Polytene Chromosomes


Polytene chromosomes are specific interphase chromosomes consisting of thousands of deoxyribonucleic acid (DNA) strands. For this reason they are very large and display a characteristic band–interband morphology. Polyteny arises in tissues, organs and at developmental stages when there is need for the rapid development of an organ at an unaltered high level of function. Organs containing cells with polytene chromosomes are, as a rule, involved in intense secretory functions accomplished during a short time against a background of rapid growth. Chromosome rearrangements and in situ hybridization on polytene chromosomes allow genes to be mapped to a resolution of a few tens of kilobases. Polytene chromosomes allow a specific narrow region to be dissected out with a micromanipulator and a library of DNA clones to be derived from the region.

Key concepts:

  • Polytene chromosomes are specific type of interphase chromosomes consisting of thousands of DNA strands.

  • Polytene chromosomes have been found in many tissues of the representatives of two orders of insects: Diptera and Collembola, in the macronuclear anlagen of Infusoria, in certain organs and tissues of mammals and also in the cells of the synergids, antipods and endosperm of angiospermous plants.

  • Polyteny arises in tissues, organs and at developmental stages when there is need for the rapid development of an organ at an unaltered high level of function. Organs containing cells with polytene chromosomes are, as a rule, involved in intense secretory functions accomplished during a short time against a background of rapid growth.

  • Along the linear axis polytene chromosome have variation in the concentration of the chromatin. Regions of high concentrations are known as chromomeres (bands), and regions with low concentrations are known as interchromomeres (interbands).

  • The pattern of bands and interbands in each polytene chromosome is specific for the species, and in general is characteristic of that particular chromosome in different tissues or at different developmental stages.

  • Polytene chromosomes are now considered to be very important objects for the analysis of numerous features of interphase chromosome organization and the genome as a whole.

Keywords: genes; puffs; bands; interbands; heterochromatin

Figure 1.

First drawings of polytene chromosome made by Balbiani in (1881) (a) and (1890) (b). (a) Salivary gland cells of Chironomus plumosus and (b) Macronucleus (anlagen?) of Loxophyllum meleagris.

Figure 2.

Drawing of a polytene chromosome set of Drosophila melanogaster. The chromosomes have been spread out by squashing them on a microscopic slide. Each parental chromosome is tightly paired with its homologue (somatic synapsis). There are regions where two homologous chromosomes are separated (asynapsis). All the chromosomes are linked together by the pericentromeric regions to create a single chromocentre. In the left lower corner mitotic chromosomes from ovarian tissue are shown at the same magnification. From Painter T (1934) Salivary chromosomes and the attack on the gene. Journal of Heredity 25: 465–476.

Figure 3.

Arrangement and degree of conjugation of chromatids in classic polytene chromosomes (a), cryptic polyteny (b) and pompon‐like chromosomes (c). (a) Individual chromatids with chromomeres (shown as black rectangles) contact each other tightly, the chromomeres forming bands. (b) The chromatids contact each other only in some of the chromomeres, forming a broom‐like structure. (c) The conjugation of the chromatids is completely disturbed and a ‘pompon’ is formed. Open circles indicate the centromeric region.

Figure 4.

The polytene chromosome set of Chironomus thummi. The chromosomes of this species lie separately from each other; they do not have a common chromocentre. BR, Balbiani rings; NU, nucleolus; CEN, pericentromeric regions. Courtesy of LI Gunderina, unpublished.

Figure 5.

Electron microscopic view of part of the 3R chromosome of Drosophila melanogaster. Polytene chromosome bands and interbands are seen as black and white transverse stripes. Courtesy of VF Semeshin, unpublished.

Figure 6.

Electron microscopic view of ecdysone‐ and heat shock‐induced puffs in Drosophila melanogaster. Chromosome region 63A–E is shown before (b) and after (c) heat shock, before (b) and after (a) induction of ecdysone. Inactive genes located in compact chromatin form bands. The bands shown in (b) and (c) are activated after administration of an agent inducing gene activity: ecdysone for 63E2–3 or heat shock for 63B9. As a result, the material of the bands loosens, becomes decompacted and local swelling of the chromosome region occurs. Courtesy of VF Semeshin, unpublished.

Figure 7.

View of heterozygous deletion in Drosophila melanogaster polytene chromosomes, showing normal and deleted chromosome regions. Redrawn from Painter (1934).

Figure 8.

The first drawing of heterozygous inversion in the X‐chromosome of Drosophila melanogaster. Synapsis is complete except at the points where the chromosome fragment is inverted. From Painter (1934).



Alverdes F (1912) Die Entwicklung des Kernfadens in der Speicheldruse der Chironomus larve. Zoologischer Anzeiger 39: 1–6.

Andreyeva EN, Kolesnikova TD, Demakova OV et al. (2007) High‐resolution analysis of Drosophila heterochromatin organization using SuUR Su(var)3‐9 double mutants. Proceedings of the National Academy of Science of the USA 104: 12819–12824.

