Accordingly, the different translational efficiencies of different transcripts in the tissues of Ts mice might reflect their intrinsic ability to compete for limited numbers of functional 60S subunits. It is not clear if the molecular phenotype of Ts mice represents a hypomorphic phenotype with no relevance to physiological regulatory processes or if it has uncovered a new bona fide regulatory mechanism.
If the latter case is true, it suggests that regulated production of the RNA and protein components of the ribosome could be relevant for the control of specific developmental processes. Interestingly, analysis of the levels and distribution of a large set of ribosomal proteins in the mouse embryo revealed an unexpectedly high degree of tissue-specific expression Kondrashov et al. Particularly interesting are ribosomal proteins, such as Rps25, that have been suggested to interact with IRES Nishiyama et al.
An important question that remains to be addressed is whether translational control mechanisms similar to those observed in Ts mice are vertebrate specific or even mouse specific or if they represent an evolutionarily conserved control mechanism. Our discussion here reveals a remarkably wide spectrum of regulatory mechanisms involved in the control of Hox expression, many of which have been evolutionarily conserved between insects and mammals Table 1. However, it must be noted that the presence of similar regulatory mechanisms in flies and mice does not necessarily imply a common origin and could instead be the result of convergent evolution.
Although each Hox-regulating mechanism is likely to have its own intrinsic properties, it is important to note that many of the mechanisms presented seem to be linked to one another either by the regulatory input imparted by common factors or other forms of functional coupling. Summary of the main molecular mechanisms controlling Hox gene expression in Drosophila and mice. Examples in Drosophila show, for instance, that the process of alternative promoter usage affecting the expression of mRNAs Oh et al.
Further examples of gene expression coupling include the effects of transcriptional elongation rates on the spectrum of alternatively spliced forms of Ubx de la Mata et al.
In vertebrates, Hox cluster miRNAs seem to follow a temporal expression pattern highly similar to that of their targets, leading to the suggestion that miRNAs could be an integral part of the mechanisms behind a long known, but still poorly understood, property of Hox genes: posterior prevalence Yekta et al.
Interestingly, it has been shown that the role of miRNAs in posterior prevalence can be reinforced by a lncRNA transcribed from the same genomic area Gummalla et al. Therefore, the coordinated evolution of the different regulatory processes might be a core feature underlying the robustness of the Hox expression programme. In addition, we have discussed the impact of 3D chromatin conformation on several aspects of Hox gene regulation.
Although it is still too early to draw a clear picture of this process, it is plausible that initial stages of vertebrate Hox gene activation involve a sequential relocation of Hox chromatin from transcriptionally silent nuclear domains into nuclear areas engaged in active transcription.
In this context, it is conceivable that recently discovered regulatory players, including non-coding RNAs, such as lncRNAs or enhancer-associated transcripts, might influence chromatin structure and cluster-wide control mechanisms. Yet these functional links across the many processes involved in gene expression are not a unique feature of the Hox genes.
Indeed, more than a decade ago Tom Maniatis and Robin Reed suggested the existence of a pervasive level of functional coupling across all the molecular machines involved in gene expression control Maniatis and Reed, However, most work addressing the mechanisms and biological implications of gene expression coupling has so far been conducted in mammalian cultured cells or yeast leaving the question of the extent to which these interconnections play a relevant role within the physiological context of development largely unexplored.
In this context, Hox genes might provide an excellent system in which to investigate both the mechanisms and biological roles of the many interconnections across different gene regulatory levels that are traditionally studied in isolation. A possible scenario with regards to the biological roles of a highly interconnected network of Hox-regulatory interactions is that this has emerged to increase robustness of the Hox expression programme, ensuring that correct spatial and temporal patterns of Hox expression are achieved despite intrinsic molecular variation and extrinsic fluctuations in embryonic environment.
More generally, the existence of this highly interconnected form of control might suggest that animal embryos must carefully control Hox gene expression in order to complete development successfully. This interlocked regulatory network arrangement might also provide an explanation for why core features of Hox expression, especially those related to expression domains, have been maintained largely unchanged during the extended periods of bilaterian evolution. Work in the C.
