The role of histone modifications in epigenetic transitions during normal and perturbed development.

Epigenetic mechanisms control eukaryotic development beyond DNA-stored information. DNA methylation, histone modifications and variants, nucleosome remodeling and noncoding RNAs all contribute to the dynamic make-up of chromatin under distinct developmental options. In particular, the great diversity of covalent histone tail modifications has been proposed to be ideally suited for imparting epigenetic information. While most of the histone tail modifications represent transient marks at transcriptionally permissive chromatin, some modifications appear more robust at silent chromatin regions, where they index repressive epigenetic states with functions also outside transcriptional regulation. Under-representation of repressive histone marks could be indicative of epigenetic plasticity in stem, young and tumor cells, while committed and senescent (old) cells often display increased levels of these more stable modifications. Here, we discuss profiles of normal and aberrant histone lysine methylation patterns, as they occur during the transition of an embryonic to a differentiated cell or in controlled self-renewal vs pro-neoplastic or metastatic conditions. Elucidating these histone modification patterns promises to have important implications for novel advances in stem cell research, nuclear reprogramming and cancer, and may offer novel targets for the combat of tumor cells, potentially leading to new diagnostic and therapeutic avenues in human biology and disease.

Functional interaction of Oct transcription factors with the family of repeats in Epstein-Barr virus oriP.

The family of repeats (FR) is a major upstream enhancer of the Epstein-Barr virus (EBV) latent C promoter (Cp) that controls transcription of six different latent nuclear proteins following interaction with the EBV nuclear protein EBNA1. Here, it was shown that Cp could also be activated by octamer-binding factor (Oct) proteins. Physical binding to the FR by the cellular transcription factors Oct-1 and Oct-2 was demonstrated by using an electrophoretic mobility-shift assay. Furthermore, Oct-1 in combination with co-regulator Bob.1, or Oct-2 alone, could drive transcription of a heterologous thymidine kinase promoter linked to the FR in both B cells and epithelial cells. Cp controlled by the FR was also activated by binding of Oct-2 to the FR. This may have direct implications for B cell-specific regulation of Cp.

Context-dependent Pax-5 repression of a PU.1/NF-kappaB regulated reporter gene in B lineage cells.

Enhancers located in the 3' end of the locus in part regulate immunoglobulin heavy chain (IgH) gene expression. One of these enhancers, HS 1,2, is developmentally regulated by DNA binding proteins like NF-kappaB, Pax-5 and the protein complex NF-alphaP in B lineage cells. Here we report that NF-alphaP is the ets protein PU.1. A glutathione-S-transferase (GST)-pulldown assay demonstrated that PU.1 can physically interact with NF-kappaB in solution. Experiments in COS cells showed that PU.1 and NF-kappaB (p50/c-Rel) can activate transcription of an enhancer linked reporter gene. The paired domain protein Pax-5 has previously been shown to repress enhancer-dependent transcription. Additional co-transfection experiments revealed that PU.1/NF-kappaB dependent transcription could be repressed in a context dependent manner by Pax-5, but not by the paired domain of Pax-5. When the PU.1 binding site was substituted with a binding site for the ets-protein Elf-1, Pax-5 could no longer repress reporter gene activity. Our data indicate a model where Pax-5 mediated repression of the HS 1,2 enhancer requires the recruitment of a co-factor which is dependent on Pax-5/PU.1 but which cannot be recruited by Pax-5/Elf-1.

NFE, a new transcriptional activator that facilitates p50 and c-Rel-dependent IgH 3' enhancer activity.

The induction of immunoglobulin heavy chain (IgH) 3' enhancer activity has been coupled to ligand/receptor-dependent activation of resting B cells. To search for transcriptional target sites that account for this induction, extracts from lipopolysaccharide (LPS)-stimulated B cells and cell lines were used. Here we describe, by gel-retardation analysis, the identification of an NF-kappaB site and an adjacent nuclear factor ets-like (NFE) site in the 3' enhancer. The NFE motif binds four protein complexes in resting B cell extracts, of which two are down-regulated upon LPS stimulation. Gel shift-shift experiments of the NF-kappaB complexes with specific antibodies identified p50 and c-Rel proteins to be the predominant factors in primary LPS-stimulated cell extracts. Site-directed mutagenesis of these motifs demonstrates that they contribute to part of the enhancer activity in plasma cells. One copy of the NFkappaB/NFE motifs, linked to a heterologous reporter construct, displays lymphoid-restricted reporter gene activity in transient transfection assays. Mutation of either site abrogates all promoter activity. Complementation experiments demonstrate that although p50 and c-Rel expression vectors reconstitute transcription of an intact NF-kappaB/NFE reporter construct in a dose-dependent manner, mutation of the NFE site or the NF-kappaB site abrogates essentially all transcriptional activity in both plasma cells and in COS cells. Taken together, we provide evidence for the existence of an activator, NFE, which in combination with the p50 and c-Rel proteins, are part of the transcription factor machinery that regulates 3' enhancer activity, and thus the control of the IgH locus in late B lymphocyte development.

