The individual chromatin fibers that make up a puff can be visualized with an electron microscope. In favorable cases, loops are seen, much like those observed in amphibian lampbrush chromosomes. When genes in the loop are not expressed, the loop assumes a thickened structure, possibly that of a folded 30-nm fiber, but when gene expression is occurring, the loop becomes more extended. In electron micrographs, the chromatin located on either side of the decondensed loop appears considerably more compact, suggesting that a loop constitutes a distinct functional domain of chromatin structure.
Observations in human cells also suggest that highly folded loops of chromatin expand to occupy an increased volume when a gene within them is expressed. For example, quiescent chromosome regions from 0.4 to 2 million nucleotide pairs in length appear as compact dots in an interphase nucleus when visualized by fluorescence microscopy. However, the same DNA is seen to occupy a larger territory when its genes are expressed, with elongated, punctate structures replacing the original dot.
New ways of visualizing individual chromosomes have shown that each of the 46 interphase chromosomes in a human cell tends to occupy its own discrete ter- ritory within the nucleus: that is, the chromosomes are not extensively entangled with one another (Figure 4–53). However, pictures such as these present only an average view of the DNA in each chromosome. Experiments that specifically localize the heterochromatic regions of a chromosome reveal that they are often
Figure 4–53 Simultaneous visualization of the chromosome territories for all of the human chromosomes in a single interphase nucleus. Here, a mixture of DNA probes for each chromosome has been labeled so as to fluoresce with a different spectra; this allows DNA–DNA hybridization to be used to detect each chromosome, as in Figure 4–10. Three-dimensional reconstructions were then produced. below the micrograph, each chromosome is identified in a schematic of the actual image. Note that homologous chromosomes (e.g., the two copies of chromosome 9) are not in general co-located. (From m.R. Speicher and N.P. Carter, Nat. Rev. Genet. 6:782–792, 2005. with permission from macmillan Publishers ltd.)
Figure 4–54 The distribution of gene-rich regions of the human genome in an interphase nucleus. gene-rich regions have been visualized with a fluorescent probe that hybridizes to the Alu interspersed repeat, which is present in more than a million copies in the human genome (see page 292). For unknown reasons, these sequences cluster in chromosomal regions rich in genes. In this representation, regions enriched for the Alu sequence are green, regions depleted for these sequences are red, while the average regions are yellow. The gene-rich regions are seen to be largely absent in  the DNA near the nuclear envelope. (From A. bolzer et al., PLoS Biol. 3:826–842, 2005.) closely associated with the nuclear lamina, regardless of the chromosome examined. And DNA probes that preferentially stain gene-rich regions of human chromosomes produce a striking picture of the interphase nucleus that presumably reflects different average positions for active and inactive genes (Figure 4–54).
How is most of the chromatin in each interphase chromosome condensed when its genes are not being expressed? A powerful extension of the chromosome conformation capture method described previously (see Figure 4–48), which exploits a high-throughput DNA sequencing technology called massive parallel sequencing (see Panel 8–1, pp. 478–481), allows the connections between all of the different one-megabase (1 Mb) segments of the human genome to be mapped in human interphase chromosomes. The results reveal that most regions of our chromosomes are folded into a conformation referred to as a fractal globule: a knot-free arrangement that facilitates maximally dense packing while, at the same time, preserving the ability of the chromatin fiber to unfold and fold (Figure 4–55).