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Close mobile search navigation Article navigation. Volume , Issue Previous Article Next Article. Article contents. Key features of Hox genes. Hox transcriptional regulation in space and time.
The chromatin component of Hox gene regulation. Adding active and inactive chromatin-associated marks to Hox chromatin. Long non-coding RNAs in the regulation of Hox gene expression. Hox gene regulation via RNA processing.
Hox gene regulation via miRNAs. Translational control. Concluding remarks. Article Navigation. This site. Google Scholar. Claudio R. Alonso Claudio R. Author and article information. Competing interests statement The authors declare no competing financial interests. Online Issn: Published by The Company of Biologists Ltd. Development 19 : — Cite Icon Cite.
View large Download slide. Table 1. View Large. Funding Work in the C. Search ADS. Unraveling cis-regulatory mechanisms at the abdominal-A and Abdominal-B genes in the Drosophila bithorax complex. A Hox gene mutation that triggers nonsense-mediated RNA decay and affects alternative splicing during Drosophila development. Truncation of the Mll gene in exon 5 by gene targeting leads to early preimplantation lethality of homozygous embryos. Polycomb-dependent regulatory contacts between distant Hox loci in Drosophila.
Genetic analysis of a conserved sequence in the HoxD complex: regulatory redundancy or limitations of the transgenic approach? The expression pattern of the murine Hoxa gene and the sequence recognition of its homeodomain reveal specific properties of Abdominal B-like genes. A bivalent chromatin structure marks key developmental genes in embryonic stem cells.
Evolutionary conservation of the structure and expression of alternatively spliced Ultrabithorax isoforms from Drosophila.
Multiple levels of transcriptional and post-transcriptional regulation are required to define the domain of Hoxb4 expression. The distribution of polycomb-group proteins during cell division and development in Drosophila embryos: impact on models for silencing. Different forms of Ultrabithorax proteins generated by alternative splicing are functionally equivalent.
The molecular genetics of the bithorax complex of Drosophila: characterization of the products of the Abdominal-B domain. The molecular genetics of the bithorax complex of Drosophila: cis-regulation in the Abdominal-B domain. Chromatin decondensation and nuclear reorganization of the HoxB locus upon induction of transcription. Nuclear re-organisation of the Hoxb complex during mouse embryonic development.
Multiple coding and non-coding RNAs in the Hoxb3 locus and their spatial expression patterns during mouse embryogenesis. Regulation of the Hoxb-8 gene: synergism between multimerized cis-acting elements increases responsiveness to positional information. Multiple promoters and alternative splicing: Hoxa5 transcriptional complexity in the mouse embryo.
Integration of RNA processing and expression level control modulates the function of the Drosophila Hox gene Ultrabithorax during adult development. Polycomb: a paradigm for genome organization from one to three dimensions. Developmental regulation of the Hox genes during axial morphogenesis in the mouse. Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. The structural and functional organization of the murine HOX gene family resembles that of Drosophila homeotic genes.
Colinearity and functional hierarchy among genes of the homeotic complexes. El Tayebi. Ring1B compacts chromatin structure and represses gene expression independent of histone ubiquitination. Analysis of the murine Hoxa-9 cDNA: an alternatively spliced transcript encodes a truncated protein lacking the homeodomain. Phosphorylation, expression and function of the Ultrabithorax protein family in Drosophila melanogaster. Interspecies exchange of a Hoxd enhancer in vivo induces premature transcription and anterior shift of the sacrum.
Multiple epigenetic maintenance factors implicated by the loss of Mll2 in mouse development. The murine and Drosophila homeobox gene complexes have common features of organization and expression. Regulatory role for a conserved motif adjacent to the homeodomain of Hox10 proteins. Regulation of Antennapedia transcript distribution by the bithorax complex in Drosophila. Generation of alternative Ultrabithorax isoforms and stepwise removal of a large intron by resplicing at exon-exon junctions.
Genetic analysis of a Hoxd regulatory element reveals global versus local modes of controls in the HoxD complex. Spatial regulation of the Antennapedia and Ultrabithorax homeotic genes during Drosophila early development. Enhancer timing of Hox gene expression: deletion of the endogenous Hoxc8 early enhancer.
