Search

Transcription of the several hundred of mouse and human Ribosomal RNA (rRNA) genes accounts for the majority of RNA synthesis in the cell nucleus and is the determinant of cytoplasmic ribosome abundance, a key factor in regulating gene expression. The rRNA genes, referred to globally as the rDNA, are clustered as direct repeats at the Nucleolar Organiser Regions, NORs, of several chromosomes, and in many cells the active repeats are transcribed at near saturation levels. The rDNA is also a hotspot of recombination and chromosome breakage, and hence understanding its control has broad importance. Despite the need for a high level of rDNA transcription, typically only a fraction of the rDNA is transcriptionally active, and some NORs are permanently silenced by CpG methylation. Various chromatin-remodelling complexes have been implicated in counteracting silencing to maintain rDNA activity. However, the chromatin structure of the active rDNA fraction is still far from clear. Here we have combined a high-resolution ChIP-Seq protocol with conditional inactivation of key basal factors to better understand what determines active rDNA chromatin. The data resolve questions concerning the interdependence of the basal transcription factors, show that preinitiation complex formation is driven by the architectural factor UBF (UBTF) independently of transcription, and that RPI termination and release corresponds with the site of TTF1 binding. They further reveal the existence of an asymmetric Enhancer Boundary Complex formed by CTCF and Cohesin and flanked upstream by phased nucleosomes and downstream by an arrested RNA Polymerase I complex. We find that the Enhancer Boundary Complex is the only site of active histone modification in the 45kbp rDNA repeat. Strikingly, it not only delimits each functional rRNA gene, but also is stably maintained after gene inactivation and the re-establishment of surrounding repressive chromatin. Our data define a poised state of rDNA chromatin and place the Enhancer Boundary Complex as the likely entry point for chromatin remodelling complexes. [ABSTRACT FROM AUTHOR]

The binding of histones in chromatin core particles and in core particles depleted of histones H2A and H2B has been studied by high-resolution proton nuclear magnetic resonance (NMR) at 270 MHz. At low ionic strengths it is shown that histones H3 and H4 are bound in the core particle. Further, whereas the apolar regions of H2A and H2B are also bound to the core particle, the basic N-terminal and C-terminal regions are more mobile and give rise to sharp resonances in the NMR spectrum of the core particle. Between 0.3 and 0.6 M NaCl there is further release of basic regions of histones H3 and H4 from the complex. The dissociation of the core particle between 0.6 and 2.0 M NaCl is accompanied by the release of the structured apolar regions of the histones as evidenced by the appearance of a complex aromatic spectrum and perturbed upfield ring-currentshifted methyl resonances. Arginine residues are implicated in the binding between histones and DNA and 69% of these residues are found in the apolar regions of the histones. The interactions between histones and DNA in the core particle thus involves H3 and H4 and the apolar regions of H2A and H2B. It is suggested that these basic regions of H2A and H2B have binding sites outside the core particle. [ABSTRACT FROM AUTHOR]

It has been shown by high-resolution proton magnetic resonance (PMR)-spectroscopy and circular dichroism (CD) that an H2A/H2B histone complex exists after salt extraction of these histones from chromatin and that this complex can be fully renatured from both urea-denatured acid-extracted and from urea-denatured salt-extracted histones. The histone complex is shown to involve specific secondary and tertiary structure. Formation of this complex is observed to be critically dependent on pH, occurring at and above pH 5. It cannot be induced below pH 5 by increase in ionic strength. From CD spectra the H2A/H2B complex is shown to contain about 37%, α helix but no β structure. the latter being confirmed by infrared spectroscopy in the 6-μm region. The PMR spectra show that the structured region includes most of the aromatic residues of' both histones. at least two histidine residues of H2B and probably histidines 31 and 82 of histone H2A. The secondary structure of histones H2A and H2B is predicted using the Chou and Fasman procedure and comparisons are made between the predictions for histones of different species. These results in conjunction with the experimental evidence lead to the conclusion that at least residues 31-95 of H2A and residues 37-114 of H2B, i.e. the more apolar regions of the molecules: are involved in the tertiary structure of the H2A/H2B complex. [ABSTRACT FROM AUTHOR]

Sites of interaction between histones H3 and H4 have been probed by investigating complex formation, firstly between histone H4 and three peptides cleaved by chemical means from histone H3 (residues 1-90 and 1-120 using cyanogen bromide and residues 42-135 using N-bromosuccinimide), secondly between historic H3 and two peptides cleaved from historic H4 (residues 1-84 using cyanogen bromide and residues 38-102 using chymotrypsin) and thirdly between the H4 peptide (residues 38-102) and the three H3 peptides (residues 1-90, 1-120 and 42-135). The criterion for complex formation is the appearance of characteristic perturbed resonances in the aromatic region of the 270-MHz proton resonance spectrum of the peptide mixture. It is concluded that loss of 37 N-terminal residues from historic H4 and 41 N-terminal residues from histone H3 does not prevent complex formation, whilst the loss of 18 C-terminal residues from H4 and 45 C-terminal residues from H3 does prevent it; the last 15 C-terminal residues of H3 are, however, not required for forming a complex. The regions important for complex formation are therefore defined as residues 42-120 in histone H3 and residues 38-102 in historic H4. [ABSTRACT FROM AUTHOR]