Why are homeotic genes important in animals?

Evolution

Homeobox genes are found in plants, fungi, and animals, and even in slime molds (Dictyostelium). Although now several prokaryotic genomes have been sequenced, no true homeobox gene has been found in these organisms. Thus, it appears likely that the first homeobox appeared sometime in eukaryote evolution, probably derived from a helix–turn–helix factor. In the ancestral organism from which eventually plants, fungi, and animals were derived, at least two different homeobox genes must have existed already: one a typical 60-amino acid homeobox gene, and one TALE homeobox gene. This ancestral TALE homeobox gene had a conserved upstream domain from which the KNOX, MEIS, and PBC domains are derived. While in plants and fungi some proliferation of different types of homeobox genes has taken place, by far the largest expansion has happened in animals, where there are now dozens of different classes and families of homeobox genes (see Classes of Homeobox Genes). The emergence of the different classes of homeobox genes seems to have happened early in metazoan evolution, since in sponges and cnidaria many different types of homeobox genes are found, and in the Bilaterialia phyla essentially all classes and many families are present.

Homeobox genes are known as transcriptional regulators that are involved in various aspects of developmental processes in many organisms. In plants, many types of homeobox genes have been identified, and mutational or expression pattern analyses of these genes have indicated the involvement of several classes of homeobox genes in developmental processes. The fundamental body plan of plants is established during embryogenesis, whereas morphogenetic events in the shoot apical meristem (SAM) continue after embryogenesis. Knotted1-like homeobox genes (knox genes) are preferentially expressed in both the SAM and the immature embryo. Therefore, these genes are considered to be key regulators of plant morphogenesis. In this review, we discuss the regulatory role of knox genes and other types of homeobox genes in SAM establishment during embryogenesis and SAM maintenance after embryogenesis, mainly in rice.

Introduction

Homeobox genes were discovered in Drosophila melanogaster as being responsible, when mutated, for phenotypic changes during early embryonic development such as body segment replacement (antenna toward pedia) or duplication (thoracic segment T2)1–7. Sequence homology studies with these two initial genes (called Antenapedia and Ultrabithorax) led to the isolation of similar genes in many other species from the Nematode to Zebra Fish, Xenope, Mouse and Human8. A highly conserved sequence of 183bp called “homeobox” was found present in these genes4, and genes containing such a homeobox sequence were named “homeobox genes”. The homeobox encodes a protein domain (61 amino acids) called the “homeodomain”, which can bind to specific DNA sequences5. With time and the achievement of whole-genome sequencing, the homeobox gene family has been extended, in humans, to a total number of 300 loci corresponding to 235 functional genes and 65 pseudo-genes9. Within this important superfamily, two groups can be distinguished. The first group corresponds to “HOX” homeobox genes that are organized into four clusters in mammalian genomes. These clusters, probably obtained by successive duplications10, are localized on different chromosomes (Table 14.1) and contain 13 series of paralog genes8,11,12. The second group corresponds to all other homeobox genes, divergent from HOX homeobox genes and dispersed in genomes9. The Dlx homeobox genes are peculiar divergent homeobox genes since they are also organized in clusters and are furthermore located on the same chromosomes as HOX clusters (Table 14.1).

Table 14.1. Chromosome localization of the HOX and DLX gene clusters in mouse and human

MouseHumanHOX-ADLX5-DLX6Chr 6Chr 7HOX-BDLX3-DLX4Chr 11Chr 17HOX-CChr 15Chr 12HOX-DDLX1-DLX2Chr 2Chr 2

The present chapter provides a review of the current state of knowledge of the Dlx homeobox genes with a special focus on the implication of these genes in bone formation and bone tumors.