Cytogenetic analysis of chromosome 3 in Drosophila melanogaster: the homoeotic gene complex in polytene chromosome interval 84a-B. Ribosome-mediated specificity in Hox mRNA translation and vertebrate tissue patterning. Structure and expression of a family of Ultrabithorax mRNAs generated by alternative splicing and polyadenylation in Drosophila. Transcriptional activation and repression by Ultrabithorax proteins in cultured Drosophila cells. Different transcripts of the Drosophila Abd-B gene correlate with distinct genetic sub-functions.
A histone H3 lysine 27 demethylase regulates animal posterior development. Early retinoic acid-induced F9 teratocarcinoma stem cell gene ERA alternate splicing creates transcripts for a homeobox-containing protein and one lacking the homeobox.
Structure of transcripts from the homeotic Antennapedia gene of Drosophila melanogaster: two promoters control the major protein-coding region.
UTX, a histone H3-lysine 27 demethylase, acts as a critical switch to activate the cardiac developmental program. Three Drosophila Hox complex microRNAs do not have major effects on expression of evolutionarily conserved Hox gene targets during embryogenesis. Genetic analysis of the Antennapedia gene complex Ant-C and adjacent chromosomal regions of Drosophila melanogaster.
Polytene chromosome segments 84AB1,2. RNA processing and its regulation: global insights into biological networks. Comprehensive mapping of long-range interactions reveals folding principles of the human genome.
In ovo application of antagomiRs indicates a role for miR in patterning the chick axial skeleton through Hox gene regulation. Thus, the breaks found in the Drosophila Hox complexes may be exceptional cases of rearrangements that bypassed deleterious effects.
Based on our current understanding of Hox gene regulation in vertebrates and invertebrates, it now seems likely that at least some of the reason for preserving collinearity diverged during the evolutionary history of the two lineages. In mammals, collinearity seems to be preserved primarily due to the sharing of distal enhancer elements.
This sharing of enhancers presumably provides evolutionary pressure to keep the Hox genes clustered. Furthermore, it seems that distance from these enhancers controls the timing and ultimate location of Hox gene expression, providing pressure to preserve collinearity.
However, this is not the case in invertebrates. In Drosophila , Hox gene expression is controlled by gene-specific enhancers located within the complex itself.
It is perhaps for this reason that invertebrate Hox complexes are generally larger than their vertebrate counterparts and why the Drosophila Hox complex could be split in two. These fly Hox genes correspond to mammalian orthologs Hox4 and Hox5 , respectively. These genes correspond to the fly genes abd-A and Abd-B. As in the case of miR10, a miRNA gene is found at a similar location in arthropods, though the primary sequence of the miRNA genes differ between the two lineages.
In Drosophila , this miRNA gene is transcribed on both strands, giving rise to miR-iab-4 on one strand, and miR-iab-8 on the other strand. Recent work from our lab on the iab-8 -ncRNA has led to a number of interesting results, and provide additional reasons for the preservation of Hox clustering.
Hox genes were discovered through mutations that affect the identities of the segments that form along the AP axis of the fly. Many of these mutations were identified within the posterior Hox complex of the fly, called the BX-C Lewis, for review, see Maeda and Karch, These parasegments form the posterior thorax and all the abdominal segments of the fly posterior T2, T3 and all eight abdominal segments A1—A8 1.
Before the molecular genetic era, classical genetic analysis revealed the existence of mutations that affect the identities of each of the segments under the control of the BX-C. These mutations defined nine segment-specific functions.
By genetic mapping, Ed Lewis discovered that these nine segments-specific functions are aligned along the chromosome in the same order as the segments they specify along the AP axis. This was the first identification of colinearity. Molecular analysis later revealed that the BX-C encoded only three, homeotic genes and that the genetically identified segment-specific functions were probably regulatory in nature.
This was confirmed by antibody staining in mutant embryos. Antibody staining showed that Ubx , abd-A , and Abd-B are expressed in overlapping domains in the posterior half of the embryo see also below. These expression patterns are intricate and finely tuned from one parasegment to the next see for example Figure 2. By staining various mutant embryos it was shown that the segment-specific functions correspond to cis -regulatory regions that regulate the expression of Ubx.
