Broad Chromatin Domains: An Important Facet of Genome Regulation

Chromatin composition differs across the genome, with distinct compositions characterizing regions associated with different properties and functions. Whereas many histone modifications show local enrichment over genes or regulatory elements, marking can also span large genomic intervals defining broad chromatin domains. Here we highlight structural and functional features of chromatin domains marked by histone modifications, with a particular emphasis on the potential roles of H3K27 methylation domains in the organization and regulation of genome activity in metazoans.     

EZH2在人脂肪肉瘤的表达情况及EZH2抑制剂抗人脂肪肉瘤效果及机制研究

摘要 目的：探索组蛋白H3K27me3甲基转移酶EZH2在人脂肪瘤、高分化脂肪肉瘤和去分化脂肪肉瘤的表达情况及EZH2酶活性小分子抑制剂GSK126对人脂肪肉瘤细胞系SW872的影响,并初步探索其可能机制。方法：筛选脂肪瘤、高分化脂肪肉瘤和去分化脂肪肉瘤患者术后活检标本共计23例,其中脂肪瘤7例,高分化脂肪肉瘤9例,去分化脂肪肉瘤7例,制成组织芯片,免疫组化染色检测EZH2的蛋白表达情况。体外培养SW872 脂肪肉瘤细胞系,采用CCK-8 法检测不同浓度GSK126对细胞生存的抑制作用,流式细胞技术检测细胞凋亡情况,Realtime PCR法检测细胞的凋亡与抗凋亡（Caspase-1、Caspase-3、Caspase-7、Caspase-9、Bcl-2、Bag-3）、血管生成（VEGF-α）、干性（CD133、CD44、CD24）相关基因的表达,Western blot 检测内质网应激相关蛋白Bip和ATF4蛋白的表达量。结果：EZH2在去分化脂肪肉瘤的表达高于高分化脂肪肉瘤,在良性脂肪瘤中的阳性表达少见（均P＜0.05）。EZH2酶活性抑制剂GSK126对SW872 细胞的存活有明显的抑制作用,给药后细胞凋亡率增加（P＜0.05）,凋亡相关基因Caspase-1、Caspase-3、Caspase-7、Caspase-9均表达增强（均P＜0.05）,血管生成基因VEGF-?琢表达降低（P＜0.01）,干性基因CD133表达降低（P＜0.01）,其余基因表达无明显差别。GSK126组的内质网应激相关蛋白Bip和ATF4蛋白的表达增加。结论：EZH2蛋白表达量与脂肪肉瘤细胞分化程度呈负相关,EZH2有望成为脂肪肉瘤的生物学标志物及恶性程度标志物。EZH2抑制剂可能成为脂肪肉瘤潜在的化疗药物,可能通过增强内质网应激发挥作用。     

Competition between PRC2.1 and 2.2 subcomplexes regulates PRC2 chromatin occupancy in human stem cells

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Design and synthesis of (E)-1,2-diphenylethene-based EZH2 inhibitors

Enhancer of zeste homolog 2 (EZH2) serves as the catalytic subunit of the polycomb repression complex 2 (PRC2), which is implicated in cancer progression metastasis and poor prognosis. Based on our EZH2 inhibitor SKLB1049 with low nanomolar activity, we extended the “tail” region to get a series of (E)-1,2-diphenylethene derivatives as novel EZH2 inhibitors. SAR exploration and preliminary assessment led to the discovery of the potent novel EZH2 inhibitor 9b (EZH2^WT IC₅₀ = 22.0 nM). Compound 9b inhibited the proliferation of WSU-DLCL2 and SU-DHL-4 cell lines (IC₅₀ = 1.61 µM and 2.34 µM, respectively). The biological evaluation showed that 9b was a potent inhibitor for wild-type EZH2 and greatly reduced the overall levels of H3K27me3 in a concentration-dependent manner. Further study indicated that 9b could significantly induce apoptosis of SU-DHL-4 cells. These findings indicated that 9b would be an attractive lead compound for further optimization and evaluation.     

