Chromatin structure outside and inside the nucleus

Abstract

The structure of the 30-nm chromatin fiber has provided, over the years, an important reference in chromatin studies. Originally derived from electron microscopic studies of soluble chromatin fibers released by restriction digestion, the gross structural features of such fragments have been supported by biophysical methods such as low angle X-ray and neutron scattering, sedimentation, light scattering, and electric dichroism. Electron microscopy and sedimentation velocity measurements demonstrated that reconstituted chromatin fibers, prepared from repeating arrays of high affinity nucleosome positioning sequences, retain the same overall features as observed for native chromatin fibers. It had been suggested that the 30 nm fiber might be the form assumed in vivo by transcriptionally silent chromatin, but individual gene or genome-wide studies of chromatin released from nuclei do not reveal any such simple correlation. Furthermore, even though the 30 nm fiber has been thought to represent an intermediate in the hierarchical folding of DNA into chromosomes, most analyses of chromatin folding within the nucleus do not detect any regular extended compact structures. However, there are important exceptions in chicken erythroid cell nuclei as well as in transcribed regions that form extended loops. Localized domains within the nucleus, either at the surface of chromosome domains or constrained as a specialized kind of constitutive heterochromatin by specific DNA binding proteins, may adopt 30 nm fiber-like structures.

Figure 1. The 30-nm chromatin fiber

(A) The one-start helical model proposed by Klug and coworkers; the linker DNA shown in yellow is bent in a continuously supercoiled fashion between nucleosomes ^,,. (B) The two-start twisted ribbon model with a linker DNA approximately parallel to the fiber axis ^, (C) The two-start cross-linked model in which the linker DNA is perpendicular to the fiber axis and occupies the center of the fiber originally proposed by Williams et al. and Smith et al.. Figure reproduced from Dorigo et al. with permission (need to get) of the American Association for the Advancement of Science.

Figure 2. Effects of histone modifications on compactness of a constitutive heterochromatin structure

(A) ChIP assay depicting the percentage of nucleosomes containing the H4Ac modification in both untreated cells (blue), cells treated with TSA (1 μM for 4 h; red) and cells that were given 5 days to recovery after removal of the TSA (green). Data show the mean ± s.e.m of three (untreated and recovery) or six (TSA) independent ChIP experiments. *P < 0.05, **P < 0.01. (B) Nuclei from 6C2 cells either untreated or treated with TSA (for 16 h) were digested with MspI, floated out of the nuclei, sedimented on a sucrose gradient and analysed by quantative PCR (copied from Giles et al.).