Higher order chromatin structure

Gerchman, S.E. and Ramakrishnan, V. (1987) Chromatin higher-order structure studied by neutron scattering and scanning transmission electron microscopy. Proc. Natl. Acad. Sci. USA 84,... 

Histone deacetylases (HDAGs) catalyze the removal of acetyl groups from the Ne atom of histone lysines in a nucleosomal context, ensuring the reversibility of histone acetylation. Histone deacetylation is often associated vdth transcriptional repression and silencing since it promotes chromatin higher order structures and the recruitment of silencers [34]. As other enzymes involved in chromatin... 

Chromatin is composed of nucleosomes, where each comprise 147 base pairs of DNA wrapped around an octamer oftwo copies of each histone H2A, H2B, H3, and H4. Nucleosomes are folded into higher-order structures that are stabilized by linker histones. Chromatin structure can be altered by enzymes that posttranslationally modify histones (e.g., through phosphorylation, acetylation, methylation, or ubiquitination) or by ATP-driven chromatin-remodeling complexes that alter nucleosome position and/or composition. 

HIGHER-ORDER STRUCTURES PROVIDE FOR THE COMPACTION OF CHROMATIN... 

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... 

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. 

Higher Order Structures of Chromatin and Histone Fibers... 

Simpson RT, Thoma F, Brubaker JM (1985) Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones a model system for study of higher order structure. Cell 42 799-808 Sugiyama S, Yoshino T, Kanahara H, Kobori T, Ohtani T (2003) Atomic force microscopic imaging of 30 nm chromatin fiber from partially relaxed plant chromosomes. Scanning 25 132-136 Sugiyama S, Yoshino T, Kanahara H, Shichiri M, Fukushi D, Ohtani T (2004) Effects of acetic acid treatment on plant chromosome structures analyzed by atomic force microscopy. Anal Biochem 324 39 4... 

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... 

In Section 2.2, we shall describe advances (or lack of same) in our understanding of higher-order structure in chromatin. Again, the role of lysine-rich histone remains unclear. Although it is evident that they are required for maximum compaction, what structural role they play therein remains elusive. 

Simpson, R.T., Thoma, F., and Brubaker, J.M. (1985) Chromatin reconstituted from tandemly repeated cloned DNA fragments and core histones. A model system for study of higher order structure. Cell 42, 799-808. 

Widom, J, Finch, J.T., and Thomas, J.O. (1985) Higher-order structure of long repeat chromatin. EMBO J. 4, 3189-3194. 

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. 

Cui, Y. and Bustamante, C. (2000) Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure. Proc. Natl. Acad. Sci. USA 97, 127-132. 

Histones are very basic proteins with an isoelectric point between 10.31 and 11.27 for human complement. They are present in virtually all eukaryotes (with the exception of dinoflagellates [14]) where they are associated with most of the nuclear DNA. The DNA is wrapped around an octamer formed by the four core histones H2A, H2B, H3 and H4 to build a nucleosome. This particle is the fundamental repeating unit of chromatin [15]. A string of nudeosomes can fold into a higher order structure, the exact molecular nature of which is still not fully understood but clearly has a strong influence on gene expression. 

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