Dependence of heterochromatic histone H3 methylation patterns on the Arabidopsis gene DDM1

The Arabidopsis gene DDM1 is required to maintain DNA methylation levels and is responsible for transposon and transgene silencing. However, rather than encoding a DNA methyltransferase, DDM1 has similarity to the SWI/SNF family of adenosine triphosphate-dependent chromatin remodeling genes, suggesting an indirect role in DNA methylation. Here we show that DDM1 is also required to maintain histone H3 methylation patterns. In wild-type heterochromatin, transposons and silent genes are associated with histone H3 methylated at lysine 9, whereas known genes are preferentially associated with methylated lysine 4. In ddm1 heterochromatin, DNA methylation is lost, and methylation of lysine 9 is largely replaced by methylation of lysine 4. Because DNA methylation has recently been shown to depend on histone H3 lysine 9 methylation, our results suggest that transposon methylation may be guided by histone H3 methylation in plant genomes. This would account for the epigenetic inheritance of hypomethylated DNA once histone H3 methylation patterns are altered.     

Role of histone H3 lysine 27 methylation in Polycomb-group silencing

Polycomb group (PcG) proteins play important roles in maintaining the silent state of HOX genes. Recent studies have implicated histone methylation in long-term gene silencing. However, a connection between PcG-mediated gene silencing and histone methylation has not been established. Here we report the purification and characterization of an EED-EZH2 complex, the human counterpart of the Drosophila ESC-E(Z) complex. We demonstrate that the complex specifically methylates nucleosomal histone H3 at lysine 27 (H3-K27). Using chromatin immunoprecipitation assays, we show that H3-K27 methylation colocalizes with, and is dependent on, E(Z) binding at an Ultrabithorax (Ubx) Polycomb response element (PRE), and that this methylation correlates with Ubx repression. Methylation on H3-K27 facilitates binding of Polycomb (PC), a component of the PRC1 complex, to histone H3 amino-terminal tail. Thus, these studies establish a link between histone methylation and PcG-mediated gene silencing.     

ATP-driven exchange of histone H2AZ variant catalyzed by SWR1 chromatin remodeling complex

The conserved histone variant H2AZ has an important role in the regulation of gene expression and the establishment of a buffer to the spread of silent heterochromatin. How histone variants such as H2AZ are incorporated into nucleosomes has been obscure. We have found that Swr1, a Swi2/Snf2-related adenosine triphosphatase, is the catalytic core of a multisubunit, histone-variant exchanger that efficiently replaces conventional histone H2A with histone H2AZ in nucleosome arrays. Swr1 is required for the deposition of histone H2AZ at specific chromosome locations in vivo, and Swr1 and H2AZ commonly regulate a subset of yeast genes. These findings define a previously unknown role for the adenosine triphosphate-dependent chromatin remodeling machinery.     

Clustering of human H1 and core histone genes

An H1 histone gene was isolated from a 15-kilobase human DNA genomic sequence. The presence of H2A, H2B, H3, and H4 genes in this same 15-kilobase fragment indicates that mammalian core and H1 histone genes are clustered.     

FSH处理对猪颗粒细胞中类固醇合成酶基因的表达及其调控区组蛋白H3修饰的影响

【目的】研究FSH处理对猪卵巢颗粒细胞类固醇合成酶、垂体激素受体、凋亡相关等基因表达的影响及此过程中组蛋白H3修饰的变化情况。【方法】首先,采集猪卵巢组织并用注射器抽取方法收集卵泡颗粒细胞,用含血清体系体外培养颗粒细胞至贴壁,血清饥饿16h后用终浓度5IU·mL~(-1)的FSH处理24h,并收集细胞。其次,提取细胞m RNA,采用qRT-PCR方法检测类固醇合成酶(STAR、CYP11A1、HSD3B和CYP19A1)、垂体激素受体(FSHR和LHR)、凋亡相关基因(XIAP和Fas L)m RNA的表达变化,最后,相同处理后固定细胞,采用染色质免疫沉淀结合q PCR(Ch IP-q PCR)方法检测类固醇合成酶基因STAR、CYP19A1和HSD3B上游转录调控区组蛋白H3修饰(H3K4me2、H3K4me3、H3K9ac和H3K14ac)状况。【结果】5IU·mL~(-1)的FSH处理引起类固醇合成酶基因STAR、CYP19A1和HSD3B分别为2倍(P0.01)、2.8倍(P0.01)和3.6倍(P0.05)的显著上调,而CYP11A1表达水平没有显著变化;FSH处理对垂体激素受体FSHR、LHR和凋亡相关基因XIAP、Fas L影响不显著。在上调的三个类固醇合成酶基因中,HSD3B调控区组蛋白H3修饰变化最为显著,H3K4me2、H3K4me3、H3K9ac和H3K14ac结合分别有14.7倍(P0.01)、13.6倍(P0.01)、19.7(P0.01)倍和2.5倍(P0.05)的显著上调;STAR基因调控区的H3K9ac在处理后有11.1倍的显著下降(P0.05);CYP19A基因调控区的H3K4me3和H3K9ac分别有0.5倍的上调(P0.01)和10.4倍(P0.01)的下降,其余组蛋白修饰在处理前后没有显著变化。【结论】FSH处理24h对颗粒细胞类固醇合成酶基因转录有显著上调作用,对其转录过程有H3组蛋白修饰参与,组蛋白修饰模式具有基因特异性。垂体激素受体和凋亡相关基因的应答可能需要FSH和其他因素的联合作用。     