Replication initiation and DNA topology: The twisted life of the origin

Genomic propagation in both prokaryotes and eukaryotes is tightly regulated at the level of initiation, ensuring that the genome is accurately replicated and equally segregated to the daughter cells. Even though replication origins and the proteins that bind onto them (initiator proteins) have diverged throughout the course of evolution, the mechanism of initiation has been conserved, consisting of origin recognition, multi‐protein complex assembly, helicase activation and loading of the replicative machinery. Recruitment of the multiprotein initiation complexes onto the replication origins is constrained by the dense packing of the DNA within the nucleus and unusual structures such as knots and supercoils. In this review, we focus on the DNA topological barriers that the multi‐protein complexes have to overcome in order to access the replication origins and how the topological state of the origins changes during origin firing. Recent advances in the available methodologies to study DNA topology and their clinical significance are also discussed. J. Cell. Biochem. 110: 35–43, 2010. © 2010 Wiley‐Liss, Inc.     

Dephosphorylation-induced EZH2 activation mediated RECK downregulation by ERK1/2 signaling

The reversion-inducing cysteine-rich protein with Kazal motifs (RECK) gene, a widely known cancer inhibitor, could effectively suppress cancer metastasis and angiogenesis. Downregulation or loss of RECK expression frequently occurs during cancer progression. However, the mechanism underlying RECK dysregulation has not been fully elucidated. Herein, we reported for the first time that enhancer of zeste homolog 2 (EZH2), a histone methyltransferase, could epigenetically attenuate RECK expression via catalyzing H3K27 trimethylation (H3K27me3) within the RECK promoter. Furthermore, we also proved, for the first time, the involvement of EZH2 in the inhibition of RECK by extracellular signal-related kinases (ERK)-1/2 signaling. Next, we revealed that the modulation of the enzymic activity of EZH2 resulting from posttranslational phosphorylation at the serine-21 site was responsible for the increased enrichment of H3K27me3 at the RECK promoter region by ERK1/2 signaling. Collectively, the results of our study shed more light on the mechanisms responsible for the dysregulation of RECK by the ERK1/2 pathway.     

Proteomic profiling reveals distinct phases to the restoration of chromatin following DNA replication

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Overexpression of MYC and EZH2 cooperates to epigenetically silence MST1 expression

Hippo-like MST1 protein kinase regulates cell growth, organ size, and carcinogenesis. Reduction or loss of MST1 expression is implicated in poor cancer prognosis. However, the mechanism leading to MST1 silencing remains elusive. Here, we report that both MYC and EZH2 function as potent suppressors of MST1 expression in human prostate cancer cells. We demonstrated that concurrent overexpression of MYC and EZH2 correlated with the reduction or loss of MST1 expression, as shown by RT-qPCR and immunoblotting. Methylation sensitive PCR and bisulfite genomic DNA sequencing showed that DNA methylation caused MST1 silencing. Pharmacologic and RNAi experiments revealed that MYC and EZH2 silenced MST1 expression by inhibiting its promoter activity, and that EZH2 was a mediator of the MYC-induced silencing of MST1. In addition, MYC contributed to MST1 silencing by partly inhibiting the expression of microRNA-26a/b, a negative regulator of EZH2. As shown by ChIP assays, EZH2-induced DNA methylation and H3K27me3 modification, which was accompanied by a reduced H3K4me3 mark and RNA polymerase II occupancy on the MST1 promoter CpG region, were the underlying cause of MST1 silencing. Moreover, potent pharmacologic inhibitors of MYC or EZH2 suppressed prostate cancer cell growth in vitro, and the knockdown of MST1 caused cells’ resistance to MYC and EZH2 inhibitor-induced growth retardation. These findings indicate that MYC, in concert with EZH2, epigenetically attenuates MST1 expression and suggest that the loss of MST1/Hippo functions is critical for the MYC or EZH2 mediation of cancer cell survival.     

Overexpression of MYC and EZH2 cooperates to epigenetically silence MST1 expression

Hippo-like MST1 protein kinase regulates cell growth, organ size, and carcinogenesis. Reduction or loss of MST1 expression is implicated in poor cancer prognosis. However, the mechanism leading to MST1 silencing remains elusive. Here, we report that both MYC and EZH2 function as potent suppressors of MST1 expression in human prostate cancer cells. We demonstrated that concurrent overexpression of MYC and EZH2 correlated with the reduction or loss of MST1 expression, as shown by RT-qPCR and immunoblotting. Methylation sensitive PCR and bisulfite genomic DNA sequencing showed that DNA methylation caused MST1 silencing. Pharmacologic and RNAi experiments revealed that MYC and EZH2 silenced MST1 expression by inhibiting its promoter activity, and that EZH2 was a mediator of the MYC-induced silencing of MST1. In addition, MYC contributed to MST1 silencing by partly inhibiting the expression of microRNA-26a/b, a negative regulator of EZH2. As shown by ChIP assays, EZH2-induced DNA methylation and H3K27me3 modification, which was accompanied by a reduced H3K4me3 mark and RNA polymerase II occupancy on the MST1 promoter CpG region, were the underlying cause of MST1 silencing. Moreover, potent pharmacologic inhibitors of MYC or EZH2 suppressed prostate cancer cell growth in vitro, and the knockdown of MST1 caused cells’ resistance to MYC and EZH2 inhibitor-induced growth retardation. These findings indicate that MYC, in concert with EZH2, epigenetically attenuates MST1 expression and suggest that the loss of MST1/Hippo functions is critical for the MYC or EZH2 mediation of cancer cell survival.     

