Thus polytene chromosomes form when multiple rounds of replication produce many sister chromatids which stay fused together.
In Drosophila melanogaster, for example, the chromosomes of the larval salivary glands undergo many rounds of endoreduplication to produce large quantities of adhesive mucoprotein ("glue") before pupation.
Another example within the fly itself is the tandem duplication of various polytene bands located near the centromere of the X chromosome which results in the Bar phenotype of kidney-shaped eyes.
Their primary functions are: to act as binding sites for RNA pol II, to initiate replication and, to start nucleosome remodeling of short fragments of DNA.
[2] Polytene chromosomes were originally observed in the larval salivary glands of Chironomus midges by Édouard-Gérard Balbiani in 1881.
[8] Balbiani described the chromosomal puffs among the tangled thread inside the nucleus, and named it "permanent spireme".
"[9] The hereditary nature of these structures was not confirmed until they were studied in Drosophila melanogaster in the early 1930s by German biologists Emil Heitz and Hans Bauer.
In 1930, Heitz studied different species of Drosophila (D. melanogaster, D. simulans, D. hydei, and D. virilis) and found that all their interphase chromatins in certain cells were swollen and messy.
In 1932, he collaborated with Karl Heinrich Bauer with whom he discovered that the tangled chromosomes having distinct bands are unique to the cells of the salivary glands, midgut, Malphigian tubules, and brain of the flies Bibio hurtulunus and Drosophila funebris.
[11][12] Learning of this, Heitz accused Painter of deliberately ignoring their original publication to claim priority of discovery.
Some of the largest polytene chromosomes described thus far occur in larval salivary gland cells of the chironomid genus Axarus.