Hox gene

Hox genes (a subset of homeotic genes) are a group of related genes that control the body plan of an embryo along the cranio-caudal (head-tail) axis. After the embryonic segments have formed, the Hox proteins determine the type of segment structures (e.g. legs, antennae, and wings in fruit flies or the different types of vertebrae in humans) that will form on a given segment. Hox proteins thus confer segmental identity, but do not form the actual segments themselves.

An analogy for the Hox genes can be made to the role of a play director that calls which scene the actors should carry out next. If the play director calls the scenes in the wrong order, the overall play will be presented in the wrong order. Similarly, mutations in the Hox genes can result in body parts and limbs in the wrong place along the body. Like a play director, the Hox genes do not act in the play or participate in limb formation themselves.

The protein product of each Hox gene is a transcription factor. Each Hox gene contains a well-conserved DNA sequence known as the homeobox. In many animals, the organization of the Hox genes in the chromosome is the same as the order of their expression along the anterior-posterior axis of the developing animal, and are thus said to display colinearity.[1][2]

Hox genes code for transcription factors

The products of Hox genes are Hox proteins. Hox proteins are transcription factors, which are proteins that are capable of binding to specific nucleotide sequences on the DNA called enhancers where they either activate or repress genes. The same Hox protein can act as a repressor at one gene and an activator at another. The ability of Hox proteins to bind DNA is conferred by a part of the protein referred to as the homeodomain. The homeodomain is a 60-amino-acid-long DNA-binding domain (encoded by its corresponding 180-base-pair DNA sequence, the homeobox). This amino acid sequence folds into a "helix-turn-helix" (i.e. homeodomain fold) motif that is stabilized by a third helix. The consensus polypeptide chain is (typical intron position noted with dashes):[3]


The sequence and function of Hox genes is highly conserved

The homeodomain protein motif is highly conserved across vast evolutionary distances. In addition, homeodomains of individual Hox proteins usually exhibit greater similarity to homeodomains in other species than to proteins encoded by adjacent genes within their own Hox cluster. These two observations led to the suggestions that Hox gene clusters evolved from a single Hox gene via tandem duplication and subsequent divergence and that a prototypic Hox gene cluster containing at least seven different Hox genes was present in the common ancestor of all bilaterian animals.[4]

The functional conservation of Hox proteins can be demonstrated by the fact that a fly can function perfectly well with a chicken Hox protein in place of its own.[5] So, despite having a last common ancestor that lived over 670 million years ago,[6] the chicken and fly version of the same Hox gene can actually take each other's places when swapped.

Hox gene function in Drosophila

Homeobox (Hox) gene expression in Drosophila melanogaster

Drosophila melanogaster is an important model for understanding body plan generation and evolution. The general principles of Hox gene function and logic elucidated in flies will apply to all bilaterian organisms, including humans. Drosophila, like all insects, has eight Hox genes. These are clustered into two complexes, both of which are located on chromosome 3. The Antennapedia complex (not to be confused with the Antp gene) consists of five genes: labial (lab), proboscipedia (pb), deformed (Dfd), sex combs reduced (Scr), and Antennapedia (Antp). The Bithorax complex, named after the Ultrabithorax gene, consists of the remaining three genes: Ultrabithorax (Ubx), abdominal-A (abd-A) and abdominal-B (abd-B).


The lab gene is the most anteriorly expressed gene. It is expressed in the head, primarily in the intercalary segment (an appendageless segment between the antenna and mandible), and also in the midgut. Loss of function of lab results in the failure of the Drosophila embryo to internalize the mouth and head structures that initially develop on the outside of its body (a process called head involution). Failure of head involution disrupts or deletes the salivary glands and pharynx. The lab gene was initially so named because it disrupted the labial appendage; however, the lab gene is not expressed in the labial segment, and the labial appendage phenotype is likely a result of the broad disorganization resulting from the failure of head involution.[7]


The pb gene is responsible for the formation of the labial and maxillary palps. Some evidence shows pb interacts with Scr.[8]


