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Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution.

Marlétaz F, Maeso I, Faas L, Isaacs HV, Holland PW - BMC Biol. (2015)

Bottom Line: We found that one paralogue, Cdx4, has a much stronger effect on gene expression than the others, including a strong regulatory effect on FGF and Wnt genes.The data also reveal a colinear-like effect of Cdx genes on Hox genes, with repression of Hox paralogy groups 1 and 2, and activation increasing from Hox group 5 to 11.We therefore suggest that developmental programmes were extensively rewired after whole genome duplication in the early evolution of vertebrates.

View Article: PubMed Central - PubMed

Affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK. ferdinand.marletaz@gmail.com.

ABSTRACT

Background: The functional consequences of whole genome duplications in vertebrate evolution are not fully understood. It remains unclear, for instance, why paralogues were retained in some gene families but extensively lost in others. Cdx homeobox genes encode conserved transcription factors controlling posterior development across diverse bilaterians. These genes are part of the ParaHox gene cluster. Multiple Cdx copies were retained after genome duplication, raising questions about how functional divergence, overlap, and redundancy respectively contributed to their retention and evolutionary fate.

Results: We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xenopus tropicalis followed by RNA-seq. We found that one paralogue, Cdx4, has a much stronger effect on gene expression than the others, including a strong regulatory effect on FGF and Wnt genes. Functional annotation revealed distinct and overlapping roles and subtly different temporal windows of action for each gene. The data also reveal a colinear-like effect of Cdx genes on Hox genes, with repression of Hox paralogy groups 1 and 2, and activation increasing from Hox group 5 to 11. We also highlight cases in which duplicated genes regulate distinct paralogous targets revealing pathway elaboration after whole genome duplication.

Conclusions: Despite shared core pathways, Cdx paralogues have acquired distinct regulatory roles during development. This implies that the degree of functional overlap between paralogues is relatively low and that gene expression pattern alone should be used with caution when investigating the functional evolution of duplicated genes. We therefore suggest that developmental programmes were extensively rewired after whole genome duplication in the early evolution of vertebrates.

No MeSH data available.


Gene set enrichment analysis of Cdx MO effects. Functional annotation derived from Panther pathways and the GO biological process version of Panther database were employed for term enrichment analysis using distinct tests accounting for direction of expression change: distinct directional (DD), mixed directional (MD), non-directional (ND), as well as UP or DOWN regulation. The scheme yielding the best enrichment score was retained as the one providing the best description of the enrichment for the term (bubble fill colour). Displayed terms were retained as showing an enrichment >5 in at least one condition
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Fig4: Gene set enrichment analysis of Cdx MO effects. Functional annotation derived from Panther pathways and the GO biological process version of Panther database were employed for term enrichment analysis using distinct tests accounting for direction of expression change: distinct directional (DD), mixed directional (MD), non-directional (ND), as well as UP or DOWN regulation. The scheme yielding the best enrichment score was retained as the one providing the best description of the enrichment for the term (bubble fill colour). Displayed terms were retained as showing an enrichment >5 in at least one condition

Mentions: To further evaluate the degree of functional divergence between the Cdx paralogues, we conducted an enrichment analysis using gene sets derived from biological annotation: Panther pathways and Gene Ontology Biological Processes (Fig. 4). These analyses measure the consistency of significance statistics (P value) and gene expression variation (fold-change) over a gene set corresponding to a given annotation term. We identified important pathways and biological functions, such as Wnt signalling pathways (Panther) and ‘mitosis’ processes (GO Biological Processes), that are represented in gene sets regulated by all three paralogues. Such broad terms often do not exhibit a comprehensive up- or down-regulation, most likely because they encompass genes with antagonist interactions within the same pathway (e.g. intracellular effectors). Few annotation terms show such a shared enrichment, while many other pathways or biological processes appear regulated by one or two paralogues only. For instance, the genes affected by Cdx1 and Cdx2 disruption are enriched in down-regulated members of the ‘heme biosynthesis’ pathway (Fig. 4), consistent with a role of Cdx genes in blood cell specification [27]. Similarly, these same two Cdx genes are involved in the repression of the PDGF signalling pathway, as their disruption causes up-regulated expression of genes belonging to this category (Fig. 4). Enrichment analysis indicates only limited functional overlap of Cdx4 with Cdx1 and Cdx2, with several pathways seemingly only affected by Cdx4; these include Hedgehog signalling, the Gonadotropin pathway, and Slit/Robo axon guidance (Fig. 4). Finally, the triple morpholino treatment recapitulates the enrichment effects observed for individual Cdx genes in most cases. However, a few pathways, such as TGF-beta signalling, are only detected when all three Cdx are disrupted simultaneously (Fig. 4). These categories could correspond to gene sets of which individual members are regulated by distinct Cdx genes, and which only pass significance threshold when all members are activated simultaneously. Alternatively, these gene sets could reflect functional redundancy between co-expressed Cdx genes, or compensatory regulation after disruption of any one Cdx gene.Fig. 4


Cdx ParaHox genes acquired distinct developmental roles after gene duplication in vertebrate evolution.