ATR protects ongoing and newly assembled DNA replication forks through distinct mechanisms

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Single-copy locus proteomics of early- and late-firing DNA replication origins identifies a role of Ask1/DASH complex in replication timing control

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组蛋白H3甲基转移酶Ezh2与小鼠脂肪细胞分化关系研究

目的:探索组蛋白H3K27me3甲基转移酶Ezh2对小鼠白色、棕色和米色脂肪细胞分化的影响。方法:构建诱导型Ezh2全身敲除小鼠(Ezh2~(flox/flox) CAGcre)并于6周龄时腹腔注射他莫昔芬诱导敲除,以同窝、同性别、相同基因型假诱导(腹腔注射玉米油)小鼠作为对照。诱导完成后在光镜下观察脂肪细胞形态,采用Western Blot法检测脂肪组织中H3K27me3、Ezh2和Ucp1的蛋白表达量。采用Realtime PCR法检测不同部位脂肪组织的脂肪分化相关基因(Pparγ、Adipoq和Fabp4)、棕色脂肪标志基因(Ucp1、Cidea和Prdm16)和米色脂肪标志基因(CD137、Tmem26和Tbx1)的表达。检测敲除组小鼠的冷耐受能力,并予以高脂饮食诱导肥胖,观察小鼠体重增长情况、诱导结束后小鼠的糖耐量和胰岛素敏感性指标。结果:Ezh2敲除小鼠Ezh2和H3K27me3的蛋白含量降低,背部棕色脂肪细胞脂滴明显小于对照组,Ucp1的基因和蛋白表达明显高于对照组(P0.05);敲除组小鼠白色脂肪细胞分化较差,米色脂肪分化增加,米色脂肪的Ucp1和Tbx1基因表达增加(P0.05)。敲除小鼠可以更好地耐受冷刺激,并抵抗高脂饮食诱导的肥胖和胰岛素抵抗。结论:Ezh2在体内促进白色脂肪细胞的分化,抑制棕色和米色脂肪细胞分化。     

Genomic profiling of HIV-1 integration in microglia cells links viral integration to the topologically associated domains

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A human cancer cell line initiates DNA replication normally in the absence of ORC5 and ORC2 proteins

The origin recognition complex (ORC), composed of six subunits, ORC1–6, binds to origins of replication as a ring-shaped heterohexameric ATPase that is believed to be essential to recruit and load MCM2–7, the minichromosome maintenance protein complex, around DNA and initiate DNA replication. We previously reported the creation of viable cancer cell lines that lacked detectable ORC1 or ORC2 protein without a reduction in the number of origins firing. Here, using CRISPR-Cas9–mediated mutations, we report that human HCT116 colon cancer cells also survive when ORC5 protein expression is abolished via a mutation in the initiator ATG of the ORC5 gene. Even if an internal methionine is used to produce an undetectable, N terminally deleted ORC5, the protein would lack 80% of the AAA+ ATPase domain, including the Walker A motif. The ORC5-depleted cells show normal chromatin binding of MCM2–7 and initiate replication from a similar number of origins as WT cells. In addition, we introduced a second mutation in ORC2 in the ORC5 mutant cells, rendering both ORC5 and ORC2 proteins undetectable in the same cells and destabilizing the ORC1, ORC3, and ORC4 proteins. Yet the double mutant cells grow, recruit MCM2–7 normally to chromatin, and initiate DNA replication with normal number of origins. Thus, in these selected cancer cells, either a crippled ORC lacking ORC2 and ORC5 and present at minimal levels on the chromatin can recruit and load enough MCM2–7 to initiate DNA replication, or human cell lines can sometimes recruit MCM2–7 to origins independent of ORC.