The Dfd gene is responsible for the formation of the maxillary and mandibular segments in the larval head.[9] The mutant phenotypes of Dfd are similar to those of labial. Loss of function of Dfd in the embryo results in a failure of head involution (see labial gene), with a loss of larval head structures. Mutations in the adult have either deletions of parts of the head or transformations of head to thoracic identity.[7]

Sex combs reduced

The Scr gene is responsible for cephalic and thoracic development in Drosophila embryo and adult.[10]


Main article: Antennapedia

The second thoracic segment, or T2, develops a pair of legs and a pair of wings. The Antp gene specifies this identity by promoting leg formation and allowing (but not directly activating) wing formation. A dominant Antp mutation, caused by a chromosomal inversion, causes Antp to be expressed in the antennal imaginal disc, so that, instead of forming an antenna, the disc makes a leg, resulting in a leg coming out of the fly's head.

Wild type (left), mutant (right)


Main article: Ultrabithorax

The third thoracic segment, or T3, bears a pair of legs and a pair of halteres (highly reduced wings that function in balancing during flight). Ubx patterns T3 largely by repressing genes involved in wing formation. The wing blade is composed of two layers of cells that adhere tightly to one another, and are supplied with nutrient by several wing veins. One of the many genes that Ubx represses is blistered, which activates proteins involved in cell-cell adhesion, and spalt, which patterns the placement of wing veins. In Ubx loss-of-function mutants, Ubx no longer represses wing genes, and the halteres develop as a second pair of wings, resulting in the famous four-winged flies. When Ubx is misexpressed in the second thoracic segment, such as occurs in flies with the "Cbx" enhancer mutation, it represses wing genes, and the wings develop as halteres, resulting in a four-haltered fly.


In Drosophila, abd-A is expressed along most of the abdomen, from abdominal segments 1 (A1) to A8. Expression of abd-A is necessary to specify the identity of most of the abdominal segments. A major function of abd-A in insects is to repress limb formation. In abd-A loss-of-function mutants, abdominal segments A2 through A8 are transformed into an identity more like A1. When abd-A is ectopically expressed throughout the embryo, all segments anterior of A4 are transformed to an A4-like abdominal identity.[7] The abd-A gene also affects the pattern of cuticle generation in the ectoderm, and pattern of muscle generation in the mesoderm.[8]


Gene abd-B is transcribed in two different forms, a regulatory protein, and a morphogenic protein. Regulatory abd-B suppress embryonic ventral epidermal structures in the eighth and ninth segments of the Drosophila abdomen. Both the regulatory protein and the morphogenic protein are involved in the development of the tail segment.[8]

Classification of Hox proteins

Proteins with a high degree of sequence similarity are also generally assumed to exhibit a high degree of functional similarity, i.e. Hox proteins with identical homeodomains are assumed to have identical DNA-binding properties (unless additional sequences are known to influence DNA-binding). To identify the set of proteins between two different species that are most likely to be most similar in function, classification schemes are used. For Hox proteins, three different classification schemes exist: phylogenetic inference based, synteny-based, and sequence similarity-based.[11] The three classification schemes provide conflicting information for Hox proteins expressed in the middle of the body axis (Hox6-8 and Antp, Ubx and abd-A). A combined approach used phylogenetic inference-based information of the different species and plotted the protein sequence types onto the phylogenetic tree of the species. The approach identified the proteins that best represent ancestral forms (Hox7 and Antp) and the proteins that represent new, derived versions (or were lost in an ancestor and are now missing in numerous species).[12]

Genes regulated by Hox proteins

Hox genes act at many levels within developmental gene hierarchies: at the "executive" level they regulate genes that in turn regulate large networks of other genes (like the gene pathway that forms an appendage). They also directly regulate what are called realisator genes or effector genes that act at the bottom of such hierarchies to ultimately form the tissues, structures, and organs of each segment. Segmentation involves such processes as morphogenesis (differentiation of precursor cells into their terminal specialized cells), the tight association of groups of cells with similar fates, the sculpting of structures and segment boundaries via programmed cell death, and the movement of cells from where they are first born to where they will ultimately function, so it is not surprising that the target genes of Hox genes promote cell division, cell adhesion, apoptosis, and cell migration.[13]