Similarly the iab-2 through iab-4 cis -regulatory regions direct the parasegment-specific expression patterns of abd-A in PS7, PS8, and PS9 Figures 1 and 2 ; for review, see Maeda and Karch, Thus, the collinearity that exists in flies extends beyond the genes themselves to the cis -regulatory elements that drive the Hox gene expression.
Synopsis of the BX-C. The genomic region of the BX-C is marked off in kilobases according to the numbering of Martin et al. The three transcription units Ubx , abd-A, and Abd-B with their exons marked as thick lines and the arrows showing the transcription polarity are drawn below the DNA map.
The horizontal and colored brackets above the DNA line indicate the extends of the segment-specific cis- regulatory regions with the following color code.
These segmental boundaries are depicted with the same colors on the fly above the BX-C map. Note that the parasegmental boundaries are visible in the thoracic segments where PS5 corresponds to the posterior part of T2 and the anterior part of T3.
PS6 corresponds to posterior T3 and anterior A1. Panels A , B , and C show pelts of stage 13 embryos. In these preparations, embryos were cut along the dorsal midline and flattened on a slide. Anterior is at the top. In stage 13 embryos, Hox gene expression is mostly visible in the epidermis with abd-A displayed in red and Abd-B in green. In these parasegments, Abd-B is produced from promoter A under the regulation of, respectively the iab-5, iab-6, iab-7, and iab-8 regulatory regions see also text.
Both abd-A and Abd-B are displayed in panel C. Note that their overall expression domains appear complementary to each other. Original observations published in Celniker et al. Introns are numbered with latin numbers and exons with regular numbering. Note that the polarity of transcription is the same as that for abd-A and Abd-B.
Note also the presence of one exon for each of the iab cis -regulatory regions to the exception of 2 exons in iab Like in vertebrates, most Drosophila Hox genes are expressed in broad domains along the AP axis. This is the case for the Antp gene that specifies the identity of PS4.
While its segmental specification role is restricted to this single parasegments, Antp remains expressed in all the more posterior parasegments, until PS12 Hafen et al. Thus these three Hox genes remain expressed posterior to the parasegments they specify respectively though, in each parasegment, expression is limited to a subset of cells, see below. Looking at the overall parasegment-specific expression pattern of Ubx and abd-A , or that of abd-A and Abd-B Figure 2 , their respective expression domains appear complementary to each other.
A similar negative, trans -regulatory interaction exists between Ubx and Antp , the Hox gene responsible for PS4 specification. In this case, Ubx is known to repress Antp Hafen et al. As a result of these negative cross-regulatory interactions, each parasegement is a mosaic of cells expressing different combinations of Hox genes.
In Peifer et al. This model predicts that each cell within a parasegment expresses a single Hox gene. In order to test his hypothesis, we carefully reexamined Hox gene expression in the Drosophila embryo using confocal microscopy analysis with antibodies directed against Ubx , abd-A , and Abd-B.
The general rule that a given Hox gene represses expression of the immediately anterior expressed Hox gene appears mostly true. However, there is a notable exception with abd-A and Abd-B in the central nervous system CNS , where both proteins are found co-expressed in many cells Figure 3.
Interestingly, we often found that cells with the highest levels of Abd-A protein also express high levels of Abd-B protein Figure 3. CNS of stage 15 embryos stained for abd-A red and Abd-B green were dissected and mounted on a slide with anterior on top. Parasegments boundaries are shown. Note the presence of neurons in PS10 to PS12 expressing both proteins as seen by the yellow color.
Often the neurons expressing high level of abd-A also express Abd-B. The finding of cells expressing both abd-A and Abd-B contradicted the posterior transcriptional dominance rule of Hox genes as established by previous experiments. This prompted us to reexamine some of these experiments in more detail.
Previously, it was shown that in the absence of Abd-B protein, abd-A protein becomes ectopically expressed in more posterior parasegments Karch et al. This finding supported the idea that Abd-B and the posterior dominance rule restricted abd-A to more anterior abdominal parasegments. When we examined Abd-B null mutants in detail, we found that while we do indeed observe an extension of abd-A expression in PS13 in the epidermis, expression in the CNS remains unaffected Figure 4B.
