It is thought that the interphase chromosomes of all eukaryotes are similarly arranged in loops. Although these loops are normally too small and fragile to be easily observed in a light microscope, other methods can be used to infer their presence. For example, modern DNA technologies have made it possible to assess the frequency with which any two loci along an interphase chromosome are held together, thus revealing likely candidates for the sites on chromatin that form the bases of loop structures (Figure 4–48). These experiments and others suggest that the DNA in human chromosomes is likely to be organized into loops of various lengths. A typical loop might contain between 50,000 and 200,000 nucleotide pairs of DNA, although loops of a million nucleotide pairs have also been suggested (Figure 4–49).
Further insight has come from another unusual class of cells—the polytene cells of flies, such as the fruit fly Drosophila. Some types of cells, in many organisms, grow abnormally large through multiple cycles of DNA synthesis without cell division. Such cells, containing increased numbers of standard chromosomes, are said to be polyploid. In the salivary glands of fly larvae, this process is taken to an extreme degree, creating huge cells that contain hundreds or thousands of copies of the
Figure 4–47 lampbrush chromosomes.
(A) A light micrograph of lampbrush chromosomes in an amphibian oocyte. Early in oocyte differentiation, each chromosome replicates to begin meiosis, and the homologous replicated chromosomes pair to form this highly extended structure containing a total of four replicated DNA double helices, or chromatids. The lampbrush chromosome stage persists for months or years, while the oocyte builds up a supply of materials required for its ultimate development into a new individual. (b) An enlarged region of a similar chromosome, stained with a fluorescent reagent that makes the loops active in RNA synthesis clearly visible. (Courtesy of Joseph g. gall.) genome. Moreover, in this case, all the copies of each chromosome are aligned side by side in exact register, like drinking straws in a box, to create giant polytene chromosomes. These allow features to be detected that are thought to be shared with ordinary interphase chromosomes, but are normally hard to see.
When polytene chromosomes from a fly’s salivary glands are viewed in the light microscope, distinct alternating dark bands and light interbands are visible (Figure 4–50), each formed from a thousand identical DNA sequences arranged side by side in register. About 95% of the DNA in polytene chromosomes is in bands, and 5% is in interbands. A very thin band can contain 3000 nucleotide pairs, while a thick band may contain 200,000 nucleotide pairs in each of its chromatin strands. The chromatin in each band appears dark because the DNA is more condensed than the DNA in interbands; it may also contain a higher concentration of proteins (Figure 4–51). This banding pattern seems to reflect the same sort of organization detected in the amphibian lampbrush chromosomes described earlier.
There are approximately 3700 bands and 3700 interbands in the complete set of Drosophila polytene chromosomes. The bands can be recognized by their different thicknesses and spacings, and each one has been given a number to generate a chromosome “map” that has been indexed to the finished genome sequence of this fly.
The Drosophila polytene chromosomes provide a good starting point for examining how chromatin is organized on a large scale. In the previous section, we saw that there are many forms of chromatin, each of which contains nucleosomes with a different combination of modified histones. Specific sets of non-histone proteins assemble on these nucleosomes to affect biological function in different ways. Recruitment of some of these non-histone proteins can spread for long distances along the DNA, imparting a similar chromatin structure to broad tracts
DNA product is obtained only if proteins hold the two DNA sequences close together in the cell