Examples of targs
Organism Target gene Normal function of target gene Regulated by
Drosophila distal-less activates gene pathway for limb formation ULTRABITHORAX[14]

(represses distal-less)

distal-less activates gene pathway for limb formation ABDOMINAL-A[14]

(represses distal-less)

decapentaplegic triggers cell shape changes in the gut that are

required for normal visceral morphology


(activates decapentaplegic)

reaper Apoptosis: localized cell death creates the segmental

boundary between the maxilla and mandible of the head


(activates reaper)

decapentaplegic prevents the above cell changes in more posterior



(represses decapentaplegic)

Mouse EphA7 Cell adhesion: causes tight association of cells in

distal limb that will form digit, carpal and tarsal bones


(activates EphA7)

Cdkn1a Cell cycle: differentiation of myelomonocyte cells into

monocytes (white blood cells), with cell cycle arrest


(activates Cdkn1a)

Enhancer sequences bound by homeodomains

The DNA sequence bound by the homeodomain protein contains the nucleotide sequence TAAT, with the 5' terminal T being the most important for binding.[18] This sequence is conserved in nearly all sites recognized by homeodomains, and probably distinguishes such locations as DNA binding sites. The base pairs following this initial sequence are used to distinguish between homeodomain proteins, all of which have similar recognition sites. For instance, the nucleotide following the TAAT sequence is recognized by the amino acid at position 9 of the homeodomain protein. In the maternal protein Bicoid, this position is occupied by lysine, which recognizes and binds to the nucleotide guanine. In Antennapedia, this position is occupied by glutamine, which recognizes and binds to adenine. If the lysine in Bicoid is replaced by glutamine, the resulting protein will recognize Antennapedia-binding enhancer sites.[19]

However, all homeodomain-containing transcription factors bind essentially the same DNA sequence. The sequence bound by the homeodomain of a Hox protein is only six nucleotides long, and such a short sequence would be found at random many times throughout the genome, far more than the number of actual functional sites. Especially for Hox proteins, which produce such dramatic changes in morphology when misexpressed, this raises the question of how each transcription factor can produce such specific and different outcomes if they all bind the same sequence. One mechanism that introduces greater DNA sequence specificity to Hox proteins is to bind protein cofactors. Two such Hox cofactors are Extradenticle (Exd) and Homothorax (Hth). Exd and Hth bind to Hox proteins and appear to induce conformational changes in the Hox protein that increase its specificity.[20]

Regulation of Hox genes

Just as Hox genes regulate realisator genes, they are in turn regulated themselves by gap genes and pair-rule genes, which are in their turn regulated by maternally-supplied mRNA. This results in a transcription factor cascade: maternal factors activate gap or pair-rule genes; gap and pair-rule genes activate Hox genes; then, finally, Hox genes activate realisator genes that cause the segments in the developing embryo to differentiate. Regulation is achieved via protein concentration gradients, called morphogenic fields. For example, high concentrations of one maternal protein and low concentrations of others will turn on a specific set of gap or pair-rule genes. In flies, stripe 2 in the embryo is activated by the maternal proteins Bicoid and Hunchback, but repressed by the gap proteins Giant and Kruppel. Thus, stripe 2 will only form wherever there is Bicoid and Hunchback, but not where there is Giant and Kruppel.[21]

MicroRNA strands located in Hox clusters have been shown to inhibit more anterior hox genes ("posterior prevalence phenomenon"), possibly to better fine tune its expression pattern.[22]

Non-coding RNA (ncRNA) has been shown to be abundant in Hox clusters. In humans, 231 ncRNA may be present. One of these, HOTAIR, silences in trans (it is transcribed from the HOXC cluster and inhibits late HOXD genes) by binding to Polycomb-group proteins (PRC2).[23]

The chromatin structure is essential for transcription but it also requires the cluster to loop out of the chromosome territory.[24]

In higher animals including humans, retinoic acid regulates differential expression of Hox genes along the anteroposterior axis.[25] Genes in the 3' ends of Hox clusters are induced by retinoic acid resulting in expression domains that extend more anteriorly in the body compared to 5' Hox genes that are not induced by retinoic acid resulting in expression domains that remain more posterior.

