Induces Histone Modifications Research Articles

Gene expression patterns in a rodent model for depression

Disturbances in sleep are encountered in the majority of patients with depression. To elucidate the possible molecular mechanisms behind this relationship we examined gene expression changes in a rodent model for depression and disturbed sleep. Animals were treated with daily injections of clomipramine in their early infancy, after which gene expression in basal forebrain was examined using Affymetrix Rat 230.2 chips. We tested the levels of both single transcripts and involved pathways, and searched for common nominators (i.e. transcription factors) that could explain these changes. We identified 72 differentially expressed gene transcripts, many of which are involved in epigenetic regulation, such as DNMT2. Analysis of functional pathways revealed statistically significant changes of the biological process of synaptic transmission, the cellular compartment of the synapse and the molecular function of GABA signalling, showing that transcripts with altered expression are functionally related. Finally, promoter analysis of the differentially expressed genes showed a clear enrichment of binding sites for the transcription factor CREB1, a molecule also involved in epigenetic regulation (cAMP response element-binding protein induces histone modifications). These results indicate that CREB1 may constitute one of the major links between disturbed sleep and mood. The results also highlight the molecular mechanisms in the murine clomipramine model, previously shown to be a valid model for depression.

L. pneumophila induce histone modifications in human lung epithelial cells

L. pneumophila induce histone modifications in human lung epithelial cells

Nutritional Modulation of Terminal End Buds: Its Relevance to Breast Cancer Prevention

Findings with experimental rodent models reveal that exposures to dietary factors during the in utero and pubertal periods when the mammary gland is undergoing extensive modeling and re-modeling, alter susceptibility to develop mammary tumors. Similar observations have been made in humans: childhood exposure to genistein in soy or to some other bioactive food components reduces later breast cancer risk, although they may have no effect if consumed during adulthood. Thus, food components may be more effective in affecting cancer risk in some periods of life than others. Many of these dietary exposures modify fetal and postnatal hormonal environment, including changing the concentrations of estrogens and leptin. The hormonal alterations then may induce persistent epigenetic changes by affecting gene promoter regions or by inducing histone modifications that affect chromatin transcription. The targets of epigenetic changes are likely to be the terminal end buds (TEBs), the structures where carcinogen-induced mammary tumors in rats and mice are initiated. More specifically, the site of these changes in TEBs may be the stem cells and their niche; this might explain how an exposure early in life affects the risk of breast cancer decades later. Similar structures in women, called terminal ductal lobular units, are the sites where most human breast cancers rise. According to this hypothetical model, cancer is initiated only when the epigenetically altered cells are exposed to carcinogens/radiation, etc. during adult life. In a "normal" stem cell or its niche, cancer initiating exposures do not necessarily cause cancer, because the cells can either repair the damage or undergo apoptosis. Thus, the most likely molecular targets of early life dietary exposures are genes that regulate DNA adduct formation, repair DNA damage or induce apoptosis, such as genes affecting cellular metabolism, tumor suppressor genes or genes promoting cell survival. It is possible that some of these epigenetic changes also explain why the number of TEBs generally, but not always, correlates with breast cancer risk. This hypothesis may imply that adult intake of some bioactive dietary components reduces cancer risk increased by early life dietary exposures or inhibits tumor growth by reversing epigenetic changes in various molecular targets.

CpG Island Methylator Phenotype Is a Strong Determinant of Poor Prognosis in Neuroblastomas

Neuroblastoma, one of the most common pediatric solid tumors, is characterized by two extreme disease courses, spontaneous regression and life-threatening progression. Here, we conducted a genome-wide search for differences in DNA methylation that distinguish between neuroblastomas of the two types. Three CpG islands (CGI) and two groups of CGIs were found to be methylated specifically in neuroblastomas with a poor prognosis. By quantitative analysis of 140 independent cases, methylation of all the five CGI (groups) was shown to be closely associated with each other, conforming to the CpG island methylator phenotype (CIMP) concept. The presence of CIMP was sensitively detected by methylation of the PCDHB CGIs and associated with significantly poor survival (hazard ratio, 22.1; 95% confidence interval, 5.3-93.4; P < 0.0001). Almost all cases with N-myc amplification (37 of 38 cases) exhibited CIMP. Even in 102 cases without N-myc amplification, the presence of CIMP (30 cases) strongly predicted poor survival (hazard ratio, 12.4; 95% confidence interval, 2.6-58.9; P = 0.002). Methylation of PCDHB CGIs, located in their gene bodies, did not suppress gene expression or induce histone modifications. However, CIMP was significantly associated with methylation of promoter CGIs of the RASSF1A and BLU tumor suppressor genes. The results showed that neuroblastomas with CIMP have a poor prognosis and suggested induction of silencing of important genes as an underlying mechanism.

