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Actin plays central roles in the organization and dynamics of the cytoskeleton. Within a few decades of the first isolation of actin from muscle in 1941, it was shown that actin filaments form the main architecture of the cytoskeleton, and that the dynamics of the cytoskeleton are regulated by the assembly/disassembly of the filament, which depends on the adenosine diphosphate/triphosphate (ADP/ATP) exchange and on association with various actin-binding proteins. Because of these characteristics of actin, previous researchers hypothesized that actin and/or its evolutionarily related molecules were involved in the organization and dynamics of the nucleus. However, actin filaments were observed only in the cytoplasm, and no molecule evolutionarily related to actin was identified at the time. The hypothesis was therefore regarded with skepticism for a long time.

Normal human cells in culture enter senescence upon passages or treatment with various agents. Among the treatments, 5-bromodeoxyuridine (BrdU) is unique in that it most clearly induces a senescence-like phenomenon in every type of mammalian cells ( Michishita et al. 1999 ). This system ensures genetic and biochemical approaches to study cellular senescence. In contrast, normal cells stop proliferation by stochastic accumulation of senescent cells over a long period of culture. 5-Bromodeoxyuridine is well known as a modulator of cellular differentiation. Therefore, studies of the molecular basis for BrdU facilitate understanding of chromatin-mediated cellular differentiation and cellular senescence.

Various types of proteins are required for nuclear organization, which confers a variety of nuclear functions in eukaryotic cells. A set of proteins forms the chromosomal backbone ( Paulson and Laemmli 1977 ) and different sets of proteins including chromatin-remodeling factors regulate the utilization of genetic code in chromosomal DNA ( Boulikas 1995 ; Moazed 2001 ; Muchardt and Yaniv 2001 ). Eukaryotic chromosomes are topologically attached to the nuclear matrix (NM) or scaffold, a network of protein fibers referred to as the skeletal framework of the nucleus. The NM or scaffold is operationally defined as the residual structures that remain insoluble after extraction of nuclei with a high concentration of either salt or detergent. Several members of the group of proteins classified as components of the NM can directly bind to particular segments of chromosomal DNA. A DNA segment to which matrix and scaffold proteins can bind is termed a matrix or scaffold attachment region (MAR/SAR) ( Cockerill and Garrard 1986 ; Gasser and Laemmli 1986 ; Cockerill et al. 1987 ; Jarman and Higgs 1988 ). One significant role of MAR/SARs that was revealed by structural analyses of the nucleus and chromosomes is the matrix- or scaffold-mediated stabilization of chromosomal structure. Chromosomal loops with an approximate length of ∼60 kilobases yield compact configurations of chromosomes.

“Preformation” and “epigenesis” were the two antithetical concepts theoretical biologists of the early 18th century advocated to explain ontogenesis. Apparently their repercussions still remain and keep vibrating, at least in a subject of the current biological study; i.e. how the usage of “genetic” information, an ultimate “preformed” material, is controlled by the “epigenetics,” a derivative of “epigenesis,” and conversely, how such “epigenetic” regulations are restricted by the cisacting “genetic” elements. The genetic elements described in the latter issue are experimentally defined as “boundary elements” or “insulators,” and have been studied extensively for decades ( Gerasimova and Corces 2001 ). Here I am going to summarize some of the recent advances to unravel the mechanics of boundary elements that hinder spread of epigenetic heterochromatin. They appear to be classified functionally into two groups, the antagonistic chromosomal effect and the structural tethering in the nucleus.

During the latest decade, the studies that have attempted to understand the regulatory mechanism of the structure and function of chromatin have had a great research impact with respect to the research in the field related to nuclear functions, including transcription and replication. The analysis of the molecular mechanism of replication and transcription began with the dissection and reconstitution of cell-free systems that mimicked the accurate enzymatic processes in test tubes. The cell-free replication system of the adenovirus genome DNA replication—the first cell-free eukaryotic DNA replication system—was reconstituted with purified viral proteins and host cell factors. Using this system, NF-I was identified as one of the host factors, and it was shown to be a sequence-specific DNA binding protein—one of the first cases of such paradigm proteins. The reconstituted cell-free SV40 DNA replication system has provided us with an important basis for understanding cellular genome replication. The cell-free transcription system that used nuclear extracts and a DNA fragment corresponding to the adenovirus major late promoter region built a basic sculpture/landscape of the molecular mechanism of transcription.