Quantitative PCR has shown several trends regarding colinearity: the system is in equilibrium and the total number of transcripts depends on the number of genes present according to a linear relationship.[26]

Colinearity of Hox genes

In some organisms, especially vertebrates, the various Hox genes are situated very close to one another on the chromosome in groups or clusters. Interestingly, the order of the genes on the chromosome is the same as the expression of the genes in the developing embryo, with the first gene being expressed in the anterior end of the developing organism. The reason for this colinearity is not yet completely understood. The diagram above shows the relationship between the genes and protein expression in flies.

Hox nomenclature

The Hox genes are named for the homeotic phenotypes that result when their function is disrupted, wherein one segment develops with the identity of another (e.g. legs where antennae should be). Hox genes in different phyla have been given different names, which has led to confusion about nomenclature. The complement of Hox genes in Drosophila is made up of two clusters, the Antennapedia complex and the Bithorax complex, which together were historically referred to as the HOM-C (for Homeotic Complex). Although historically HOM-C genes have referred to Drosophila homologues, while Hox genes referred to vertebrate homologues, this distinction is no longer made, and both HOM-C and Hox genes are called Hox genes.

Human genes

Humans have Hox genes in four clusters: [27]

Cluster Chromosome Genes
HOXA 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


The Hox genes are so named because mutations in them cause homeotic transformations. Homeotic transformations were first identified and studied by William Bateson in 1894, who coined the term "homeosis". After the rediscovery of Mendel's genetic principles, Bateson and others realized that some examples of homeosis in floral organs and animal skeletons could be attributed to variation in genes.

Definitive evidence for a genetic basis of some homeotic transformations was obtained by isolating homeotic mutants. The first homeotic mutant was found by Calvin Bridges in Thomas Hunt Morgan's laboratory in 1915. This mutant shows a partial duplication of the thorax and was therefore named Bithorax (bx). It transforms the third thoracic segment (T3) toward the second (T2). Bithorax arose spontaneously in the laboratory and has been maintained continuously as a laboratory stock ever since.[28]

The genetic studies by Morgan and others provided the foundation for the systematic analyses of Edward B. Lewis and Thomas Kaufman, which provided preliminary definitions of the many homeotic genes of the Bithorax and Antennapedia complexes, and also showed that the mutant phenotypes for most of these genes could be traced back to patterning defects in the embryonic body plan.

Ed Lewis, Christiane Nüsslein-Volhard and Eric F. Wieschaus identified and classified 15 genes of key importance in determining the body plan and the formation of body segments of the fruit fly D. melanogaster. For their work, Lewis, Nüsslein-Volhard, and Wieschaus were awarded the Nobel Prize in Physiology or Medicine in 1995.[29]

In 1983, the homeobox was discovered independently by researchers in two labs: Ernst Hafen, Michael Levine, and William McGinnis (in Walter Gehring's lab at the University of Basel, Switzerland) and Matthew P. Scott and Amy Weiner (in Thomas Kaufman's lab at Indiana University in Bloomington).

