Epigenetics of Hox Genes

Last update: Sep 2020

Hox genes play an essential role in the development of a number of species, including humans. This section will use the example of mice to explain the phenomenon in which this gene is sequentially activated over the course of embryonic development.

A Word on Epigenetics

The sequential activation of the Hox gene is in related to epigenetic modifications of the DNA sequence, namely to the histone protein methylation and acetylation. Before diving deeper into the topic, let's have a look at what those terms mean.

Histones are proteins that associate with DNA molecules in order to make nucleosomes, which assemble into highly compact structures that make up chromatin. Each nucleosome consists of 8 histone proteins and around 147 bp of DNA wrapped around them. Histone proteins can undergo many post-translational modifications (PTMs) that can result in the alteration of the chromatin structure and thus influence gene expression. Post-translational modifications affect chromatin structure through the recruitment of various proteins to the modification sites. Tightly packed chromatin, dubbed heterochromatin, is associated with gene repression, and loosely packed chromatin called euchromatin is associated with gene activation.

Histones can undergo many modifications, including methylation, acetylation, and phosphorylation, on certain amino-acid residues, especially lysine denoted as K. Histone methylation is mediated by histone methyltransferase and is associated with gene repression. As shown in the picture, the presence of grey circles (lollipops) that denote H3K27 methylation (on 27th lysine of the 3rd histone protein) is related to tightly packed heterochromatin that is characteristic in gene repression. Methylation of residues other than lysine does not necessarily inhibit transcription. On the contrary, histone acetylation, shown as pink circles, is often related to transcriptionally active euchromatin regions.

Figure 1. Sequential activation of Hox genes proceeding with time

Sequential Activation of Hox Genes

Histone modifications often result in the recruitment of various chromatin-modifying enzymes to the chromatin. As a result, histone methylation/demethylation and acetylation/deacetylation can cause a self-propagating change in chromatin structure. This “domino effect” spreads the chromatin structure modification along the chromosome (in the direction of arrows in Fig.1).

This effect is thought to be a crucial mechanism in the sequential activation of Hox genes during mouse embryo development. In the picture, you can see the chromatin structure of the region encoding Hox genes in samples collected from tail-tips of 8.5- and 9.5- day old mouse embryos. At day 8.5, the genes Hoxd1-9 are in the heavily acetylated euchromatin region and are actively expressed. However, Hoxd10-13 genes are still in the heterochromatin region and are heavily methylated, so they are not expressed, though some sites within Hoxd10 are beginning to get acetylated. At day 9.5, the acetylation has propagated along the chromatin, prompting the formation of euchromatin, and the Hoxd10-13 genes are starting to be expressed.

This “domino effect” is also observed in the case of H3K27 methylation, which results in progressive repression of genes.

Hox Genes in Axial Patterning

Hox genes play an essential role in vertebrate axial patterning during development. In line with the previous paragraph, Hox genes in insects and invertebrates are expressed in temporal and spatial order in which they are arranged on the chromosomes, that is, 1,2,3, etc. In other words, the order of genes on the chromosome reflects the spatial pattern of expression of those genes in the embryo. This is illustrated in Fig.2, where 4 genes are expressed in order along the anterior-posterior axis. Their expression pattern provides the cells with their position values.

It is also worth noting that, “anterior” Hox genes are expressed before the “posterior” Hox genes, which illustrates the temporal order of expression.

Figure 2. Model of gene expression pattern along the anterior-posterior axis

The Hox gene-mediated axial patterning has been demonstrated in mice embryos. Fig.3 below shows the lateral view of the expression patterns of Hoxb1, Hoxb4, and Hoxb9 genes in 9.5-day old mouse embryos that have undergone neurulation. Those 3 Hox genes are usually expressed in neural tube and mesoderm. The triangles show the anterior boundary of expression. The sequence in the top right corner shows the position of the 3 genes within the Hoxb gene complex. As you can see, all 3 genes have a distinct expression pattern that extends posteriorly, with a clear anterior border. Hoxb1 is expressed in the tissues closer to the anterior end of the embryo. Hoxb4 gene, which comes after Hoxb1 on the DNA sequence, is expressed further down the anterior-posterior axis. Hoxb9 gene, whose sequence follows that of the other 2 genes, is expressed yet further away, close to the posterior end of the mouse embryo. You can also see that the 3 expression patterns overlap, as all 3 genes are expressed, starting at their respective anterior borders, all the way until the posterior end. Therefore, pretty much every mesoderm region along the anterior-posterior axis has a unique combination of expressed Hox genes, which contributes to establishing position values. This observation agrees with the Hox expression pattern model in Fig.2.

Figure.3 Hox genes in mouse embryos expressed in order in which they are arranged on the chromosomes



[1] Wolpert, L. and Tickle, C., 2011. Principles of Development. 4th ed. New York: Oxford University Press.

[2] Li G, Zhou L (2013) Genome-Wide Identification of Chromatin Transitional Regions Reveals Diverse Mechanisms Defining the Boundary of Facultative Heterochromatin. PLoS ONE 8(6): e67156. https://doi.org/10.1371/journal.pone.0067156

[3] Mariño-Ramírez, L., Kann, M. G., Shoemaker, B. A., & Landsman, D. (2005). Histone structure and nucleosome stability. Expert review of proteomics, 2(5), 719–729. https://doi.org/10.1586/14789450.2.5.719

[4] Quinonez, S. C., & Innis, J. W. (2014). Human HOX gene disorders. Molecular genetics and metabolism, 111(1), 4–15. https://doi.org/10.1016/j.ymgme.2013.10.012


Figure 1. Wolpert, L. , Tickle, C., Martinez Arias, A. 2015. Principles of Development. 5th ed. New York: Oxford University Press.

Figure 2&3. Wolpert, L. and Tickle, C., 2011. Principles of Development. 4th ed. New York: Oxford University Press.