Chromatin, organization levels

On the other hand, there is no question that enormous strides have been made. It is now possible to describe in detail the chromatin structures in many specific promoters, and then show how they are remodeled for transcriptional activation. Different kinds of chromatin organization are now recognized for different levels of developmental control. Despite the remarkable advance in detailed information that the past 25 years have provided, the overall picture of transcription in chromatin remains strangely obscured. There is almost too much... 

Gerdes, M. G., Carter, K. C., Moen, P. T., Jr., and Lawrence, J. B, (1994). Dynamic changes in the higher-level chromatin organization of specific sequences revealed by in situ hybridization to nuclear halos. J. Cell Biol. 126, 289-304. 

We have reported earlier that the coordinate development of periodic changes in chromatin organization in DNA excision repair is signMcantly impaired in poly(ADP-ribose)-depleted cells (Fig. 1) (3). This disturbance at the chromatin organizational level apparently represents the earliest poly(ADP-ribosyl)ation-dependent event in the course of DNA excision repair observed so far (8). Here we present evidence suggesting the rearrangement of newly synthesized repair patches into free DNA domains is a prerequisite for efficient excision of a bulky adduct and that this rearrangement process involves poly(ADP-ribosyl)ation of chromosomal proteins. 

Therefore, various histone fractions have different specializations in chromatin structure. The phosphorylation of HI histone determines the molecular level of chromatin organization the phosphorylation of H2a histone determines the heterochromatization pf chromatin and the superphosphorylation of H1 histone, and normal phosphorylation of H3 histone affects the microscopic level of organization (Curley et al., 1978). 

Since 1974, evidence has accumulated in the literature which indicates that chromatin itself may be considered as an assembly system. It is true that chromatin is more complex than assembly systems analyzed to date, both with respect to the size of the nucleic acid involved and therefore the amount (and variety) of protein complexed with it and with respect to the dynamic aspect of the multilevel higher order structure. Nevertheless, at least at the lower levels of organization, the interpretation of chromatin as an assembly system may be valid. Evidence for this derives from three basic lines of research described in previous sections (1) the reconstitution of the nucleosome, (2) the self-assembly of the octamer, and (3) the putative self-organization of nucleosomes into higher order structures. 

Direct visualization of chromatin structures, from single nucleosome particles to large-scale chromatin fiber in relatively unperturbed nuclei, has had a major impact on our understanding of how DNA is organized in eukaryotic cells. Without images of chromatin at all levels of organization, our interpretations of more indirect biochemical data would be impaired. We predict that advances in chromatin structure and function research will continue to rely on developments in imaging techniques. 

Chromatin structure is organized at several levels. The basic structure of chromatin—either heterochromatin or euchromatin—is called the nucleosome. The nucleosome is a complex of 146 base pairs of DNA, wound in two turns around the outside of a disk-like complex of eight proteins (called histones). The histone core contains two copies each of four histones, H2A, H2B, H3, and H4. The histone octamer is wrapped by very close to two turns of DNA. Linker DNA and another histone (HI) join together the nucleosomes (about 65 base pairs worth). HI binds cooperatively to nucleosomes, so that a gene can be zipped up all at once by the binding of many HI molecules successively. See Figure 12-1. 

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