DNA methylation as an epigenetic regulator of neural 5-lipoxygenase expression: evidence in human NT2 and NT2-N cells.

Increased expression of 5-lipoxygenase is associated with various neuropathologies and may be related to epigenetic gene regulation. DNA methylation in promoter regions is typically associated with gene silencing. We found that human NT2 cells, which differentiate into neuron-like NT2-N cells, express 5-lipoxygenase and we investigated the relationship between 5-lipoxygenase expression and the methylation state of the 5-lipoxygenase core promoter. We used the demethylating agent 5-aza-2'-deoxycytidine and the histone deacetylase inhibitor valproate to alter DNA methylation and to induce histone modifications. 5-Lipoxygenase expression and DNA methylation were assayed with RT-PCR and bisulfite genomic sequencing, respectively. Neuronal differentiation of proliferating NT2 precursors decreased 5-lipoxygenase expression. 5-Aza-2'-deoxycytidine increased 5-lipoxygenase mRNA levels only in proliferating cells, whereas valproate increased 5-lipoxygenase mRNA levels in a cell cycle-independent manner. In both precursors and differentiated cells, CpG dinucleotides of the promoter were poorly methylated. In precursors, both 5-aza-2'-deoxycytidine and valproate further reduced the number of methylated CpGs. Moreover, we found evidence for cytosine methylation in CpWpG (W=adenine or thymine) and other asymmetrical sequences; CpWpG methylation was reduced by valproate in NT2-N but not in NT2 cells. This is the first report demonstrating that the dynamics of DNA methylation relates to neural 5-lipoxygenase gene expression.

Chemically-induced histone modification as a predictor of carcinogenicity

The interaction between carcinogens and DNA is believed to initiate neoplastic transformation, but evidence suggests that epigenetic mechanisms may also be of importance. Because the histone proteins have important roles in chromatin structure and cellular function, they provide a reasonably well understood epigenetically-based system for the detection of carcinogens. In this study, human foreskin fibroblastic cells were exposed to one of several mutagens and/or carcinogens for 3, 12, or 24 h to determine if induced histone modification may be a means of predicting chemical carcinogenicity. Butyric acid (5 mM), known to result in acetylation of histones H3 and H4, and 12-O-tetradecanoylphorbol-13-acetate (3 microM), known to result in phosphorylated histone H1, were tested initially. Electrophoresis of the histone fractions was capable of resolving multiple forms of histones H1, H3, and H4. Propane sultone (0.1 mM) induced a broadening of the H2A and H2B bands after a 24 h exposure and carbon tetrachloride (1 mM) induced the formation of new histone forms in the H1 fraction after 24 h and in the H3 fraction after 3 h. Experimental variability limited the statistically significant modifications to carbon tetrachloride and propane sultone, two known carcinogens, where new forms of modified histone were detected. Therefore, the histone modification assay, with further experimentation, may be an alternate method of detecting carcinogens, especially when conventional genotoxic tests prove unreliable.

Rat liver histone modifications and their relationship to DNA-dependent RNA polymerase activities during alpha-hexachlorocyclohexane induced liver proliferation.

The time course of histone acetylation, methylation and phosphorylation during α-hexachlorocyclohexane (α-HCH) induced liver cell proliferation has been studied and correlated to other biochemical events in rat liver caused by α-HCH. Both in vitro acetylation and methylation showed an initial increase 1 and 2 h after α-HCH which obviously precedes the beginning of increased nuclear in vitro RNA synthesis. Separation of in vitro acetylated liver histones isolated 1 and 2 h after α-HCH application results in a preferential accumulation of radiactive acetate in the range of F 3, F 2b, F 2a2 histone fractions and in F 2a1. A second peak of increased histone acetylation at 24 h and methylation at 36 h occurs during a period of increased nuclear RNA polymerase activities and the beginning increase of DNA synthesis. An increased in vitro histone phosphorylation was measured 42 h after α-HCH application. From the different time courses of these nuclear events it seems possible that the early histone acetylation and methylation might be involved in the beginning increase of transcriptional activity. Further experiments will be necessary to find out whether the α-HCH induced histone modifications occurring 1, 2 h and 24, 36, 42 h are biologically significant in the sense of a causal connection for α-HCH caused increase of transcriptional activity, DNA replication or enzyme induction or whether they are independent of each other and merely coincide.