Histone variants and chromatin structure during sea urchin development

At the late blastula stage of sea urchin development a changeover of histone synthesis and chromatin composition takes place. Synthesis of the early histone variants declines while another set, the late histone variants, begins to be detected. During subsequent development the late histones accumulate steadily. In the 9-day larva only late histone variants are detectable. Micrococcal nuclease acts differentially on early and late nuclei. There is a depressed release of acid-soluble DNA when chromatin containing the late histones is digested. Nucleosomal repeat lengths change systematically and in parallel with the changing histone composition. Blastula and preblastula chromatin have a significantly shorter major repeat length than does the chromatin of 9-, 11-, and 16-day larvae. Intermediate stages of development have chromatin with intermediate periodicities. These differences are observed when the determinations are made under denaturing conditions of electrophoresis. Repeat lengths were found to be independent of the extent of digestion at all stages examined except the pluteus, in which there is an increase of the apparent repeat length as digestion proceeds. Pancreatic DNase I digests nuclei from blastulae and 9-day larvae similarly. Changes in the histone composition of chromatin, in nuclease accessibility of chromatin, and in nucleosomal repeat length are all very closely correlated, implying that there are underlying causal relationships.     

Nucleosome DNA repeat length and histone complement in a fungus exhibiting condensed chromatin

Fungal chromatins are reported to exhibit unusually short nucleosomal DNA repeat lengths. To test whether this is a phylogenetic feature of fungi or rather is correlated with an apparent absence of condensed chromatin in the organisms studied, we have examined the chromatin organization and the complement of basic nuclear proteins in the fungus Entomophthora, an organism which exhibits marked chromatin condensation. Micrococcal nuclease digestion of Entomophthora chromatin revealed a nucleosomal DNA repeat length of 197 +/- 1.2 base pairs (bp). This repeat length is 20-40 bp longer than that reported for any fungus. Entomophthora nucleosomes exhibited an HI-like protein which was much less basic than the HI histones reported for higher eukaryotes but which was similar in basicity to the HI histone reported for the fungus Neurospora. However, the nucleosomal DNA repeat length of Neurospora chromatin is reported to be unusually short, whereas that of Entomophthora was found to be typical of the repeat lengths observed for chromatins of higher eukaryotes. Thus, repeat length, at least in fungi, would not appear to be directly determined by the basicity of the fungal cognate of histone HI.     

An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length

In the nucleus of eukaryotic cells, histone proteins organize the linear genome into a functional and hierarchical architecture. In this paper, we use the crystal structures of the nucleosome core particle, B-DNA and the globular domain of H5 linker histone to build the first all-atom model of compact chromatin fibers. In this 3D jigsaw puzzle, DNA bending is achieved by solving an inverse kinematics problem. Our model is based on recent electron microscopy measurements of reconstituted fiber dimensions. Strikingly, we find that the chromatin fiber containing linker histones is a polymorphic structure. We show that different fiber conformations are obtained by tuning the linker histone orientation at the nucleosomes entry/exit according to the nucleosomal repeat length. We propose that the observed in vivo quantization of nucleosomal repeat length could reflect nature's ability to use the DNA molecule's helical geometry in order to give chromatin versatile topological and mechanical properties.     

A nuclear protein-modifying enzyme is responsive to ordered chromatin structure.

Poly (ADP-ribose) polymerase, a nuclear protein-modifying enzyme, binds to the internucleosomal linker region of chromatin, although it modifies certain core nucleosomal histones in addition to histone H1. The activity per unit of DNA chromatin changes with the nucleosome repeat number. It reaches a maximum on chromatin of 8-10 nucleosomes in length. As the complexity of chromatin with respect to nucleosome repeat number and compactness increases, a decline and stabilization of specific activity is noted. The difference in specific activity is maintained through resedimentation and dialysis of particles. It does not appear due to differences in polymer chain length or differential degradation of poly (ADP-ribose). The data suggest a relationship between ADP-ribosylation and chromatin organization and vice versa.