Rearrangements Involving HOX Genes

HOX genes are frequently overexpressed in leukemia (37). HOX genes are expressed in early hematopoietic progenitors but are undetectable in terminally differentiated cells. Gene expression profiling analysis showed that the HOXA4, HOXA9, HOXA10, PBX3, and MEIS1 homeobox genes are coexpressed across diverse cytogenetic groups, suggesting a coregulated pathway with pathogenetic relevance in a subgroup of AML (38). HOX genes are mainly disrupted via chromosomal translocation. For instance, HOXA9 and HOXD13 are deregulated through the t(7;11) and t(2;11) translocations, respectively, giving rise to fusion proteins between the HOX protein and the nucleoporin 98-kD (NUP98) nuclear protein (39). The NUP98 moiety of HOXA9-NUP98 has transactivating capacity and interacts with the transcriptional coactivator creb binding protein (CBP)/p300. Overexpression of HOXA6, HOXA7, HOXA9, and the HOX cofactor myeloid ecotropic viral integration site 1 (MEIS1) has also been correlated with chromosome 11q23 abnormalities involving the MLL protein, which directly regulates the expression of HOX genes.

HOXA

Homeobox genes have been identified in multiple organisms, from mammals to insects and lower organisms, and they appear to affect structural symmetry during organogenesis. Research has identified homeobox genes as important for the normal development of the genitourinary tract. Cohn31 reviewed the research that found that homeobox genes were needed for the normal growth and differentiation of the urethral plate and distal genital tubercle. Development of the genital tubercle parallels that of development of the limb buds in the embryo; without HOXA genes, growth of the distal genital tubercle remains rudimentary.

Mutations in the homeobox genes have also been associated with abnormal development of the external genitalia, often in the setting of a syndrome of developmental abnormalities. One such novel syndrome is X-linked lissencephaly with abnormal genitalia (XLAG), in which patients have frameshift or point mutations in the Aristaless-related homeobox gene (ARX).32 Affected patients present with neural malformations, including agenesis of the corpus callosum, abnormalities of midline structures in the brain, disorganized and incomplete development of the cerebral cortex, and micropenis with bilateral undescended testicles. Some patients also have associated renal phosphate wasting.33

The importance of the homeobox genes in regulating normal organogenesis is underscored by duplication of function. HOXA and HOXD genes have been found to have compensatory activity for mild mutations such that affected embryos may develop without significant congenital abnormalities. However, more severe or extensive mutations in either gene cannot be compensated by the remaining normal gene.34 Work by Utsch and colleagues34 found that novel mutations in the homeobox genes associated with the hand-foot-genital syndrome may reflect the limitations of duplicated function in compensatory genes.

The HOX Cluster in HSC Self-Renewal

Homeobox (HOX) genes encode homeodomain-containing transcription factors critical for embryonic patterning, organized into four paralogous clusters (A, B, C, and D) on four chromosomes.306 Because of limited DNA sequence specificity and selectivity, HOX proteins function through interaction with DNA-binding cofactors, in particular, PBX and/or myeloid ectopic insertion site (MEIS) family members.307,308 At least 22 of the 52 HOX genes (none from the HOXD cluster) are expressed in mouse and human HSPCs and are subsequently downregulated to permit lineage commitment.309 Therefore, continuous HOX expression generally blocks differentiation and leads to rapid expansion of preleukemic HSPCs. In mice, overexpression of HOXA10 has been shown to block myeloid and lymphoid differentiation leading to AML.310 This is also the case for Hoxa9, in particular conjunction with Meis1 or the E2A-Pbx1 fusion gene.311–313 HOXA9 overexpression belongs to a gene signature that distinguishes AML from ALL, and in AML patients highly correlates with treatment failure.314

A number of leukemic chromosomal translocations, either directly or indirectly, lead to the overexpression of HOX genes. The nuclear pore complex protein NUP98 was first implicated in hematologic malignancies by the discovery of NUP98-HOXA9 fusions in AML.315,316 Approximately half of all NUP98 translocations involve HOX genes, most commonly HOXA9 in AML, MDS, CML and CMML, but also HOXA11 and HOXA13 as well as their paralogues in the B and C cluster.317,318 While the overall prevalence of these fusions is low, they are associated with a poor prognosis.319

In normal HSPCs, the expression of HOX genes is regulated by MLL1,320 as part of a multiprotein complex that regulates the chromatin structure at HOX clusters.321,322 MLL1 fusion proteins in MLL1-rearranged leukemias further induce the transcription of specific HOX genes including HOXA5, HOXA9 and HOXA10.323,324 Indeed, HOX gene overexpression is essential for MLL1-fusion induced leukemogenesis as demonstrated by the dependence of transplanted AMLs induced by both MLL1-ENL and MLL1-AF4 rearrangements on HOXA9.325,326