Marlétaz F, Maeso I, Faas L, Isaacs HV, Holland PW - BMC Biol. (2015)

Gene set enrichment analysis of Cdx MO effects. Functional annotation derived from Panther pathways and the GO biological process version of Panther database were employed for term enrichment analysis using distinct tests accounting for direction of expression change: distinct directional (DD), mixed directional (MD), non-directional (ND), as well as UP or DOWN regulation. The scheme yielding the best enrichment score was retained as the one providing the best description of the enrichment for the term (bubble fill colour). Displayed terms were retained as showing an enrichment >5 in at least one condition
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4522105&req=5

Fig4: Gene set enrichment analysis of Cdx MO effects. Functional annotation derived from Panther pathways and the GO biological process version of Panther database were employed for term enrichment analysis using distinct tests accounting for direction of expression change: distinct directional (DD), mixed directional (MD), non-directional (ND), as well as UP or DOWN regulation. The scheme yielding the best enrichment score was retained as the one providing the best description of the enrichment for the term (bubble fill colour). Displayed terms were retained as showing an enrichment >5 in at least one condition
Mentions: To further evaluate the degree of functional divergence between the Cdx paralogues, we conducted an enrichment analysis using gene sets derived from biological annotation: Panther pathways and Gene Ontology Biological Processes (Fig. 4). These analyses measure the consistency of significance statistics (P value) and gene expression variation (fold-change) over a gene set corresponding to a given annotation term. We identified important pathways and biological functions, such as Wnt signalling pathways (Panther) and ‘mitosis’ processes (GO Biological Processes), that are represented in gene sets regulated by all three paralogues. Such broad terms often do not exhibit a comprehensive up- or down-regulation, most likely because they encompass genes with antagonist interactions within the same pathway (e.g. intracellular effectors). Few annotation terms show such a shared enrichment, while many other pathways or biological processes appear regulated by one or two paralogues only. For instance, the genes affected by Cdx1 and Cdx2 disruption are enriched in down-regulated members of the ‘heme biosynthesis’ pathway (Fig. 4), consistent with a role of Cdx genes in blood cell specification [27]. Similarly, these same two Cdx genes are involved in the repression of the PDGF signalling pathway, as their disruption causes up-regulated expression of genes belonging to this category (Fig. 4). Enrichment analysis indicates only limited functional overlap of Cdx4 with Cdx1 and Cdx2, with several pathways seemingly only affected by Cdx4; these include Hedgehog signalling, the Gonadotropin pathway, and Slit/Robo axon guidance (Fig. 4). Finally, the triple morpholino treatment recapitulates the enrichment effects observed for individual Cdx genes in most cases. However, a few pathways, such as TGF-beta signalling, are only detected when all three Cdx are disrupted simultaneously (Fig. 4). These categories could correspond to gene sets of which individual members are regulated by distinct Cdx genes, and which only pass significance threshold when all members are activated simultaneously. Alternatively, these gene sets could reflect functional redundancy between co-expressed Cdx genes, or compensatory regulation after disruption of any one Cdx gene.Fig. 4

Bottom Line: We found that one paralogue, Cdx4, has a much stronger effect on gene expression than the others, including a strong regulatory effect on FGF and Wnt genes.The data also reveal a colinear-like effect of Cdx genes on Hox genes, with repression of Hox paralogy groups 1 and 2, and activation increasing from Hox group 5 to 11.We therefore suggest that developmental programmes were extensively rewired after whole genome duplication in the early evolution of vertebrates.

View Article: PubMed Central - PubMed

Affiliation: Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK. ferdinand.marletaz@gmail.com.

ABSTRACT

Background: The functional consequences of whole genome duplications in vertebrate evolution are not fully understood. It remains unclear, for instance, why paralogues were retained in some gene families but extensively lost in others. Cdx homeobox genes encode conserved transcription factors controlling posterior development across diverse bilaterians. These genes are part of the ParaHox gene cluster. Multiple Cdx copies were retained after genome duplication, raising questions about how functional divergence, overlap, and redundancy respectively contributed to their retention and evolutionary fate.

Results: We examined the degree of regulatory and functional overlap between the three vertebrate Cdx genes using single and triple morpholino knock-down in Xenopus tropicalis followed by RNA-seq. We found that one paralogue, Cdx4, has a much stronger effect on gene expression than the others, including a strong regulatory effect on FGF and Wnt genes. Functional annotation revealed distinct and overlapping roles and subtly different temporal windows of action for each gene. The data also reveal a colinear-like effect of Cdx genes on Hox genes, with repression of Hox paralogy groups 1 and 2, and activation increasing from Hox group 5 to 11. We also highlight cases in which duplicated genes regulate distinct paralogous targets revealing pathway elaboration after whole genome duplication.

Conclusions: Despite shared core pathways, Cdx paralogues have acquired distinct regulatory roles during development. This implies that the degree of functional overlap between paralogues is relatively low and that gene expression pattern alone should be used with caution when investigating the functional evolution of duplicated genes. We therefore suggest that developmental programmes were extensively rewired after whole genome duplication in the early evolution of vertebrates.

No MeSH data available.