cells (LMPP/MPP4), we performed a lentiviral shRNA screen of 15 epigenetic factors, selected based on differential expression between myeloid-restricted and lymphoid-restricted progenitors. Following a 48 hour infection with lentiviral shRNA constructs or a non-targeting control, the lineage potential of lymphoid-primed multipotent progenitors was interrogated by myeloid and lymphoid colony forming unit (CFU) assays. From this screen, knockdown of the lysine methyltransferase Kmt5a most dramatically altered lineage output from lymphoid-primed multipotent progenitors through an expansion of myeloid lineage colonies without altering lymphoid colony production. To confirm target specificity, two independent shRNA hairpins targeting distinct locations of the Kmt5a transcript demonstrated that knockdown of Kmt5a (97.1% and 99.5% versus non-targeting control shRNA) increased macrophage colony production by 1.94 and 1.95 fold, respectively (P < 0.01 and P < 0.05, n = 3). Preliminary single cell culture experiments support that the enhanced myeloid lineage output from lymphoid-primed multipotent progenitors occurs at the single-cell level through increased cloning efficiency of myeloid-biased cells. Our results suggest that Kmt5a functions to restrict myeloid lineage output from lymphoid-primed multipotent progenitors. Mechanistically, KMT5A is responsible for monomethylation of histone H4K20 and the methylation of non-histone proteins (ex. p53K376). Our ongoing work aims to distinguish between these histone and non-histone targets to determine the precise mechanisms restricting myeloid lineage output from lymphoid-primed multipotent progenitors. This work has direct implications for a better understanding of the molecular drivers of transient myeloid lineage reprogramming of lymphoid-primed multipotent progenitors during hematopoietic regeneration, age associated myeloid lineage skewing of hematopoiesis, and myeloid malignancies. DisclosuresNo relevant conflicts of interest to declare.

Lysine-specific demethylase 1 inhibitor rescues the osteogenic ability of mesenchymal stem cells under osteoporotic conditions by modulating H3K4 methylation.

Bone tissue engineering may be hindered by underlying osteoporosis because of a decreased osteogenic ability of autologous seed cells and an unfavorably changed microenvironment in these patients. Epigenetic regulation plays an important role in the developmental origins of osteoporosis; however, few studies have investigated the potential of epigenetic therapy to improve or rescue the osteogenic ability of bone marrow mesenchymal stem cells (BMMSCs) under osteoporotic conditions. Here, we investigated pargyline, an inhibitor of lysine-specific demethylase 1 (LSD1), which mainly catalyzes the demethylation of the di- and mono-methylation of H3K4. We demonstrated that 1.5 mmol·L−1 pargyline was the optimal concentration for the osteogenic differentiation of human BMMSCs. Pargyline rescued the osteogenic differentiation ability of mouse BMMSCs under osteoporotic conditions by enhancing the dimethylation level of H3K4 at the promoter regions of osteogenesis-related genes. Moreover, pargyline partially rescued or prevented the osteoporotic conditions in aged or ovariectomized mouse models, respectively. By introducing the concept of epigenetic therapy into the field of osteoporosis, this study demonstrated that LSD1 inhibitors could improve the clinical practice of MSC-based bone tissue engineering and proposes their novel use to treat osteoporosis.

FOXA1 Directs H3K4 Monomethylation at Enhancers via Recruitment of the Methyltransferase MLL3

SummaryFOXA1 is a pioneer factor that binds to enhancer regions that are enriched in H3K4 mono- and dimethylation (H3K4me1 and H3K4me2). We performed a FOXA1 rapid immunoprecipitation mass spectrometry of endogenous proteins (RIME) screen in ERα-positive MCF-7 breast cancer cells and found histone-lysine N-methyltransferase (MLL3) as the top FOXA1-interacting protein. MLL3 is typically thought to induce H3K4me3 at promoter regions, but recent findings suggest it may contribute to H3K4me1 deposition. We performed MLL3 chromatin immunoprecipitation sequencing (ChIP-seq) in breast cancer cells, and MLL3 was shown to occupy regions marked by FOXA1 occupancy and H3K4me1 and H3K4me2. MLL3 binding was dependent on FOXA1, indicating that FOXA1 recruits MLL3 to chromatin. MLL3 silencing decreased H3K4me1 at enhancer elements but had no appreciable impact on H3K4me3 at enhancer elements. We propose a mechanism whereby the pioneer factor FOXA1 recruits the chromatin modifier MLL3 to facilitate the deposition of H3K4me1 histone marks, subsequently demarcating active enhancer elements.