See also


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  3. http://www.csb.ki.se/groups/tbu/homeo/consensus.gif
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  5. Lutz, B.; H.C. Lu; G. Eichele; D. Miller; T.C. Kaufman (1996). "Rescue of Drosophila labial null mutant by the chicken ortholog Hoxb-1 demonstrates that the function of Hox genes is phylogenetically conserved". Genes & Development. 10 (2): 176–184. doi:10.1101/gad.10.2.176. PMID 8566751.
  6. Ayala, F.J.; A. Rzhetskydagger (20 January 1998). "Origin of the metazoan phyla: Molecular clocks confirm paleontological estimates". Proc. Natl. Acad. Sci. USA. 95 (2): 606–11. doi:10.1073/pnas.95.2.606. PMC 18467Freely accessible. PMID 9435239.
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  8. 1 2 3 Brody, Thomas (1996). "The Interactive Fly".
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  10. Pattatucci AM, Kaufman TC (October 1991). "The homeotic gene Sex combs reduced of Drosophila melanogaster is differentially regulated in the embryonic and imaginal stages of development". Genetics. 129 (2): 443–61. PMC 1204635Freely accessible. PMID 1683847.
  11. Hueber S.D.; Weiller G.F., Djordjevic, M. A, Frickey, T. (2010). "Improving Hox Protein Classification across the Major Model Organisms". PLoS ONE. 5 (5): e10820. doi:10.1371/journal.pone.0010820. PMC 2876039Freely accessible. PMID 20520839.
  12. Hueber S.D.; Rauch J., Djordjevic M.A., Gunter H. Weiller G.F., Frickey T. (2013). "Analysis of central Hox protein types across bilaterian clades: On the diversification of central Hox proteins from an Antennapedia/Hox7-like protein". Developmental Biology. 383 (2): 175–185. doi:10.1016/j.ydbio.2013.09.009. PMID 24055174.
  13. 1 2 Pearson, JC; Lemons, D.; McGinnis, W. (2005). "Modulating Hox gene functions during animal body patterning". Nature Rev. Genet. 6: 893–904. doi:10.1038/nrg1726.
  14. 1 2 Vachon, G. et al. Homeotic genes of the bithorax complex repress limb development in the abdomen of the Drosophila embryo through the target gene Distal-less. Cell 71, 437–450 (1992).
  15. 1 2 Capovilla, M.; Botas, J. (1998). "Functional dominance among Hox genes: repression dominates activation in the regulation of dpp". Development. 125: 4949–4957.
  16. Lohmann, I.; McGinnis, N.; Bodmer, M.; McGinnis, W. (2002). "The Drosophila Hox gene Deformed sculpts head morphology via direct regulation of the apoptosis activator reaper". Cell. 110: 457–466. doi:10.1016/s0092-8674(02)00871-1.
  17. Bromleigh, V. C.; Freedman, L. P. (2000). "p21 is a transcriptional target of HOXA10 in differentiating myelomonocytic cells". Genes Dev. 14: 2581–2586. doi:10.1101/gad.817100.
  18. Gilbert, Developmental Biology, 2006
  19. Hanes and Brent 1989, 1991
  20. Mann, Richard S.; Lelli, Katherine M.; Joshi, Rohit (2009). "Chapter 3 Hox Specificity: Unique Roles for Cofactors and Collaborators". Current Topics in Developmental Biology. 88: 63–101. doi:10.1016/S0070-2153(09)88003-4.
  21. Small, S; Blair, A; Levine, M (Nov 1992). "Regulation of even-skipped stripe 2 in the Drosophila embryo". EMBO J. 11 (11): 4047–57.
  22. Lempradl, A; Ringrose, L (2008). "How does noncoding transcription regulate Hox genes?". BioEssays. 30 (2): 110–21. doi:10.1002/bies.20704.
  23. Rinn, JL; Kertesz, M; Wang, JK; Squazzo, SL; Xu, X; Brugmann, SA; Goodnough, LH; Helms, JA; et al. (2007). "Functional Demarcation of Active and Silent Chromatin Domains in Human HOX Loci by Non-Coding RNAs". Cell. 129 (7): 1311–23. doi:10.1016/j.cell.2007.05.022. PMC 2084369Freely accessible. PMID 17604720.
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  25. Duester, G (September 2008). "Retinoic Acid Synthesis and Signaling during Early Organogenesis". Cell. 134 (6): 921–31. doi:10.1016/j.cell.2008.09.002. PMC 2632951Freely accessible. PMID 18805086.
  26. Montavon; Le Garrec, JF; Kerszberg, M; Duboule, D (2008). "Modeling Hox gene regulation in digits: reverse collinearity and the molecular origin of thumbness". Genes Dev. 22 (3): 346–59. doi:10.1101/gad.1631708. PMC 2216694Freely accessible. PMID 18245448.
  27. https://www.youtube.com/watch?v=n64OKxEghiU
  28. Gehring, Walter J. (1998). Master Control Genes in Development and Evolution: The Homeobox Story. Yale Univ. Press.
  29. "The Nobel Prize in Physiology or Medicine 1995". Nobelprize.org.

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