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A homeobox is a DNA sequence found within genes that are involved in the regulation of patterns of development (morphogenesis) in animals, fungi and plants.


They were discovered independently in 1983 by Walter Jakob Gehring and his colleagues at the University of Baselmarker, Switzerlandmarker, and Matthew P. Scott and Amy Weiner, who were then working with Thomas Kaufman at Indiana Universitymarker in Bloomingtonmarker.


A homeobox is about 180 base pairs long. It encodes a protein domain (the homeodomain) which when expressed (e.g. as protein) can bind DNA.

Homeobox genes encode transcription factors which typically switch on cascades of other genes. The homeodomain binds DNA in a specific manner.

However, the specificity of a single homeodomain protein is usually not enough to recognize only its desired target genes. Most of the time, homeodomain proteins act in the promoter region of their target genes as complexes with other transcription factors, often also homeodomain proteins. Such complexes have a much higher target specificity than a single homeodomain protein.

Homeodomains are found both in genes of the Hox gene clusters and in other genes throughout the genome.

Hox genes

Molecular evidence shows that some limited number of Hox genes have existed in the Cnidaria since before the earliest true Bilatera, making these genes pre-Paleozoic.

They are essential metazoan genes as they determine the identity of embryonic regions along the anterio-posterior axis. The first vertebrate Hox gene was isolated in Xenopus by Eddy De Robertis and colleagues in 1984, marking the beginning of the young science of Evo-devo.

In vertebrates, the four paralog clusters are partially redundant in function, but have also acquired several derived functions. In particular, HoxA and HoxD specify segment identity along the limb axis.

The main interest in this set of genes stems from their unique behaviour. They are typically found in an organized cluster. The linear order of the genes within a cluster is directly correlated to the order of the regions they affect as well as the timing in which they are affected. This phenomenon is called colinearity. Due to this linear relationship, changes in the gene cluster due to mutations generally result in similar changes in the affected regions.

For example, when one gene is lost the segment develops into a more anterior one, while a mutation that leads to a gain of function causes a segment to develop into a more posterior one. This is called ectopia. Famous examples are Antennapedia and bithorax in Drosophila, which can cause the development of antennae instead of legs and the development of a duplicated thorax, respectively.


The homeobox genes were first found in the fruit fly Drosophila melanogaster and have subsequently been identified in many other species, from insects to reptiles and mammals.

Homeobox genes were previously only identified in bilateria but recently cnidaria have also been found to contain homeobox domains and the "missing link" in the evolution between the two has been identified.

Homeobox genes have even been found in fungi, for example the unicellular yeasts, and in plants.


The well known homeotic genes in plants (MADS-box genes) are not homologous to Hox genes in animals. Plants and animals do not share the same homeotic genes, and this suggests that homeotic genes arose independently in the early evolution of animals and plants.

Human genes

Humans generally contain homeobox genes in four clusters:

name chromosome gene
HOXA (or sometimes HOX1) - chromosome 7 HOXA1, HOXA2, HOXA3, HOXA4, HOXA5, HOXA6, HOXA7, HOXA9, HOXA10, HOXA11, HOXA13
HOXB - chromosome 17 HOXB1, HOXB2, HOXB3, HOXB4, HOXB5, HOXB6, HOXB7, HOXB8, HOXB9, HOXB13
HOXC - chromosome 12 HOXC4, HOXC5, HOXC6, HOXC8, HOXC9, HOXC10, HOXC11, HOXC12, HOXC13
HOXD - chromosome 2 HOXD1, HOXD3, HOXD4, HOXD8, HOXD9, HOXD10, HOXD11, HOXD12, HOXD13

There is also a "distal-less homeobox" family: DLX1, DLX2, DLX3, DLX4, DLX, and DLX6.

"HESX homeobox 1" is also known as HESX1.

Short stature homeobox gene is also known as SHOX.

Additional human proteins containing this domain per UniProt annotation:


Mutations to homeobox genes can produce easily visible phenotypic changes.

Two examples of homeobox mutations in the above-mentioned fruit fly are legs where the antennae should be (antennapedia), and a second pair of wings.

Duplication of homeobox genes can produce new body segments, and such duplications are likely to have been important in the evolution of segmented animals.

Interestingly, there is one insect family, the xyelid sawflies, in which both the antennae and mouthparts are remarkably leg-like in structure. This is not uncommon in arthropods as all arthropod appendages are homologous.


The regulation of Hox genes is highly complex and involves reciprocal interactions, mostly inhibitory. Drosophila is known to use the Polycomb and Trithorax Complexes to maintain the expression of Hox genes after the down-regulation of the pair-rule and gap genes that occurs during larval development. Polycomb-group proteins can silence the HOX genes by modulation of chromatin structure.

See also


Further reading

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