Chromosomal Puff
 
Puffs represent sites in polytene chromosomes that are active in gene transcription. The morphology of puffs is such that they contain chromosomal material that has become dramatically decondensed. The process of generating a puff has been likened to untwisting the strands of a rope (1). It is important to note, however, that transcription also occurs at nonpuffed bands in polytene chromosomes (2). Therefore it is probable that puffing represents a specialized adaptation of chromosomal structure or is a consequence of very high levels of transcriptional activity. Evidence for transcription at sites of puffing derives from the immunofluorescent staining of RNA polymerase II and the incorporation of radioactive uridine into RNA at puff sites, as revealed by autoradiography (3).
The appearance of puffs in polytene chromosomes is developmentally regulated. Analysis of puffing patterns has been very informative for studies of gene expression. In some organisms, like the midge Chironomus, puffs become enormous, thereby providing very valuable cytological insights into transcription and RNA processing. In Drosophila melanogaster, the study of puffing induced by the hormone ecdysone has been especially valuable. Ecdysone induces several puffs in salivary gland nuclei during the late third larval instar stage of development. These fall into two classes: (1) the early puffs, which appear within minutes of hormone addition and increase in size over a 1- to 4-hour period before diminishing; and (2) the late puffs, which appear after 3 hours, reach their maximal activity after 5 to 7  hours, and then regress. Inhibition of protein synthesis using drugs, such as cycloheximide, prevents the appearance of the late puffs but not the early puffs. This result indicates a requirement for protein synthesis to generate of late puffs, most probably using messenger RNA derived from the genes in the early puffs (4). Some of the early puffs fail to diminish if protein synthesis is inhibited, suggesting that autoregulatory circuits exist in which the early puffs are turned off by their own gene products. The early puffs encode several regulatory DNA-binding proteins that carry out both gene activation and repression (5). Interestingly, chromosomal duplications or deletions of sites of early puffing indicate that more copies lead to greater and more rapid activation of the late puffs, whereas fewer copies lead to a reduced level of late puffing activity (6). Genes within the puffs, activated by ecdysone, encode proteins, such as dopa decarboxylase, an enzyme involved in cuticle formation and pigment synthesis in hypodermal cells (7), and the glue proteins required to attach the pupa to its substrate (8).
References
1. W. Beerman (1964) J. Exp. Zool. 157, 49–62. 
2. J. J. Bonner and M. L. Pardue (1977) Cell 12, 227–234. 
3. M. Jamrich, A. L. Greenleaf, and E. K. F. Bautz (1977) Proc. Natl. Acad. Sci. USA 74, 2079–2083. 
4. M. Ashburner, C. Chihara, P. Meltzer, and G. Richards (1973) Cold Spring Harbor Symp. Quant. Biol. 38, 655–662. 
5. L. D. Urness and C. S. Thummel (1995) EMBO J. 14, 6239–6246. 
6. V. K. Walker and M. Ashburner (1981) Cell 26, 269–277. 
7. G. P. Kraminsky et al. (1980) Proc. Natl. Acad. Sci. USA 77, 4175–4179. 
8. S. K. Beckendorf and F. C. Kafatos (1976) Cell 9, 365–373.