Nucleosome positioning

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. 

Sato MH, Ura K, Hohmura KI, Tokuimsu F, Yoshimura SH, Hanaoka F, Takeyasu K (1999) Atomic force microscopy sees nucleosome positioning and histone Hl-induced compaction in reconstituted chromatin. FEES Lett 452 267—271... 

C. Vaillant, B. Audit and A. Arneodo, First experimental evidence of nucleosome positioning by genomic long-range correlations. Preprint. (2006). 

The principles whereby a chain of nueleosomes can compact to form a 30 nm chromatin fiber are still not well understood. Nevertheless, important aspects of this process are becoming clear from imaging studies, employing both ECM and SFM. When isolated chicken erythrocyte chromatin or chromatin reconstituted onto six tandem 208 bp nucleosome positioning units were examined by ECM, a linker DNA stem-like architectural motif was observed at the entry-exit sites (Fig. 4) [30]. Particles consistent with an octamer are surrounded with 1.7 turns of DNA, a linker... 

Fig. 4. Images of unfixed and unstained chromatin in a frozen and hydrated state. All samples shown contain linker histone H5. (A) Soluble chromatin prepared from chicken erythrocyte nuclei. Arrow indicates a nucleosome with a linker histone stem conformation. (B-E) Chromatin reconstituted onto an array of the 5S rDNA nucleosome positioning sequence. En face views (B-D) of nucleosomes show the linker DNA entering and exiting the nucleosome tangentially, before interacting and remaining associated for 3-5 nm before separating (arrows). An edge-on view (E) shows the two gyres of DNA (arrow heads) and the apposed linker DNA (arrow) (from Ref. [30]). Scale bar 20 nm (A) and 10 nm (B-E).

AFM can visualize nucleosome positioning Addition of H1 reportedly compacts the dinucleosome suggested stem-structure formation by HI... 

AFM imaging can visualize alternative nucleosome positioning on adjacent 2Q8-bp repeats (the distribution of center-to-center distances on 208-12 is bimodal)... 

Caserta, M., Verdone, L., and Di Mauro, E. (2002) Aspects of nucleosomal positional flexibility and fluidity. Chembiochem. 3, 1172-1182. 

Buttinelli, M., Di Mauro, E., and Negri, R. (1993) Multiple nucleosome positioning with unique rotational setting for the Saccharomyces cerevisiae 5S rRNA gene in vitro and in vivo. Proc. Natl. Acad. Sci. USA 90, 9315-9319. 

Overall, histone acetylation and deacetylation represents an important tool with which transcription can be positively or negatively influenced. The nucleosomes and, in a further sense, chromatin structure assiune a central role in the regulation of transcription. Nucleosome structure and nucleosome position can decisively contribute to the accessibility of DNA elements for transcription factors. The nucleosomes function as a framework that determines the spatial arrangement of a region of the DNA. Tlie nucleosome constellation must be modified during transcription initiation, whereby the post-translational modification of histones in the form of acetylation or deacetylation plays a significant role. The participation of other non-histone proteins remains an open issue and it is also imclear how a constitutive and permanent inactivation of a section of DNA can be accomplished via the chromatin structure. 

E. Segal, Y. Fondufe-Mittendorf, L. Chen, A Thastrom, Y. Field, I. K. More, J-P. Z. Wang, J. Widom, A Genomic Code for Nucleosome Positioning, Nature 442 (2006) 772. 

Interestingly, nucleosomes can potentiate as well as repress gene activation. The stimulatory effect of nucleosome positioning appears to be related to the specific exposure of recognition sequences for transcription activators. In addition, specific nucleosome positioning may help to create a specific DNA topology which may facilitate (or hinder) transcription factor binding. 

---