Chromatin fibres

Sayers, Z. Synchrotron X-Ray Scattering Studies of the Chromatin Fibre Structure, 145, 203-232 (1987). 

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

Figure 6.5 Proposed condensation process of chromatin fibre based on scattering measurements of chicken erythrocyte chromatin from [7] (a) Maximally extended chromatin showing the helicoidal space arrangement, (b)-(d) Condensation of chromatin with final catenoideil space arrangement shown in (d). (e) View down the central cavity only for a portion of the chromatin chain, (f) View of the condensed arrangement for longer fibre than that of (e).

Considering the fact that the ensuing condensation of the chromatin fibre into the metaphase chromosome is achieved by further winding of the molecule, it is fair to assume that this follows a similar mechanism, creating a self-similar sequence, a cascade of Bonnet transformations [8]. 

Synchrotron X-Ray Scattering Studies of the Chromatin Fibre Structure... 

Scattering Patterns from Oriented Chromatin Fibres,... 

Fig. 1. Hierarchy of chromatin folding in the nucleus, during interphase, chromosomes are spread in a diffuse form and the nucleoli appear as dense structures. During metaphase chromosomes which consist of condensed sections of chromatin are formed. Chromatin in interphase nuclei and in the condensed sections of chromosomes contains looped domains which are formed by the 30 nm chromatin fibre. In vitro it is possible to further unfold the 30 nm fibre to a 3-D zig-zag structure revealing the nucleosomes that consist of histone HI, the core particle and the linker DNA...

Table 1 summarizes some of the techniques that have been used to investigate the higher order structure of chromatin. There is substantial agreement that the 30 nm chromatin fibre has a structure with about 6 nucleosomes/11 nm and that the nucleosomes are arranged with their flat faces oriented approximately parallel to the fibre axis. There are, however, still significant differences between the models proposed for the detailed structure of the drromatin fibre which will be discussed separately. 

Table 1. Survey of the physical methods used in studies of chromatin fibre structure Source of Nuclei/Chromatin...

The 30 ran chromatin fibre in intact nuclei of several types of cells has been investigated by small angle scattering si. 1.72.73,74) results which help to gain an insight into the packing of chromatin in vivo can be used for comparison with the patterns of isolated chromatin fibres in solution. Features of the scattering patterns of CE nuclei-EDTA (a) and nuclei in TE buffer with 100 mM NaCl (b) are illustrated in Fig. 5. 

Fig. 5. Scattering patterns of CE nuclei, a Scattering pattern of nuclei-EDTA. Bands indicated by arrows are the 0.025 nm" interfibre interference, the 0.06 nm intemucleosomal interference and the 0.156, 0.27 and 0.36 nm" bands which are due to the contributions from the nucleosome core particles, b Scattering pattern of nuclei at high ionic strength (150 mM NaCl). The 0.05 nm band is no longer visible but a weak band at 0.045 nm is detected. Arrows indicate the interfibre interference and the intranucleosomal bands as well as the 0.083 nm" and 0.15 nm" bands which result from the close approach of nucleosomes in the condensed chromatin fibre (Fig. 3 a) fi om Bordas et al., 1986 a)...

A theoretical analysis of the scattering by an array of fibres indicates that the intensity and position of the interference band are determined by the parameter y, which is the ratio of the centre-to-centre distance between fibres to the fibre diameter. The variation in the position of the interference band from different types of nuclei under similar ionic conditions can thus be attributed to differences in the chromatin fibre diameter... 

As discussed below scattering patterns of (partially) oriented chromatin fibres and chromatin gels can be used to determine the origin of the various bands observed from nuclei. 

The 0.045 nm band attributed to the fibre transform in the nuclei patterns is absent in the oriented fibre patterns. This could be due to the aggregated state of chromatin in the oriented gels Bordas et al. report that the 0.045 nm band is lost at ionic strengths higher than 100 mM NaCl (or > 5 mM MgCl ) where the chromatin fibres in solution begin to precipitate. 

Unoriented gels obtained from chromatin-EDTA fibres and chromatin fibres condensed in the presence of 100 mM NaCl also contain the interfibre interference band, as can be seen from Fig. 6 (a) and (b). However when condensation is... 

The 0.05 nm band can be used to monitor changes in the unfolded chromatin structure. Upon removal of H1/H5 histones the band is displaced to lower s-values (i.e. the average distance between successive nucleosomes increases) showing the requirement for H1/H5 for maintaining the structural scaffolding of the low ionic strength fibre. Similarly when ethidium bromide, which partly intercalates between the bases, is bound the structure of imcondensed chromatin fibre is further extended. In parallel to the shift in the position of the 0.05 nm band the and the M/L decrease. At 0.5 mM ethidium bromide with 3.5 mg DNA/ml, M/L is about... 

Studies of the condensed chromatin fibre structure and the condensation mechanism have resulted in basically two classes of models models based on a helical arrangement of nucleosomes along the fibre and those based on a linear array of globular nucleosome clusters (superbeads) along the fibre. The first class includes the solenoid, twisted ribbon and crossed linker models whereas the latter are the superbead models and related layered structures. Schematic representations of some models are shown in Fig. 10. 

Table 2. Observations resulting from studies of chromatin fibre structure compiled from the references given in table 1. Sources are noted only when values given differ from those generally reported...

Nucleosome faces and linker DNA parallel to the uncondensed chromatin fibre axis Nucleosome faces tilted 20-30° to the condensed... 

In the model proposed by Bordas et al. at low ionic strength the chromatin fibre already has a 3-D zig-zag superstructure with an outer diameter comparable to that of the condensed fibre. Upon condensation the distance between successive nucleosomes diminishes and the structure collapses in a way similar to the folding of an accordion, resulting in about a 10-fold decrease in the pitch and an... 

The twisted ribbon model of Worcel et al. and the superbead model of Zentgraf and Franke can be ruled out on the basis of X-ray diffraction studies of oriented chromatin fibres The former model predicts the 0.175,0.27 and 0.37 nm ... 

Complementary use, in future, of small angle solution synchrotron X-ray scattering methods with electron microscopy could contribute to the clarification of the path of the linker DNA. Thus further experiments seeking a universal model for the chromatin fibre structure need to be undertaken although the existence of such a universal structure is questionable. More importantly future investigations need to be aimed at imderstanding what relevance the structure of the fibre has to the control of DNA transcription and replication. 

A group of proteins known as histones bind to the DNA to form what is called a nucleosome. Many nucleosomes constitute a chromatin fibre. This fibre resembles beads on a string, each bead being one nucleosome. 

The chromosomal DNA in eukaryotic cells appears as thin chromatin fibres which consist of about 60% protein, 35% DNA and probably 5% RNA. The chromatin fibres are folded and looped into bundles in which the DNA is associated with the protein. The protein units are known as... 

Figure 11.31 shows how the DNA chains are wound around the histones, which are then tightly packed. Electron micrographs of extended chromatin fibres show how these histone units, called nucleosomes, are fastened together like a string of beads as indicated diagrammatically in Figure 11.31a). These units are then assembled into a tightly packed array as indicated in Figure 11.31b.

The DNA strands in chromatin fibres consist of regions known as exons and introns (Figure 11.32). While the introns appear to be useless for genetic purposes (junk DNA), an exon or series of exons constitute the gene which contains the correct base sequences to convey hereditary information. 

Solenoid (Greek solen, pipe) or 30 nm chromatin fibre... 

---