Polytene chromosomes are giant interphase chromosomes with several DNA strands placed side by side. They were discovered in the year 1881 by Balbiani in salivary glands, intestine, muscles, malpighian tubules, and hypoderm of larvae Chironomus plumosus. Hence, these are also called "Salivary gland chromosomes." These are found in insects of the order Diptera and Collembola; in certain organs of mammals; and synergids, antipodes of flowering plants. Polytene chromosomes are also regularly observed in cells of salivary gland in Drosophila.

There are certain differences between cells with polytene chromosomes and mitotically dividing cells. First is the absence of cell division after DNA replication that results in the accumulation of a large number of chromatids. Second is the failure of DNA strands to segregate after each round of DNA replication, resulting in several thousand chromatids arranged side by side. Third is the intact nuclear membrane and nucleolus during consecutive DNA replication cycles.

Banding patterns

Variation in the chromatin compaction can result in different concentrations of chromatin along the length of the polytene chromosome. Since the homologous chromosomes have identical chromatin compaction and are arranged side by side, it results in multiple compact dark bands called chromomeres. The regions between the bands are called interband or inter-chromomere regions. Interbands are lightly stained and are made up of decondensed chromatin. The chromomere patterns are specific for a species; although the number and size of chromomeres can change during the organism's lifetime.

Puffs

In certain instances, the interband region forms expanded structures called puffs that are loosely coiled, to allow RNA synthesis. Therefore, the puffs are excellent models to study the process of transcription. Exceptionally large puffs called “Balbiani rings” are found in salivary glands of certain species. These have decondensed chromatin that supports a very high rate of transcription.