Polytene chromosome puffing and in situ hybridization measure different aspects of RNA metabolism.

Direct autoradiography of Drosophila melanogaster polytene chromosomes which have incorporated 3H-uridine suggests that the chromosomal puffs are the most active sites of incorporation; that the puffs are not the only sites of incorporation; and that there are sites which do not incorporate at all. In situ hybridization of 3H-RNA from salivary gland nuclei labels all three types of chromosomal sites. Labeling by in situ hybridization is not proportional to labeling by direct autoradiography. The differences may be explained by several models. Nuclear RNA of salivary glands probably contains transcripts from multiply repeated genes; these transcripts may hybridize to many chromosomal sites. The data furthermore suggest that the phenomenon of puffing may not be a simple reflection of transcription rate, since several puffs hybridize RNAs with quite different metabolic characteristics.