Ashburner M (1970) Function and structure of polytene chromosomes during insect development. In: Beament JWL, Treherne JE and Wigglesworth VB (eds) Advances in Insect Physiology, vol. 7, pp. 1–95. London: Cambridge University Press.

Ashburner M and Richards G (1976) The role of ecdysone in the control of gene activity in the polytene chromosomes of Drosophila. In: Lawrence PA (ed.) Insect Development, pp. 203–225. Oxford: Blackwell.

Balbiani EG (1881) Sur la structure du noyau des cellules salivares chez les larves de Chironomus. Zoologischer Anzeiger 4: 637–641, 662–666.

Balbiani EG (1890) Sur la structure intime du noyau du Loxophyllum meleagris. Zoologischer Anzeiger 13: 110–115, 132–136.

Bauer H (1935) Der Aufbau der Chromosomen aus den Speicheldrusen von Chironomus thummi Kiefer (Untersuchungen an den Riesenchromosomen der Dipteren I). Zeitschrift fur Zellforschung 23: 280–313.

Bauer H (1945) Chromosomen und Systematik bei Chironomiden. Archiv Fur Hydrobiologie 40: 934–1008.

Becker HJ (1962) Die Puffs der Speicheldrusenchromosomen von Drosophila melanogaster II. Die Auslosung der Puffbildung, ihre Spezifitat und ihre Beziehung zur Funktion der Ringdruse. Chromosoma 13: 341–384.

Beermann W (1950) Chromomerenkonstanz bei Chironomus. Naturwissenschaften 37: 543–544.

Beermann W (1952) Chromomerenkonstanz und spezifische Modifikationen der Chromosomenstruktur in der Entwicklung und Organdifferenzierung von Chironomus tentans. Chromosoma 5: 139–198.

Beermann W (1961) Ein Balbiani‐Ring als Locus einer Speicheldrusenmutation. Chromosoma 12: 1–25.

Beermann W (1962) Riesenchromosomen. Protoplasmatologiya 6D: 1–161.

Beermann W (1972) Chromomeres and genes. In: Beermann W (ed.) Results and Problems in Cell Differentiation, vol. 4, pp. 1–33. Berlin: Springer.

Belyaeva ES, Zhimulev IF, Volkova EI et al. (1998) Su(UR)ES – a gene suppressing DNA underreplication in intercalary and pericentric heterochromatin of Drosophila melanogaster polytene chromosomes. Proceedings of the National Academy of Science of the USA 95(13): 7532–7537.

Belyakin SN, Christophides GK, Alekseyenko AA et al. (2005) Genomic analysis of Drosophila chromosome underreplication reveals a link between replication control and transcriptional territories. Proceedings of the National Academy of Science of the USA 102: 8269–8274.

Breuer ME and Pavan C (1954) Salivary chromosome and differentiation. Proceedings of the IXth International Congress on Genetics. Caryologia 6(suppl.): 778.

Bridges CB (1935) Salivary chromosome maps with a key to the banding of the chromosomes of Drosophila melanogaster. Journal of Heredity 26: 60–64.

Clever U (1964) Actinomycin and puromycin effect on sequential gene activation by ecdysone. Science 146: 794–795.

Clever U and Karlson P (1960) Induction von Puff‐Veranderungen in den Speicheldrusenchromosomen von Chironomus tentans durch Ecdyson. Experimental Cell Research 20: 623–626.

Darlington CD (1937) Recent Advances in Cytology, 2nd edn. London: L., J. and A. Churchill.

Demakov S, Gortchakov A, Schwartz Y et al. (2004) Molecular and genetic organization of Drosophila melanogaster polytene chromosomes: evidence for two types of interband regions. Genetica 122: 311–324.

Demakov SA, Semeshin VF and Zhimulev IF (1993) Cloning and molecular genetic analysis of Drosophila melanogaster interband DNA. Molecular and General Genetics 238: 437–443.

Demakova OV, Pokholkova GV, Kolesnikova TD et al. (2007) The SU(VAR)3‐9/HP1 complex differentially regulates the compaction state and degree of underreplication of X chromosome pericentric heterochromatin in Drosophila melanogaster. Genetics 175: 609–620.

Erhard H (1910) Uber den Aufbau der Speicheldrusenkerne der Chironomuslarve. Archiv fur mikroskopische Anatomie und Entwicklungsgeschichte 76: 114–124.

Heitz E and Bauer H (1933) Beweise fur die Chromosomennatur der Kernschleifen in den Knauelkernen von Bibio hortulanus. Zeitschrift fur Zellforschung 17: 67–82.

Ilyinskaya NB (1977) A case of somatic mosaicism for heterozygous paracentric inversion of chromosome II in Chironomus plumosus. Tsitologiya 19(1): 45–49 (In Russian.).

