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A homeobox (or homoeobox) is a DNA sequence found within genes that are involved in the regulation of development (morphogenesis) of animals, fungi and plants. Genes that have a homeobox are called homeobox genes and form the homeobox gene family.

A homeobox is about 180 base pairs long; it encodes a protein domain (the homeodomain) which can bind DNA. Homeobox genes encode transcription factors which typically switch on cascades of other genes, for instance all the ones needed to make a leg. 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.

A particular subgroup of homeobox genes are the Hox genes, which are found in a special gene cluster, the Hox cluster (also called Hox complex). Hox genes function in patterning the body axis. Thus, by providing the identity of particular body regions, Hox genes determine where limbs and other body segments will grow in a developing fetus or larva. Mutations in any one of these genes can lead to the growth of extra, typically non-functional body parts in invertebrates, for example aristapedia complex in Drosophila, which results in a leg growing from the head in place of an antenna and is due to a defect in a single gene (this mutation is also known as Antennapedia). Mutation in vertebrate Hox genes usually results in spontaneous abortion. Pit-1 homeobox-containing protein bound to DNA Enlarge Pit-1 homeobox-containing protein bound to DNA

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. The diagram to the right is a structural model of the Rattus norvegicus Pit-1 homeobox-containing protein (purple) bound to DNA. Pit-1 is a regulator of growth hormone gene transcription. Pit-1 is a member of the POU DNA-binding domain family of transcription factors so it can bind to DNA using both the POU domain and the homeodomain. Homeobox genes have even been found in fungi, for example the one-cellular yeasts, and 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 were evolved once in the early evolution of animals and once again in the early evolution of plants. Humans generally contain homeobox genes in four clusters, called HOXA (or sometimes HOX1), HOXB, HOXC, or HOXD, on chromosomes 7, 17, 12, and 2, respectively.

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, 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

A haplotype is the genetic constitution of an individual chromosome. Haplotype may refer to only one locus or to an entire genome. In the case of diploid organisms such as humans, a genome-wide haplotype comprises one member of the pair of alleles for each locus (that is, half of a diploid genome). An organism's haplotype is studied using a genealogical DNA test. The term haplotype is a contraction of "haploid genotype".

In a second meaning, haplotype is a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated. It is thought that these associations, and the identification of a few alleles of a haplotype block, can unambiguously identify all other polymorphic sites in its region. Such information is very valuable for investigating the genetics behind common diseases and is collected by the International HapMap Project.