Histone acetylation facilitates association of nucleosomes with SET domain of ALL-1 methyltransferase in vitro

The inheritable methylation pattern of gene activity, created upon cell differentiation, is further maintained by the “SET” (methyltransferase)-domain proteins. However, it is still not clear how SET-proteins can decide on the required gene activity state and the way their chromatin association is maintained. Here we have found that high levels of histone acetylation - the hallmarks of active chromosome regions in vivo - can increase the affinity of reconstituted nucleosomes to the SET domain of ALL-1 histone methyltransferase in a defined system in vitro.     

Identification of the enhancer binding protein MBF-1 of the sea urchin modulator alpha-H2A histone gene

The modulator of the sea urchin alpha-H2A histone gene promoter is the only enhancer identified in the alpha-histone gene cluster. Binding of a single factor, denoted MBF-1, has previously detected in nuclear extracts from morula and gastrula embryos. Here, we describe the cloning of MBF-1 by screening a cDNA expression library with a tandem array of modulator binding sites. MBF-1 presents no similarity with other DNA binding proteins and contains nine Krüppel like Zn fingers. In vitro translated proteins and a factor from nuclear extracts interact with the modulator with identical specificity. In addition, MBF-1 expressed in human cells transactivates a reporter gene driven by an array of modulator sites. The DNA binding domain consists of the Zn fingers plus an adjacent basic region, while sequences in the N-terminal region mediates the transactivation function. MBF-1 is expressed in the unfertilized egg and in early and late developmental stages thus confirming that it is not a stage specific enhancer binding factor and that silencing of the alpha-H2A gene after hatching is not due to the lack of the transactivator.     

Epigenetic memory transmission through mitosis and meiosis in plants

Gene activities can be regulated by epigenetic modifications of nucleotides and chromatin that are stably propagated through somatic cell divisions and, in some cases, across generations. The mechanisms that control epigenetic marks have recently been uncovered using model organisms, such as the flowering plant Arabidopsis thaliana. In Arabidopsis, perturbation of epigenetic gene activity often results in heritable developmental phenotypes. Stable, but potentially reversible, changes in epigenetic status can also be sources for phenotypic variations in natural plant populations.     

Histone-binding domains: Strategies for discovery and characterization

Chromatin signaling dynamics fundamentally regulate eukaryotic genomes. The reversible covalent post-translational modification (PTM) of histone proteins by chemical moieties such as phosphate, acetyl and methyl groups constitutes one of the primary chromatin signaling mechanisms. Modular protein domains present within chromatin-regulatory activities recognize or “read” specifically modified histone species and transduce these modified species into distinct downstream biological outcomes. Thus, understanding the molecular basis underlying PTM-mediated signaling at chromatin requires knowledge of both the modification and the partnering reader domains. Over the last ten years, a number of innovative approaches have been developed and employed to discover reader domain binding events with histones. Together, these studies have provided crucial insight into how chromatin pathways influence key cellular programs. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.     

Ionic and cofactor requirements for the activity of the apoptotic endonuclease DFF40/CAD

The endonuclease DFF40/CAD mediates regulated DNA fragmentation and chromatin condensation in cells undergoing apoptosis. Here we report the enzyme's co-factor requirements, and demonstrate that the ionic changes that occur in apoptotic cells maximize DFF40/CAD activity. The nuclease requires Mg²⁺, exhibits a trace of activity in the presence of Mn²⁺, is not co-stimulated by Ca²⁺, is inhibited by Zn²⁺ or Cu²⁺, and has high activity over a rather broad pH range (7.0–8.5). The enzyme is thermally unstable, and is rapidly inactivated at 42°C. Enzyme activity is markedly affected by ionic strength. At the optimal [K⁺] of 50–125 mM, which is in the range of the cytoplasmic [K⁺] for cells undergoing apoptosis, the activity of DFF40/CAD for naked DNA cleavage is about 100-fold higher than at 0 or 200 mM [K⁺]. Although these ranges of ionic strength do not affect DFF40 homo-oligomer formation, at higher ionic strengths the enzyme introduces single-stranded nicks into supercoiled DNA.     

Computational predictions of common transcription factor binding sites on the genes of proline metabolism in plants

Proline, an imino acid, has been well documented to be associated with the stress response induced by abiotic factors such asdrought, cold and salinity in plants and biotic factors such as bacterial and fungal attacks. However, the regulatory mechanismscontrolling proline metabolism, intercellular and intracellular transport and connections of proline to other metabolic pathways arepoorly understood. F-MATCH analysis combined with composite module analysis (CMA) revealed that the binding sites matchingmatrices for O2 and OCSBF-1 were overrepresented in the promoters of differentially expressed proline metabolism genes. Thepresence of MYBAS1 consensus binding sites occurring in combination with O2 and OCSBF1 in the promoters of genes of prolinebiosynthesis pathway and SBF1 and GT1 consensus binding sites occurring in combination with O2 and OCSBF1 in the promotersof proline catabolic pathway genes suggest their involvement in modulation of proline metabolism and its accumulation in plants.