Superoxide dismutase and catalase enhance autoxidation during one-electron reduction of aminochrome by NADPH-cytochrome P-450 reductase.

NADPH-cytochrome P-450 reductase catalyzes one-electron reduction of aminochrome to the corresponding ortho-semiquinone, which was found to be unstable as indicated by the occurrence of NADPH oxidation and oxygen consumption. The addition of superoxide dismutase and catalase, alone or together, to the incubation mixture, during reduction of aminochrome catalyzed by NADPH-cytochrome P-450 reductase, did not prevent the autoxidation of ortho-semiquinone, but instead they increased NADPH oxidation. These results contrast with the almost complete inhibition of autoxidation (NADH oxidation) of ortho-hydroquinone during reduction of aminochrome catalyzed by DT-diaphorase in the presence of both superoxide dismutase and catalase. However, the effect of superoxide dismutase and catalase on oxygen consumption was found to differ from the effect on NADH or NADPH oxidation, since these enzymes, alone or together, inhibited the oxygen consumption during the reduction of aminochrome catalyzed by both NADPH-cytochrome P-450 reductase and DT-diaphorase. These results support the proposed role of NADPH-cytochrome P-450 reductase in neurodegeneration as a consequence of activation of aminochrome to reactive oxygen species. In addition, they also support the protective and antioxidant role of DT-diaphorase, together with superoxide dismutase and catalase, by competing with NADPH-cytochrome P-450 reductase to reduce aminochrome to ortho-hydroquinone and prevent the formation of reactive oxygen species. A possible mechanism is proposed.

Superoxide dismutase and catalase prevent the formation of reactive oxygen species during reduction of cyclized dopa ortho-quinone by DT-diaphorase.

Dopa was oxidized by Mn(3+)-pyrophosphate complex to the corresponding o-quinone, accompanied by the cyclization of the amino chain to form cyclized dopa ortho-quinone (cDoQ) with absorption maxima at wavelengths of 305 and 475 nm. The cyclization was found to proceed in a single step from DoQ to cDoQ without formation of cDoQH2 and oxygen consumption. DT-diaphorase catalyzes the reduction of cDoQ to the corresponding hydroquinone (cDoQH2), which was found to be unstable in the presence of oxygen. The autoxidation of the cDoQH2 was followed by recording the constant oxidation of NADH and oxygen consumption and reduction of cDoQ at a wavelength of 475 nm. It was found that three different oxidizing agents were involved in autoxidation of cDoQH2. The addition of DETAPAC resulted in a strong inhibition of NADH oxidation (65% inhibition) during the reduction of cDoQ by DT-diaphorase, suggesting that manganese was responsible for 65% of the autoxidation of cDoQH2. The addition of SOD to the incubation mixture resulted in the inhibition of NADH oxidation (79%) during the reduction of cDoQ by DT-diaphorase. In the presence of DETAPAC, the addition of SOD inhibited NADH oxidation during cDoQH2 autoxidation 75%, suggesting that superoxide radicals are responsible for 75% of the oxygen-dependent autoxidation. The remaining NADH oxidation, which was not inhibited by DETAPAC and SOD, was accompanied by a constant oxygen consumption, suggesting that this autoxidation of cDoQH2 proceeds by reducing oxygen to superoxide radical. The effect of SOD and catalase in the presence of DETAPAC was also studied. A nearly complete inhibition (90%) of oxygen consumption during the reduction of cDoQ by DT-diaphorase was observed when SOD alone or SOD and catalase were added to the incubation mixture containing DETAPAC. We conclude that SOD and catalase constitute a protective cellular system against formation of reactive oxygen species during reduction of cDoQ by DT-diaphorase.

The protective effect of superoxide dismutase and catalase against formation of reactive oxygen species during reduction of cyclized norepinephrine ortho-quinone by DT-diaphorase.

Norepinephrine was oxidized by the Mn(3+)-pyrophosphate complex to the corresponding o-quinone at pH 6.5. Cyclized norepinephrine ortho-quinone showed an absorption maximum at 289 and 483 nm. No oxygen consumption was observed during oxidation of norepinephrine to o-quinone by Mn3+ and subsequent cyclization. The reduction of cyclized norepinephrine ortho-quinone to the corresponding hydroquinone was catalyzed by DT-diaphorase. However, the hydroquinone formed proved to be unstable in the presence of oxygen, since reduction of cyclized norepinephrine o-quinone by DT-diaphorase was accompanied by continuous oxidation of NADH and oxygen consumption. Addition of the chelator DETAPAC or SOD to the incubation mixture during reduction of cyclized norepinephrine ortho-quinone by DT-diaphorase strongly inhibited NADPH oxidation and oxygen consumption, suggesting that manganese and superoxide radicals were involved in hydroquinone autoxidation. Elimination of the effects of superoxide radicals, manganese and H2O2 on autoxidation of hydroquinone by addition of SOD, catalase and DETAPAC to the incubation mixture resulted in a 79% inhibition of NADH oxidation, suggesting that 21% of the autoxidation is oxygen-dependent. However, the effect of these additions on oxygen consumption was even more pronounced (93% inhibition).