Transcriptional silencing in Saccharomyces cerevisiae is mediated by heterochromatin. There is a plethora of information regarding the roles of histone residues in transcriptional silencing, but exactly how histone residues contribute to heterochromatin structure is not resolved. We address this question by testing the effects of a series of histone H3 and H4 mutations involving residues in their aminoterminal tails, on the solvent-accessible and lateral surfaces of the nucleosome, and at the interface of the H3/H4 tetramer and H2A/H2B dimer on heterochromatin structure and transcriptional silencing. The general state, stability, and conformational heterogeneity of chromatin are examined with a DNA topology-based assay, and the primary chromatin structure is probed by micrococcal nuclease. We demonstrate that the histone mutations differentially affect heterochromatin. Mutations of lysine 16 of histone H4 (H4-K16) and residues in the LRS (loss of rDNA silencing) domain of nucleosome surface markedly alter heterochromatin structure, supporting the notion that H4-K16 and LRS play key roles in heterochromatin formation. Deletion of the aminoterminal tail of H3 moderately alters heterochromatin structure. Interestingly, a group of mutations in the globular domains of H3 and H4 that abrogate or greatly reduce transcriptional silencing increase the conformational heterogeneity and/or reduce the stability of heterochromatin without affecting its overall structure. Surprisingly, yet another series of mutations abolish or reduce silencing without significantly affecting the structure, stability, or conformational heterogeneity of heterochromatin. Therefore, histone residues may contribute to the structure, stability, conformational heterogeneity, or other yet-to-be-characterized features of heterochromatin important for transcriptional silencing.

Background: Colorectal cancer is a common malignant tumor of the digestive tract, the morbidity rate of which is rising in recent years. Ginsenoside Rh3 was reported to have anticancer activity; however, the underlying mechanism still needs to be explored in depth. Methods: Rabbit blood was used to test hemolytic effects of ginsenoside protopanaxadiol (PPD), Rh2, Rh3, and Rg3. Human colorectal cancer SW1116 cells were treated with different concentration of ginsenoside PPD, Rh2, Rh3, and Rg3 in vitro. MTT and TUNEL assay were used to examine cell proliferation and apoptosis. Semi quantitative RT-PCR, immunocytochemistry assay and flow cytometry assay were used to detect the expression of caspase3. Results: The results showed that the inhibiting effects on SW1116 cells of PPD and Rh2 were stronger than those of Rh3 (p < 0.01), but Rh3 had better solubility and slighter hemolytic effects on blood cells than those ginsenosides. Ginsenoside Rh3 inhibited the proliferation of SW1116 cells at 60 μg/mL (p < 0.01), the inhibition effect was increased sharply when the dose of Rh3 was increased from 60 to 120 μg/mL, the inhibition rate was 62.1% at 120 μg/mL, the inhibition appeared at 9 h, and the peak activity occurred at 12 h and maintained until 48 h (p < 0.01). Compared to the control group, the ratio of apoptotic cells, the expression level of mRNA and protein of caspase3 increased in 120 μg/mL Rh3 treated group. Conclusion: As a potential anticancer medicine, ginsenoside Rh3 could inhibit the proliferation of colorectal cancer cells in a dose- and time-dependent manner and induce cell apoptosis through upregulating the expression of caspase3.

Heterochromatin consists of highly ordered nucleosomes with characteristic histone modifications. There is evidence implicating chromatin remodeling proteins in heterochromatin formation, but their exact roles are not clear. We demonstrate in Saccharomyces cerevisiae that the Fun30p and Isw1p chromatin remodeling factors are similarly required for transcriptional silencing at the HML locus, but they differentially contribute to the structure and stability of HML heterochromatin. In the absence of Fun30p, only a partially silenced structure is established at HML. Such a structure resembles fully silenced heterochromatin in histone modifications but differs markedly from both fully silenced and derepressed chromatin structures regarding nucleosome arrangement. This structure likely represents an intermediate state of heterochromatin that can be converted by Fun30p to the mature state. Moreover, Fun30p removal reduces the rate of de novo establishment of heterochromatin, suggesting that Fun30p assists the silencing machinery in forming heterochromatin. We also find evidence suggesting that Fun30p functions together with, or after, the action of the silencing machinery. On the other hand, Isw1p is dispensable for the formation of heterochromatin structure but is instead critically required for maintaining its stability. Therefore, chromatin remodeling proteins may rearrange nucleosomes during the formation of heterochromatin or serve to stabilize/maintain heterochromatin structure.

Ginsenoside Rg3, a bioactive constituent isolated from Panax ginseng, exhibits antitumorigenic, antioxidative, antiangiogenic, neuroprotective and other biological activities are associated with the regulation of multiple genes. DNA methylation patterns, particularly those in the promoter region, affect gene expression, and DNA methylation is catalyzed by DNA methylases. However, whether ginsenoside Rg3 affects DNA methylation is unknown. High performance liquid chromatography assay, MspI/HpaII polymerase chain reaction (PCR) and reverse transcription‑quantitative PCR were performed to assess DNA methylation. It was demonstrated that 20(S)‑ginsenoside Rg3 treatment resulted in increased inhibition of cell growth, compared with treatment with 20(R)‑ginsenoside Rg3 in the human HepG2 hepatocarcinoma cell line. It was additionally revealed that treatment with 20(S)‑ginsenoside Rg3 reduced global genomic DNA methylation, altered cystosine methylation of the promoter regions of P53, B cell lymphoma 2 and vascular endothelial growth factor, and downregulated the expression of DNA methyltransferase (DNMT) 3a and DNMT3b more than treatment with 20(R)‑ginsenoside Rg3 in HepG2 cells. These results revealed that the modulation of DNA methylation may be important in the pharmaceutical activities of ginsenoside Rg3.

In response to DNA replication stress, DNA replication checkpoint kinase Mec1 phosphorylates Mrc1, which in turn activates Rad53 to prevent the generation of deleterious single-stranded DNA, a process that remains poorly understood. We previously reported that lagging-strand DNA synthesis proceeds farther than leading strand in rad53-1 mutant cells defective in replication checkpoint under replication stress, resulting in the exposure of long stretches of the leading-strand templates. Here, we show that asymmetric DNA synthesis is also observed in mec1-100 and mrc1-AQ cells defective in replication checkpoint but, surprisingly, not in mrc1∆ cells in which both DNA replication and checkpoint functions of Mrc1 are missing. Furthermore, depletion of either Mrc1 or its partner, Tof1, suppresses the asymmetric DNA synthesis in rad53-1 mutant cells. Thus, the DNA replication checkpoint pathway couples leading- and lagging-strand DNA synthesis by attenuating the replication function of Mrc1-Tof1 under replication stress. Significance During the S phase of the cell cycle, the DNA replication machinery accurately duplicates the genome in spite of numerous hurdles that cause replication stress. The replication checkpoint pathway deals with the replication stress, which, if left undealt with, can lead to fork collapse and genome instability, a process that remains poorly understood. Here, we show that the DNA checkpoint pathway couples leading- and lagging-strand DNA synthesis to prevent the generation of deleterious single-stranded DNA under replication stress by attenuating the replication function of Mrc1, a protein involved in both DNA replication and replication checkpoint, providing a mechanistic insight into how eukaryotic cells overcome replication stress.