Linker DNA

The histone core protects the DNA bound to the nucleosome from digestion by pan-creatic deoxyribonuclease (DNase) I or micrococcal nuclease. Nucleases, however, will cleave the linker DNA that connects the nucleosome subunits to one another. 

A rapid increase in the FPA decay rate with increasing ethidium was attributed to dye clustering and consequent excitation transfer. These data were analyzed using the (invalid) anisotropy expression, r(t) = rB(t) rE(t), wherein rE(t) is calculated via the (valid) Monte Carlo procedure described above/157 158) Satisfactory agreement with the observations was obtained by assuming that ethidium can bind only to a 28-bp stretch of DNA, which is believed to comprise about half the linker DNA. 

FPA studies at extremely low binding ratios (1/400-1/700 bp) to assess the DNA motion were carried out on ethidium intercalated in calf thymus121 60) and chicken ied-cell(61) chromatin. Under the conditions of these experiments, ethidium is believed to be intercalated only in the linker DNA, and excitation transfer is believed to be negligible. The amplitude of angular motion, or depolarization, at any given time is much lower than in... 

The nucleosome is composed of 200 base pairs of DNA and an octamer of the histones H2A, H2B, H3, and H4 as well as histone HI (Komberg, 1974, 1977). Nucleosomes can be obtained by mild digestion of chromatin with micrococcal nuclease (Noll, 1974a Axel, 1975), followed by fractionation on a sucrose gradient. Further digestion of the nucleosomes results in the formation of nucleosome core particles composed of 145 base pairs of DNA and an octamer of the histones H2A, H2B, H3, and H4 (Rill and Van Holde, 1973 Sollner-Webb and Felsenfeld, 1975 Axel, 1975 Bakayev et al., 1975 Whitlock and Simpson, 1976 Noll and Komberg, 1977). The DNA piece thus excised is called linker DNA which serves as a link... 

The genetic information of eukaryotic cells is propagated in the form of chromosomal DNA. Besides the nucleic acid component, chromosomes contain architectural proteins as stoichiometric components, which are involved in the protective compaction of the fragile DNA double strands. Together, the DNA and proteins form a nucleoprotein structure called chromatin. The fundamental repeating unit of chromatin is the nucleosome core particle. It consists of about 147 base pairs of DNA wrapped around a histone octamer of a (H3/H4)2 tetramer and two (H2A-H2B) heterodimers. One molecule of the linker histone HI (or H5) binds the linker DNA region between two nucleosome core particles (Bates and Thomas 1981). 

CHO cells, also show a lower sensitivity to bleomycin (Lopez-Larraza et al, 2006). The ATC-15 cells exhibit satisfactory growth at bleomycin doses that produce a permanent growth arrest of CHO cells, thereby suggesting that mosquito cells might have linker DNA shorter than that of mammalian cells. 

Histone HI is associated with the linker DNA found between nudeosomes to help package them into a solenoid-like structure, which is a thick 30-nm fiber. 

With the demise of the uniform fiber model in 1974, it became necessary to devise other models to account for the early electron micrographs of chromatin fibers and the X-ray diffraction studies (see Ref. [1], Chapter 1). Two models appeared in 1976, and were the major contenders for consideration in 1978. The superbead model of Franke et al. [36] envisioned the chromatin fiber as a compaction of multi-nucleosome superbeads . The solenoid model of Finch and Klug [37] postulated a regular helical array of nucleosomes, with approximately six nucleosomes per turn and a pitch of 10 nm. Although a number of competing helical models appeared in the 1980s (see Ref. [1], Chapter 7) the solenoid model remains a serious contender to this day. Structural details of this model, such as the precise disposition of linker DNA, are still lacking. 