7.4.1 Rostrocaudal Patterning: RA, FGFs, Gdf11, and the Hox Code

Hox genes are responsible for the rostrocaudal segmentation seen in animals. They are found arrayed in gene clusters, of which there are four in mammals. Typically, the Hox genes located at the 3′ end of a particular cluster are expressed in more rostral areas, while genes at the 5′ end of the cluster are most often active in caudal regions of the organism, though exceptions exist (Lemons and McGinnis, 2006). FGF signaling is responsible for the initial expression of Hox genes along the spinal cord and then continually influences their caudal expression through its secretion from the primitive knot (or Hensen's node/Spemann's organizer in various species) and the presomitic mesoderm. During development, these two areas move farther caudally, resulting in the caudal regions of spinal cord being exposed to higher concentrations of FGF, and for a longer period of time, relative to the rostral cord (Bel-Vialar et al., 2002; Dasen et al., 2003; Dubrulle and Pourquie, 2004; Liu et al., 2001). How FGF influences the expression of Hox genes is not clear, but altering expression of vertebrate caudal homeobox (Cdx) genes can mimic aberrant expression of FGF (Bel-Vialar et al., 2002). This finding, and the possibility that Cdx could bind directly to Hox regulatory elements, has led to the hypothesis that FGF may act through Cdx activity to regulate Hox gene expression (Dasen and Jessell, 2009).

Though FGF expression is responsible for Hox patterning in most regions of the spinal cord, it alone is insufficient to drive the entire Hox expression pattern seen in the spinal cord (Carpenter, 2002; Dasen and Jessell, 2009). For instance, in caudal areas of the spinal cord, Gdf11, a specific TGFβ family member, is required for proper Hox expression (Figure 7.5). Like FGF, Gdf11 is expressed by the primitive knot, which leads to its high caudal-to-rostral gradient (Dasen and Jessell, 2009). In these caudal regions, Gdf11 works in conjunction with high concentrations of FGF to ensure the appropriate expression of specific Hox genes (Liu et al., 2001).

In addition to the Gdf11 and FGF signaling needed for proper spinal Hox expression caudally, RA drives the expression of Hox genes at rostral spinal levels (Dasen and Jessell, 2009). RA is expressed by somites in the paraxial mesoderm alongside the rostral spinal cord, influencing Hox patterning in the cervical and brachial levels (Figure 7.5; Liu et al., 2001). RA also affects hindbrain Hox expression, and it imposes its influence here by binding the nuclear hormone receptor, RAR (Dasen and Jessell, 2009; Duester, 2008). In addition to shaping Hox expression patterns in the rostral spinal cord, RA is also responsible for antagonizing FGF signals from the caudal mesoderm (Dasen and Jessell, 2009; Duester, 2008), possibly helping to define borders of Hox expression. The combined signaling of RA, Gdf11, and FGF leads to 3′ Hox expression (Hox4–Hox8) at cervical and brachial levels, Hox8 and Hox9 expression at thoracic levels, and 5′ Hox expression (Hox10–Hox13) at lumbar levels (Dasen and Jessell, 2009).

IV.C HOX Genes

Homeobox (HOX) genes, which encode highly conserved, developmentally regulated transcription factors used to establish body plans, are usually thought to be expressed only during embryonic development. However, HOX gene expression has been observed in the reproductive tracts of adult mice and humans. The importance of this expression has been demonstrated by targeted disruption of the genes; there is implantation failure as well as resorption of embryos in mice deficient in either Hoxa10 or Hoxa11. In addition, the intrauterine administration of antisense oligonucleotides targeted against Hoxa10 mRNA decreases the implantation rate. Investigation of the mechanisms underlying the uterine deficits in Hoxa10 mice has found inappropriate regulation of prostaglandin E2 receptor subtypes EP3 and EP4. Down-regulation of endometrial Hoxa10 expression by an antisense strategy has been shown to decrease lumenal epithelial pinopod formation. Since pinopods develop transiently on the lumenal epithelial cells at the time of uterine receptivity, this suggests that Hoxa10 expression is required for the acquisition of receptivity.

Why are homeotic genes important in animals quizlet?

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