Splicing of these transcripts lead to the generation of a shorter isoform of Abd-B lacking the N terminal sequences of the m isoform. In agreement with this observation, the few emerging escaper flies have their fifth through eighth abdominal segments transformed into the fourth abdominal segment Karch et al.
This indicates that Abd-B is probably not responsible or at least, not exclusively responsible for abd-A repression in PS Pelts of stage 15 embryos stained for abd-A were prepared as in Figure 1.
Note the expansion of abd-A expression in PS13 in the epidermis. In the CNS, however, circled there is no expansion.
Panel D depicts the extend of the various deficiencies we used in our unsuccessful attempts to locate a second discrete repressive mechanism see page Panel E , same as panel D in Figure 2. This result indicates the existence of alternate mechanism s than Abd-B repression to keep abd-A off in PS13 original observation published in Gummalla et al.
To do this, we used the Fab-8 mutation Barges et al. Fab-8 is a mutation that removes a cis -regulatory domain boundary between iab-7 and iab Through a mechanism that is too complex to explain here, this deletion results in iab-8 , normally driving PS13 levels of Abd-B expression, being activated in PS Based on these results, two possibilities can be imagined to account for the lack of abd-A expression in PS13 of the CNS. The simplest possibility is that abd-A may not be expressed in PS13 simply because it is never turned on.
This would imply that the iab cis -regulatory domains act differently on abd-A in the epidermis versus the CNS. Alternatively, the lack of abd-A in PS13 of the CNS could results from a different, not-yet-identified repressive mechanism. Mutation analysis points to the latter hypothesis as being correct. Df 3R C4 is a large deficiency that removes the entire Abd-B transcription unit as well as iab-8 and about half of the of iab-7 Figure 4D.
As we know Abd-B is not involved in this repression, we must assume that Df 3R C4 must delete additional sequences essential for the this second repressive mechanism.
As the promoter for the iab-8 -ncRNA mapped to a region in iab-8 just next to the Fab-8 boundary, we examined abd-A expression in a larger Fab-8 deletion Fab-8 64 that also removes the ncRNA promoter. In fact, the levels of abd-A protein in PS13 resembled the levels of expression normally seen in PS The Fab-8 64 deletion removing the promoter of the iab-8ncRNA is indicated by red brackets.
Already, Sanchez-Herrero and Akam noticed the presence of a signal at the posterior end of the embryos detected with many large genomic probes. Then, several studies reported similar embryonic expression patterns in the CNS and epidermis in PS13 and 14 with strand-specific probes detecting transcripts oriented from Abd-B toward abd-A Bae et al.
The similarity between the expression patterns reported in these various studies was evident, but it was only in that it became clear that they reflected the existence of a very large transcription unit active in PS13 and PS14 Bender, At the time, it was known that the miRNA was expressed from both DNA strands and were called miR iab and miR iab respectively, based on the orientation of the transcription unit producing the miRNA.
In as much as the miRNA gene is transcribed on both strands, Bender used a classical complementation test to determine if the sterility resulted from failure in the production of one or the other or both miRNA. These observations indicate that the sterility phenotype is caused by loss of the miRNA produced from sense stand relative to abd-A and Abd-B transcription and define the region of DNA required for the production of this template RNA that spans from the region just downstream of the Abd-B transcription unit and extending to, at least, the site of the miRNA.
As the position of the promoter lies within the iab-8 regulatory domain, the transcript was named the iab ncRNA and the miRNA was renamed miR- iab-8 Bender, Remarkably, the pri-miRNA transcript is spiced, with an exon derived from each of the iab cis -regulatory domains.
A comparison with the genomic sequence data from 13 Drosophila species revealed that the transcript is conserved. The expression pattern of the iab ncRNA and thus miR- iab-8 is consistent with the location of the promoter in iab-8 , which controls the expression of Abd-B in PS The iab ncRNA transcripts first appear at the posterior end of the embryo 3 h after fertilization, at the cellular blastoderm stage Figure 7A.
When the first signs of segmentation are visible during germband elongation, Figure 7B , expression is restricted to PS13 and PS14 and mostly visible in the epidermis.
