Chromatin filaments

Widom J, Klug A (1985) Structure of the 300A chromatin filament X-ray diffraction from oriented samples. Cell 43 207-213... 

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. 

Figure 7.7 Chromatin Filament to Chromosome, (a) Proposed model of the 300 A chromatin filament. The zigzag pattern of nucleosomes (1,2,3,4) closes up to form a solenoid with 6 nucleosomes per turn, (b) Model of histone HI binding to the DNA of the nucleosome. (c) X-ray crystal structure of the nucleosome core particle. Two views are illustrated (top-left and side-right) showing histone octamer in ribbon structure form (H2A yellow H2B red H3 blue H4 green) (illustrations a), b) and c). Reproduced from Voet, Voet Pratt, 1999 [Wiley], Figs. 23-48, 23-45 and 23-44 respectively).

The cellular nudeus, during interphase, consists prindpally of a nuclear sap or caryolymph, a nudeolus and certain chromatin filaments or chro-monemata which condense into chromosomes during mitosis. 

The fact that a spermatozoid contains only half the amount of DNA present in normal cells clearly identifies DNA with the chromatin filaments which also contain protamines and histones. 

However, the nucleus also always contains some RNA located in the nucleolus (which does not contain DNA) and in the chromatin filaments. The ratio RNA/DNA varies from one spedes to another and, in the same spedes, from one organ to another. Unlike DNA whose composition is characteristic of all the cells of a spedes, the composition of RNA varies in the same cell from one point to another. Thus the RNA of the nucleus, the microsomes, and the mitochondria are all of different composition. Physiological conditions can also modify the composition of the various types of RNA in an organism, although they have no influence on the composition of the DNA. 

When mitosis occurs, the chromatin filaments combine into chromosomes which divide longitudinally and then distribute themselves between the two halves of the cell. This process is aided by the aster, a structure formed at the beginning of mitosis and surroimding the centrosome. It has been isolated from sea urchin eggs and shown to be protein in nature. 

The nucleosome forms a thin chromatin filament, with a diameter of 100 A, which is a linear array of nucleosome cores in contact with one another (Felsenfeld, 1978). Coiling of the thin fiber generates a thicker fiber with a diameter of 200-300 A, with the nucleosomes arranged in a solenoid with a lOOA hole down the center (Carpenter et al., 1976). It is not entirely clear how the chromatin is packed into the nucleus in the intact state, but a number of tentative models have been proposed (Felsenfeld, 1978). 

The native form of chromatin in cells assumes a higher order stmcture called the 30-nm filament, which adopts a solenoidal stmcture where the 10-nm filament is arranged in a left-handed cod (Fig. 5). The negative supercoiling of the DNA is manifested by writhing the hehcal axis around the nucleosomes. Chromatin stmcture is an example of toroidal winding whereas eukaryotic chromosomes are linear, the chromatin stmctures, attached to a nuclear matrix, define separate closed-circular topological domains. 

Fig. 5. Solenoid model of the 30-nm filament of chromatin, where the disks represent nucleosomes and the dark line unbound DNA.

FIGURE 1-12 A protoplasmic astrocyte abuts a blood vessel (lumen at I) in rat cerebral cortex. The nucleus shows a rim of denser chromatin, and the cytoplasm contains many organelles, including Golgi and rough endoplasmic reticulum, x 10,000. Inset (top left) Detail of perinuclear cytoplasm showing filaments. X44,000. 

Pray-Grant MG, Daniel JA, Schieltz D, Yates JR, 3rd, Grant PA (2005) Chdl chromodomain links histone H3 methylation with SAGA- and SLlK-dependent acetylation. Nature 433 434-438 Rando OJ, Zhao K, Janmey P, Crabtree GR (2002) Phosphatidylinositol-dependent actin filament binding by the SWI/SNF-hke BAF chromatin remodehng complex. Proc Natl Acad Sci USA 99 2824-2829 Roberts CW, Orkin SH (2004) The SWI/SNF complex - chromatin and cancer. Nat Rev Cancer 4 133-142... 

Stem could not form in the yeast filament, where most nucleosomes may adopt the open conformation (nucleosomes 4 and 7 in Fig. 7(b)). This in turn would be consistent with yeast chromatin high transcriptional activity [87] and DNA thermal flexibility [88,89]. 

In the filamentous fungus, Aspergillus nidulans, NIMA (never in mitosis, gene A) kinase phosphorylates H3 at Ser-10 [48]. At mitosis NIMA kinase association with chromatin increases and following metaphase NIMA locates to the mitotic spindle and spindle pole bodies. A human NIMA-related kinase (Nek6) was identified as a putative mitotic HI and H3 kinase [49]. 

Figure 27-5 (A, B) Two possible models of the 30-nm chromatin fiber.55 (A) Thoma et al.85 (B) Woodcock et al.6i 87 The fully compacted structure is seen at the top of each figure. The bottom parts of the figures illustrate proposed intermediate steps in the ionic strength-induced compaction. (C) Possible organization of the DNA within a metaphase chromosome. Six nucleosomes form each turn of a solenoid in the 30-nm filament as in (A). The 30-nm filament forms 30 kb-loop domains of DNA and some of these attach at the base to the nuclear matrix that contains topoisomerase II. About ten of the loops form a helical radial array of 250-nm diameter around the core of the chromosome. Further winding of this helix into a tight coil 700 nm in diameter, as at the top in (C), forms a metaphase chromatid. From Manuelidis91.

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