DNA is assembled into globular supranucleosomal chromatin structures by nuclear contents of amphibian oocytes

The transition structure of chromatin fibers at the nanoscale probed by cryogenic electron tomography

The naked DNA inside the nucleus interacts with proteins and RNAs forming a higher order chromatin structure to spatially and temporally control transcription in eukaryotic cells. The 30 nm chromatin fiber is one of the most important determinants of the regulation of eukaryotic transcription. However, the transition of chromatin from the 30 nm inactive higher order structure to the actively transcribed lower order nucleosomal arrays is unclear, which limits our understanding of eukaryotic transcription. Using a method to extract near-native eukaryotic chromatin, we revealed the chromatin structure at the transitional state from the 30 nm chromatin to multiple nucleosomal arrays by cryogenic electron tomography (cryo-ET). Reproducible electron microscopy images revealed that the transitional structure is a branching structure that the 30 nm chromatin hierarchically branches into lower order nucleosomal arrays, indicating chromatin compaction at different levels to control its accessibility during the interphase. We further observed that some of the chromatin fibers on the branching structure have a helix ribbon structure, while the others randomly twist together. Our finding of the chromatin helix ribbon structure on the extracted native chromatin revealed by cryo-ET indicates a complex higher order chromatin organization beyond the beads-on-a-string structure. The hierarchical branching and helix ribbon structure may provide mechanistic insights into how chromatin organization plays a central role in transcriptional regulation and other DNA-related biological processes during diseases such as cancer.

Assembling chromatin: the long and winding road

It has been over 35 years since the acceptance of the "chromatin subunit" hypothesis, and the recognition that nucleosomes are the fundamental repeating units of chromatin fibers. Major subjects of inquiry in the intervening years have included the steps involved in chromatin assembly, and the chaperones that escort histones to DNA. The following commentary offers an historical perspective on inquiries into the processes by which nucleosomes are assembled on replicating and nonreplicating chromatin. This article is part of a Special Issue entitled: Histone chaperones and Chromatin assembly.

Structural organization of the hepatitis B virus minichromosome

The replicative intermediate of hepatitis B virus (HBV), the covalently closed, circular DNA, is organized into minichromosomes in the nucleus of the infected cell by histone and non-histone proteins. In this study we investigated the architecture of the HBV minichromosome in more detail. In contrast to cellular chromatin the nucleosomal spacing of the HBV minichromosome has been shown to be unusually reduced by approximately 10 %. A potential candidate responsible for an alteration in the chromatin structure of the HBV minichromosome is the HBV core protein. The HBV core protein has been implicated in the nuclear targeting process of the viral genome. The association of the HBV core protein with nuclear HBV replicative intermediates could strengthen this role. Our findings, confirmed by in vivo and in vitro experiments indicate that HBV core protein is a component of the HBV minichromosome, binds preferentially to HBV double-stranded DNA, and its binding results in a reduction of the nucleosomal spacing of the HBV nucleoprotein complexes by 10 %. From this model of the HBV minichromosome we propose that the HBV core protein may have an impact on the nuclear targeting of the HBV genome and be involved in viral transcription by regulating the nucleosomal arrangement of the HBV regulatory elements, probably in a positive manner.

Progress in visualization of eukaryotic gene transcription

Methods for visualization of the ultrastructure of transcriptionally active eukaryotic genes have been developed using chromatin from giant nuclei of amphibian oocytes (Miller and Beatty 1969). Rapidly isolated chromatin is subjected to low salt treatment in order to dissociate most chromatin associated proteins. As a result, gene-chromatin with associated RNA polymerase particles and RNA transcripts can be directly analysed in electron microscope chromatin spread preparations. More recently, progress has been made in utilising living amphibian oocyte nuclei as a transcription system for cloned eukaryotic genes. In this article, an account of such experiments is given, with emphasis on results and problems of chromatin and transcription organization of microinjected cloned genes. The described transcription assay system possesses important potential for investigation of gene mutations and in particular for the elucidation of molecular aspects of experimental oncology and molecular human genetics.

Chromatin replication, reconstitution and assembly

Many previously held concepts about the replication of chromatin have recently been revised, or seriously challenged. For instance, within the last two years, evidence has accumulated to indicate that newly synthesized DNA is not the sole site of deposition of newly synthesized histones, and that histones are not only made, but are assembled into chromatin in the absence of DNA synthesis. Furthermore, segregation of parental histones to daughter DNA duplexes may be bidirectional, rather than the previously accepted unidirectional mechanism. The storage of histones prior to assembly apparently involves histone pairs rather than octamers, and similarly, histones associate with DNA in (apparent) pairs, rather than as pre-assembled octameric units. It is currently questioned whether or not nucleoplasmin is involved in either histone storage or nucleosome assembly. The onset of histone synthesis has recently been found to occur in late G1 rather than in S, and thus is independent of DNA synthesis; however, the cessation of histone synthesis is linked to that of DNA. Thus, there emerges from this newly accumulated data the conclusion that chromatin biosynthesis is not as straightforward as was believed just a few years ago. As we review the evidence on each of these subjects, we attempt to point out directions for future experimentation.

Macronuclear chromatin organization in Paramecium primaurelia

Chromatin organization and transcriptional activity in the macronucleus of the ciliate Paramecium primaurelia have been studied by electron microscopic examination of spread chromatin preparations. Under spreading conditions which inhibit the activity of endogenous nucleases and proteases, various morphologically distinct types of chromatin are seen: (1) Largely condensed chromatin in the form of 30-40 nm supranucleosomal globules which aggregate to form knobbly 40-60 nm fibres and unravel into 12 nm nucleosomal filaments; (2) In rapidly growing cells, extended chromatin arranged groups of 4-8 adjacent nucleofilaments, each bearing numerous and very densely packed lateral fibrils. These fibrils are 20 nm thick, have a smooth outline and extend to lengths of up to 3 micron. Such transcripts are grouped in units along the chromatin axis and are apparently organized in register in adjacent filaments; (3) In starved cells, extended nucleofilaments bearing only occasional RNP fibrils. These various morphological characteristics are discussed in terms of macronuclear transcriptional activity and the polyploid nature of macronuclei.

Identification of a novel class of tandemly repeated genes transcribed on lampbrush chromosomes of Pleurodeles waltlii

Electron microscope preparations of lampbrush chromosomes from oocytes of Pleurodeles waltlii have revealed a new class of tandemly repeated genes. These genes are highly active, as judged by the close spacing of nascent transcripts. They occur in clusters of greater than 100 copies and are transcribed in units containing roughly 940 base pairs of DNA that are separated by nontranscribed spacers of an estimated DNA content of 2,410 base pairs. The size and the pattern of arrangement of these transcription units can not be correlated with any of the repetitious genes so far described.