Functional insertion of an Alu type 2 (B2 SINE) repetitive sequence in murine class I genes

The regulation of expression of the family of MHC (major histocompatibility complex) class I genes is complex. Sequence analysis has revealed that class I genes from the H-2D subregion of the MHC (which includes the D and L genes) differ from the class I gene from the H-2K subregion (the K gene) by the insertion of a type 2 Alu-like repetitive element (the murine B2 sequence) within the 3' noncoding region of the D and L genes. The consequence of this insertion in the D and L genes is the introduction of a novel polyadenylation signal, which is preferentially used over the more distal signal, the analog of that found in the K gene. The insertion of the type 2 Alu-like sequence results in a change in the preferred site for endonucleolytic cleavage which is necessary for generating a correct 3' terminus for polyadenylation. The data demonstrate that the type 2 Alu-like sequence has a function; the data also suggest a possible regulatory role of this sequence in the expression of class I genes.     

Protein-DNA interactions in vivo upstream of a cell cycle-regulated human H4 histone gene

Cell cycle-dependent histone genes are transcribed at a basal level throughout the cell cycle, with a three- to fivefold increase during early S phase. Protein-DNA interactions in the 5' promoter region of a cell cycle-regulated human H4 histone gene have been analyzed at single-nucleotide resolution in vivo. This region contains two sites, with four potential protein-binding domains, at which the DNA is protected from reaction with dimethyl sulfate in cells and from digestion with deoxyribonuclease I in nuclei. These protein-DNA interactions persist during all phases of the cell cycle and dissociate with 0.16 to 0.2M sodium chloride.     

HLA and NK cell inhibitory receptor genes in resolving hepatitis C virus infection

Natural killer (NK) cells provide a central defense against viral infection by using inhibitory and activation receptors for major histocompatibility complex class I molecules as a means of controlling their activity. We show that genes encoding the inhibitory NK cell receptor KIR2DL3 and its human leukocyte antigen C group 1 (HLA-C1) ligand directly influence resolution of hepatitis C virus (HCV) infection. This effect was observed in Caucasians and African Americans with expected low infectious doses of HCV but not in those with high-dose exposure, in whom the innate immune response is likely overwhelmed. The data strongly suggest that inhibitory NK cell interactions are important in determining antiviral immunity and that diminished inhibitory responses confer protection against HCV.     

组蛋白乙酰化/去乙酰化与基因表达调控研究进展

在真核生物中,组蛋白是构成核小体的重要成分,其乙酰化与去乙酰化修饰在真核生物基因表达调控中起重要作用。组蛋白乙酰化异常(低乙酰化或高乙酰化)常会引起基因表达紊乱,进而引起疾病的发生。对组蛋白乙酰转移酶(Histone acetyltransferase,HAT)及组蛋白去乙酰化酶(Histone deacetylase,HDAC)的种类,组蛋白乙酰化与去乙酰化与基因表达调控、疾病发生的关系进行了综述。     

Akt-mediated phosphorylation of EZH2 suppresses methylation of lysine 27 in histone H3

Enhancer of Zeste homolog 2 (EZH2) is a methyltransferase that plays an important role in many biological processes through its ability to trimethylate lysine 27 in histone H3. Here, we show that Akt phosphorylates EZH2 at serine 21 and suppresses its methyltransferase activity by impeding EZH2 binding to histone H3, which results in a decrease of lysine 27 trimethylation and derepression of silenced genes. Our results imply that Akt regulates the methylation activity, through phosphorylation of EZH2, which may contribute to oncogenesis.     

Control of genic DNA methylation by a jmjC domain-containing protein in Arabidopsis thaliana

Differential cytosine methylation of repeats and genes is important for coordination of genome stability and proper gene expression. Through genetic screen of mutants showing ectopic cytosine methylation in a genic region, we identified a jmjC-domain gene, IBM1 (increase in bonsai methylation 1), in Arabidopsis thaliana. In addition to the ectopic cytosine methylation, the ibm1 mutations induced a variety of developmental phenotypes, which depend on methylation of histone H3 at lysine 9. Paradoxically, the developmental phenotypes of the ibm1 were enhanced by the mutation in the chromatin-remodeling gene DDM1 (decrease in DNA methylation 1), which is necessary for keeping methylation and silencing of repeated heterochromatin loci. Our results demonstrate the importance of chromatin remodeling and histone modifications in the differential epigenetic control of repeats and genes.