After germband retraction, at the developmental stage where the nerve chord become visible, expression decays rapidly in the epidermis and become predominantly expressed in the CNS in PS13 and PS14, where it remains until for some time Figure 7C. Hox patterning of the vertebrate axial skeleton. Developmental Dynamics , — Atavism: Embryology, Development and Evolution.
Gene Interaction and Disease. Genetic Control of Aging and Life Span. Genetic Imprinting and X Inactivation. Genetic Regulation of Cancer. Obesity, Epigenetics, and Gene Regulation. Environmental Influences on Gene Expression.
Gene Expression Regulates Cell Differentiation. Genes, Smoking, and Lung Cancer. Negative Transcription Regulation in Prokaryotes. Operons and Prokaryotic Gene Regulation. Regulation of Transcription and Gene Expression in Eukaryotes. The Role of Methylation in Gene Expression. DNA Transcription. Reading the Genetic Code. Simultaneous Gene Transcription and Translation in Bacteria. Chromatin Remodeling and DNase 1 Sensitivity. Chromatin Remodeling in Eukaryotes.
RNA Functions. Citation: Myers, P. Hox genes, a family of transcription factors, are major regulators of animal development. Unlike most genes, however, the order of Hox genes in the genome actually holds meaning. Aa Aa Aa. Hox Genes in Drosphila. Hox Genes in Mice and Other Vertebrates.
On the left side of the panel, a diagram of the axial skeleton is shown, with specific vertebral elements shown in the right panel marked C, cervical; T, thoracic; L, lumbar, S, sacral. Wild-type, control elements from specific vertebral positions are denoted by letter and number.
The analogous segment from the paralogous mutants are shown on the right and left, with colored boxes for each paralogous mutant group. Developmental Dynamics , Hox5, Hox6, Hox9, Hox10, and Hox11 paralogous mutants. When paralogous deletions of Hox genes are made, these features do not develop normally, resulting in skeletal deformities. For example, when the paralogous Hox5 genes are deleted, a dorsal neural arch appears on C7 and T1 arrows similar to the normal C2 vertebrae, and ribs are initiated but not completed on T1.
When the paralogous Hox6 genes are deleted, no ribs form at T1. In contrast, when the Hox9 genes are deleted, additional ribs form at L1. Ribs are also formed from L1 to S1 when the Hox10 genes are deleted, and the fused sacral wings are absent at S1 in mice lacking Hox Paralogous Knockouts in Mice.
Hox paralogous mutants. Aqua-shaded areas demonstrate the regions of anterior homeotic transformations of the somite-derived primaxial phenotypes.
Purple-shaded areas show the lateral plate-derived, abaxial phenotypes for each group. The orange background highlights the regions of phenotypic overlap between adjacent paralogous mutants. When Hox6 is deleted, no ribs form at T1 and the ribs at T2 are incomplete. Deletion of Hox9 paralogs causes the inferior thoracic ribs to attach to the sternum, and ribs form on the L1 to L4 vertebrae.
In addition, two extra lumbar vertebrae are formed. Hox10 deletion causes formation of Tlike ribs on the lumbar vertebrae and partial ribs on the sacral vertebrae as well. Hox11 deletion prevents the formation of fused sacral wings, and the sacral vertebrae and the superior tail vertebrae develop into lumbar vertebrae. Regardless of structural changes to individual vertebrae, the total number of vertebrae remains the same in all mice.
Note the differences in AP position as well as the overlap differences in the primaxial versus the abaxial phenotypes. Deletion of Hox5 , which is represented by a red bar, affects C3 to T2 in the primaxial skeleton and T1 to T8 as well as the manubrium and xiphoid processes in the abaxial skeleton.
Deletion of Hox6 , represented by a green bar, affects C6 to T6 in the primaxial skeleton and T1 to T8 and the xiphoid process in the abaxial skeleton. Deletion of Hox9 , represented by an aqua bar, affects T8 to L4 in the primaxial skeleton and T1 to T8 and the xiphoid process in the abaxial skeleton. Deletion of Hox10 , which is represented by a blue bar, affects L1 to S4. Deletion of Hox11 , which is represented by a purple bar, affects S1 through the first 5 segments of the caudal tail.
References and Recommended Reading Pearson, J. Nature Reviews Genetics 6 , — link to article Wellik, D. Article History Close.
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