Structure of Chromatin

Nucleosome assembly differs from DNA replication. Histone content of a cell doubles during cell doubling, just as the DNA content does. On the leading strand, the pre-existing histone octamers briefly dissociate from the template and then re-bind to the double helix. Newly made nucleosome core particles associate with DNA on either strand. Thus, the overall process of histone doubling is conservative (the histones stay together during replication), in contrast to DNA synthesis, which is semiconservative. 

The end of a linear chromosome is called a telomere. Telomeres require a special mechanism, because the ends of a linear chromosome can t be replicated by the standard DNA polymerases. Replication requires both a template and a primer at whose 3 end synthesis begins. The primer can t be copied by the polymerase it primes. What copies the DNA complementary to the primer In a circular chromosome, the primer site is to the 3 direction of another polymerase, but in a linear chromosome, no place exists for that polymerase to bind. As a result, unless a special mechanism for copying the ends of chromosomes is used, there will be a progressive loss of information from the end of the linear chromosome. Two characteristics about telomeres help avoid this situation. First, they consist of a short sequence—for example, AGGGTT—repeated many times at the end of each chromosome. Telomeres, therefore, are part of the highly repetitive DNA complement of a eukaryotic cell. Secondly, a specific enzyme, telomerase, carries out the synthesis of this reiterated DNA. Telomerase contains a small RNA subunit that provides the template for the sequence of the telomeric DNA. Eukaryotic somatic cells have a lifespan of only about 50 doublings, unless they are cancerous. One theory holds that a lack of telomerase in cells outside the germ line causes this limitation. 

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Chemical approach to the study of supramolecular biological structure of chromatin, nucleoproteide complex of DNA 99UK365. 

Balhom, R. (1982). A model for the structure of chromatin in mammalian sperm. J. Cell. Biol. 93 298-305. 

Although the higher order structure of chromatin is still not well understood, two models have been suggested and supported by experimental evidence (for references, see Felsenfeld, 1978 Chambon, 1978). One is the solenoid model of Finch and Klug (1976), obtained by supercoiling the chromatin thread, and the other model is the superbead model (Renz et al., 1977). Each may represent a different... 

Higher Order Structures of Chromatin and Histone Fibers... 

Woodcock CL, Frado LL, Rattner JB (1984) The higher-order structure of chromatin evidence for a hehcal ribbon arrangement. J Cell Biol 99 42-52... 

Two approaches are usually taken to study the effect of the association of DNA binding anticancer drugs upon the structure of chromatin and nucleosome. The first one is reconstitution of the model nucleosome in the presence of the drugs. This has been reported earlier in the case of mithramycin (Fox and Cons, 1993 Carpenter et al., 1993). In our laboratory, so far we have taken the second approach of comparing the association of the anticancer drugs with isolated chromatin at various levels. 

Acetylation is a reversible modification on proteins that can also contribute to protein localization and function. Acetylation of lysine residues in histone proteins can control the secondary structure of chromatin as well as gene expression levels from certain loci, and chromatin remodeling and its consequences in a variety of molecular and cell biological questions are intensely researched. Many other proteins undergo reversible acetylation, and the functional consequences of these modifications are poorly understood in many cases. 

McGhee, J.D., Nickol, J.D., Felsenfeld, G., and Rau, D.C. (1983) Higher order structure of chromatin orientation of nucleosomes within the 30 nm chromatin solenoid is independent of species and linker length. Cell 33, 831-841. 

Within the nucleosome, addition of ubiquitin to H2A occurs near the entry and exit sites of DNA and the binding site of HI [203]. Therefore, this post-translational modification is expected to have implications for both the stability of the particle and higher order structure of chromatin [45,203]. The C-terminal end of H2B and its ubiquitination site on the other hand is located at the opposite side of the nucleosome [45]. Incorporation of an ubiquitin adduct into the nucleosome at this site may have significant implications for the trajectory of the DNA and the integrity of the particle. In this regard there have been multiple biochemical results substantiating a role of H2B ubiquitination in transcriptional activation [207-210]. 

Woodcock, C.L. and Dimitrov, S. (2001) Higher-order structure of chromatin and chromosomes. Curr. Opin. Genet. Dev. 11, 130-135. 

Minsky et recently suggested that the emergence of eukaryotes led to a highly crowded environment that may have promoted DNA self-assembly, leading to extremely condensed and thermodynamically stable DNA aggregates such as nucleosomes and solenoid structures of chromatin. 

Structure of chromatin Condensed Minor changes only... 

Structure of chromatin which promotes transcription. A large protein complex takes part in this remodeling. Some of the proteins in the complex, like the CBP/p300 protein (see also 1.4.6), possess histone acetylase activity. The activated, DNA-boimd receptor possibly recruits a histone acetylase to the chromatin. It can thus create the conditions necessary for the formation of a transcription initiation complex by this histone modification. 

Histones within transcriptionally active chromatin and heterochromatin also differ in their patterns of covalent modification. The core histones of nucleosome particles (H2A, H2B, H3, H4 see Fig. 24-27) are modified by irreversible methylation of Lys residues, phosphorylation of Ser or Thr residues, acetylation (see below), or attachment of ubiquitin (see Fig. 27-41). Each of the core histones has two distinct structural domains. A central domain is involved in histone-histone interaction and the wrapping of DNA around the nucleosome. A second, lysine-rich amino-terminal domain is generally positioned near the exterior of the assembled nucleosome particle the covalent modifications occur at specific residues concentrated in this amino-terminal domain. The patterns of modification have led some researchers to propose the existence of a histone code, in which modification patterns are recognized by enzymes that alter the structure of chromatin. Modifications associated with transcriptional activation would be recognized by enzymes that make the chromatin more accessible to the transcription machinery. 

As already noted, eukaryotic RNA polymerases have little or no intrinsic affinity for their promoters initiation of transcription is almost always dependent on the action of multiple activator proteins. One important reason for the apparent predominance of positive regulation seems obvious the storage of DNA within chromatin effectively renders most promoters inaccessible, so genes are normally silent in the absence of other regulation. The structure of chromatin affects access to some promoters more than others, but repressors that... 

Tremethick, D. J. (2007). Higher-order structures of chromatin The elusive 30 nm fiber. Cell 128(4), 651-654. 

Fig. 4. Schematic diagram of proposed solenoid structure of chromatin to yield a 30 nm fiber. The structure consists of six nucleosomes per turn of the helix and hence would be three nucleosomes wide. In the diagram, only three nucleosomes of each turn are visible the other three nucleosomes per turn are hidden from view.

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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