Ilyinskaya NB (1980) Functional organization of polytene chromosomes and problems of karyosystematics. In: Novye dannye po kariosistematike dvukrylykh nasekomykh, vol.95, pp. 14–22. Leningrad: Trudy Zoologicheskogo Instituta Akademii Nauk SSSR (In Russian.).

King RL and Beams HW (1934) Somatic synapsis in Chironomus with special reference to the individuality of the chromosomes. Journal of Morphology 56: 577–588.

Koller PCh (1935) The internal mechanics of the chromosomes. IV. Pairing and coiling in salivary gland nuclei of Drosophila. Proceedings of the Royal Society of London, Series B 118: 371–397.

Koltzoff NK (1934) The structure of the chromosomes in the salivary glands of Drosophila. Science 80: 312–313.

Kostoff D (1930) Discoid structure of the spireme and irregular cell division in Drosophila melanogaster. Journal of Heredity 21: 323–324.

Mackensen O (1934) A cytological study of short deficiencies in the X chromosome of Drosophila melanogaster. American Naturalist 67: 76.

Mechelke F (1953) Reversible Strukturmodifikationen der Speicheldrusenchromosomen von Acricotopus lucidus. Chromosoma 5: 511–543.

Painter TS (1933) A new method for the study of chromosome aberrations and the plotting of chromosome maps. Science 78: 585–586.

Painter TS (1935) The morphology of the third chromosome in the salivary gland of Drosophila melanogaster and a new cytological map of this element. Genetics 20: 301–326.

Patterson JT (1932) Lethal mutations and deficiencies produced in the X chromosome of Drosophila melanogaster by X‐radiation. American Naturalist 66: 193–206.

Pavan C and Breuer ME (1952) Polytene chromosomes in different tissues of Rhynchosciara. Journal of Heredity 43: 151–157.

Pindyurin AV, Moorman C, Wit Ede et al. (2007) SUUR joins separate subsets of PcG, HP1 and B‐type lamin targets in Drosophila. Journal of Cell Science 120: 2344–2351.

Rambousek FJ (1912) Cytologick pomery slinnych zlaz u larev Chironomus plumosus L. Vestnik Kralovske Ceske Spolecnosti Nauk. Trida II, 2: 1–25 (In Czech).

Ribbert D (1979) Chromomeres and puffing in experimentally induced polytene chromosomes of Calliphora erythrocephala. Chromosoma 74: 269–298.

Ritossa F (1962) A new puffing pattern induced by temperature shock and DNP in Drosophila. Experientia 18: 571–573.

Rubin GM (1998) The Drosophila genome project: a progress report. Trends in Genetics 14: 340–343.

Semeshin VF, Belyaeva ES, Zhimulev IF et al. (1986) Electron microscopical analysis of Drosophila polytene chromosomes. IV. Mapping of morphological structures appearing as a result of transformation of DNA sequences into chromosomes. Chromosoma 93: 461–468.

Further Reading

Ashburner M (1970) Function and structure of polytene chromosomes during insect development. Advances in Insect Physiology 7: 1–95.

Ashburner M and Berendes HD (1978) Puffing of polytene chromosomes. In: Ashburner M and Wright TRF (eds) The Genetics and Biology of Drosophila, vol. 2b, pp. 316–395. London: Academic Press.

Berendes HD (1973) Synthetic activity of polytene chromosomes. International Review of Cytology 35: 61–116.

Richards G (1997) The ecdysone regulatory cascades in Drosophila. Advances in Developmental Biology 5: 81–135.

Russell S and Ashburner M (1996) Ecdysone‐regulated chromosome puffing in Drosophila melanogaster. In: Gilbert LI, Tata JR and Atkinson BG (eds) Metamorphosis: Postembryonic reprogramming of gene expression in amphibion and insect cells, pp. 109–144. London: Academic Press.

Sorsa V (1998) Polytene Chromosomes in Genetic Research. Chichester: Ellis Harwood.

Zhimulev IF (1996) Morphology and structure of polytene chromosomes. Advances in Genetics 34: 1–497.

Zhimulev IF (1998) Polytene chromosomes, heterochromatin and position effect variegation. Advances in Genetics 37: 1–566.

Zhimulev IF (1999) Genetic organization of polytene chromosomes. Advances in Genetics 39: 1–589.

Zhimulev IF and Belyaeva ES (2003) Intercalary heterochromatin and genetic silencing. BioEssays 25: 1040–1051.

Zhimulev IF, Belyaeva ES and Semeshin VF (1981) Informational content of polytene chromosome bands and puffs. CRC Critical Reviews in Biochemistry 11: 303–340.

Zhimulev IF, Belyaeva ES, Semeshin VF et al. (2004) Polytene chromosomes: 70 years of genetic research. International review of cytology 241: 203–275.

Contact Editor close
Submit a note to the editor about this article by filling in the form below.

* Required Field

How to Cite close
Zhimulev, Igor F, and Koryakov, Dmitry E(Mar 2009) Polytene Chromosomes. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0001183.pub2]