Last Update: January 24, 2007 Part I

M - 23
Polytene Chromosome-structure & function
(Ref: Genetics- Russell, Klug&Cummings, Cell and Molecular Biology, - De Robertis)

Polytene chromosome is a special type of chromosome found in various tissues (salivary,

midgut, rectal, footpads and Malpighian excretory tubules) in the larvae of Dipteran flies and
in several species of protozoan and plants. Such structures were first observed by
E.G.Balbiani in 1881 in the nuclei of certain secretory tissues of midge fly Chironomus.
Unfortunately, he did not recognize them as chromosomes, and his report remained buried in
the literature. It was not until 1933 that Theophilus Painter, Ernst Heitz, and H. Bauer
rediscovered them and realized these structures are in fact chromosomes.
Important properties
1. Polytene chromosomes consist of chromatid bundles resulting from repeated cycles of
chromosome duplication without nuclear or cell division (called endomitosis). A polytene
chromosome of Drosophila salivary glands has about 1000 DNA molecules arranged side
by side which arise from 10 rounds of DNA replication (2 10=1024). Other dipteran
species have more DNA molecules per polytene chromosome; for example, Chironomus
has 16,000.
2. Thus the polytene chromosomes may be thousand times the size of corresponding
chromosomes at meiosis or in the
nuclei of ordinary somatic cells, and
are easily detectable through
microscopic observation. Each polytene
chromosome is 200 to 600um long.
3. In each polytene chromosome, the two
homologous chromosomes are tightly
paired (called somatic pairing);
therefore the number of polytene
chromosomes per cell is half the
diploid number of chromosomes. The
number of duplicated copies of
homologous chromosome pairs per
polytene chromosome is species-
specific. This permits the identification
of deletions, inversions, and duplications as regions looped out of the chromosomes.
As a result of intimate pairing of the multiple copies of chromatids, characteristic
banding patterns are easily seen, enabling cytogeneticists to identify unambiguously any
segment of a chromosome. In Drosophila melanogaster, for example, more than 5,000
bands and interbands can be counted in the four polytene chromosomes. Each band was
originally thought to represent a single protein coding gene and the region between
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 bands was thought to represent intergenic DNA. It is now known that each band contains
an average of 30,000 base pairs (30 kb) of DNA, enough to encode several average-sized
proteins. DNA cloning and sequencing studies have shown that many bands contain a
number of genes (up to seven) that are transcribed independently. Genes are also found in
the interbands.
4. The pericentromeric heterochromatin of all the Drosophila chromosomes coalesces in a
chromocenter, where the chromosomes are joined together. The satellite DNAs of the
chromocenter are unreplicated with respect to the rest of the chromosome (i.e. they
undergo fewer round of replication).
5. One of the most remarkable characteristics of polytene chromosomes is that it is possible
to visualize in them the genetic activity of specific chromosomal sites at local
enlargements called puffs. (A puff can be considered a band in which the DNA unfolds
into open loops as a consequence of intense gene transcription). The largest puff in the
polytene chromosome of Chironomus larvae is known as Balbiani ring according to the
name of the author who first discovered it. W. Beerman and BAHR (1952) correctly
interpreated the puffing of polytene chromosomes as an expression of intense gene
transcription. In salivary glands the appearance of some puffs has been correlated with the
production of specific proteins, which are secreted in large amounts in the larval saliva.
(Puffing is a cyclic and reversible phenomenon. The puffs appear and disappear in
specific patterns at certain chromosomal loci as development proceeds, so it is fair to say
that they are developmentally controlled. Puff formation can be studied experimentally
using factors that will induce their formation. The steroid hormone ecdysone, which
induces molting in insects, will induce the formation of specific puffs when injected into
larvae or when added to salivary glands in culture. Puffs can also be induced by
temperature shock. When Drosophila larvae are exposed to high temperature (at 370C), a
series of specific genes is activated; producing nine new puffs five minutes after heat
shock, while most other genes are repressed.)

Structure of polytene chromosome in Drosophila

In Drosophila the diploid cells contain four pairs of chromosomes, of which first pair is
acrocentric sex chromosome, second and third pairs are metacentric autosomes and fourth
pair is tiny acrocentric autosome. In the larval salivary gland cells the pericentromeric
heterochromatin of all the chromosomes are fused with each other in a large chromocenter
and each pair is tightly synapsed so that a single chromosome with five arms is seen. A
single long arm is contributed by acrocentric sex chromosomes but two pairs of metacentric
autosomes produce two pairs of long arms and tiny fourth chromosomes often produce a
very short arm. The second and third chromosomes are designated by 2R (second right), 2L
(second left), 3R (third right) and 3L (third left), and they are very long among all other
arms. Each arm is provided with detectable bands, interbands and puffs.

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Importance
Polytene chromosomes provided the first evidence that eukaryotic gene activity is regulated
at the level of RNA synthesis. They constitute a valuable material for the study of gene
regulation because their transcription can be visualized directly in the microscope.