This problem first emerged from the necessity to reconcile topological and structural data of nucleosomes and chromatin. As soon as a minichromosome could be reconstituted from pure DNA and histones, the total reduction of the DNA linking number (Lk) was found to be equal to the number of nucleosomes, which was also true for the native Hl-bearing SV40 minichromosome [12]. On the other hand, the first low-resolution crystal of the core particle showed that DNA was wrapped with 1 3/4 turns of a left-handed superhelix. Assuming linker DNAs... 

Angelov, D., Vitolo, J.M., Mutskov, V., Dimitrov, S., and Hayes, J.J. (2001) Preferential interaction of the core histone tail domains with linker DNA. Proc. Natl. Acad. Sci. USA 98, 6599-6604. Tobias, I., Coleman, B.D., and Olson, W. (1994) The dependence of DNA tertiary structure on end conditions theory and implications for topological transitions. J. Chem. Phys. 101, 10990-10996. Coleman, B.D., Tobias, I., and Swigon, D. (1995) Theory of the influence of end conditions on selfcontact in DNA loops. J. Chem. Phys. 103, 9101-9109. 

Bednar, J., Horowitz, R.A., Grigoryev, S.A., Carruthers, L.M., Hansen, J.C., Koster, A.J., and Woodcock, C.L. (1998) Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc. Natl. Acad. Sci. USA 95, 14173-14178. 

Mg (but not Na" ") results in a structure that is equivalent to the 30-nm compact fiber in the extent of condensation [49]. Finally, the independent and critical function of core histone N-termini in chromatin condensation was demonstrated by showing that nucleosomal filaments reconstituted from core histones lacking their N-terminal domains are unable to condense into folded structures upon an increase of Mg " ", despite the presence of properly bound histone H5 ([50,51], see also Ref. [52] for the discussion of the special role of H3 and H4 tails). Thus, the presence of HI is not a sine-qua-non condition for salt-induced chromatin folding, which can proceed in Hi s absence and is an intrinsic property of filaments consisting of spaced core particles. A key question is how many of the features of the native 30-nm compact fiber are due to the presence of histone HI From the available data it seems that HI may influence the intrinsic folding pathway of the chromatin filament by stabilizing a single ordered conformation. This property can have much to do with the cooperativity of HI interactions within chromatin but also with the way HI is bound to the nucleosome and with the efifect it exerts on the path of linker DNA. 

An, W., van Holde, K., and Zlatanova, J. (1998) The non-histone chromatin protein HMGl protects linker DNA on the side opposite to that protected by linker histones. J. Biol. Chem. 273, 26289-26291. 

The nucleosome core particle is a relatively stable and homogenous structure that is easily prepared, and as such has formed the basis for numerous studies into chromatin structure and function. However, several recent studies have suggested that what is true for the nucleosome core may not always be true for nucleosome arrays, nor even for nucleosomes containing linker DNA. For example, the core histone tails preferentially interact with linker DNA when is it present, whereas they are constrained to bind intranucleosomal DNA in core particles [46 8]. Consequently, the activities of proteins that require access to the tails or the DNA may be affected, and it has been shown that both DNA ligase and P/CAF are less active on nucleosome core particles than other chromatin substrates [49,50]. Similar concerns apply to the interaction of HMGN proteins with nucleosome core particles, and results from studies of these complexes must be considered in the wider context of how these proteins may interact with nucleosome arrays. 

The two models for HMGN action are not mutually exclusive, as HMGN may use both mechanisms to alter chromatin structure. Several observations point to an interplay between linker histones and the core histone tails. For example, linker histone inhibits the acetylation of H3 by P/CAF [93]. The inhibition was shown to result from steric hindrance of the tail by linker histones, rather than tail inaccessibility due to chromatin folding. It has also been shown that the removal of core histone tails may reduce the affinity of linker histone HI for the nucleosome [94], and that the interaction of the C-terminal tail of core histone H2A with linker DNA is rearranged in the presence of HI [47]. It is conceivable, therefore, that HMGN modulates the activity both of the core histone tails and of linker histones within the same nucleosome. 

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