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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.


Cdx expression, cross-regulation, and pair-wise comparison. a Normalized expression of three Cdx paralogues at stage 14 derived from the control uninjected embryos. b Fold-change effect of alternative Cdx MOs on Cdx expression. Error bars indicate standard error; significance level noted as (**) and (*) for Benjamini-Hochberg-adjusted P <0.005 and <0.05, respectively. c Temporal expression profile of Cdx paralogues recovered from data of [25]. d–g Pairwise comparison of gene-specific fold-change triggered by distinct Cdx MOs. Genes with expression affected by both Cdx MOs are plotted as red dots, other genes plotted as grey dots
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Fig2: Cdx expression, cross-regulation, and pair-wise comparison. a Normalized expression of three Cdx paralogues at stage 14 derived from the control uninjected embryos. b Fold-change effect of alternative Cdx MOs on Cdx expression. Error bars indicate standard error; significance level noted as (**) and (*) for Benjamini-Hochberg-adjusted P <0.005 and <0.05, respectively. c Temporal expression profile of Cdx paralogues recovered from data of [25]. d–g Pairwise comparison of gene-specific fold-change triggered by distinct Cdx MOs. Genes with expression affected by both Cdx MOs are plotted as red dots, other genes plotted as grey dots

Mentions: We used injection of translation-blocking morpholino oligonucleotides (MOs) in X. tropicalis to investigate whether, or to what extent, duplicate genes of the Cdx homeobox gene family have distinct effects on developmental pathways in the embryo, assessed through alterations to transcriptional profiles (Fig. 1b). In X. tropicalis, all three Cdx genes are initially expressed in the early mesoderm at the start of gastrulation (stage 10) [22]. Following the end of gastrulation, the Cdx genes are expressed in both the ectoderm and mesoderm in the posterior of the neurula stage embryo (stage 14). We chose the early neurula stage, 6 hours after the initiation of Cdx expression, for transcriptomic analyses because it represents the peak of Cdx expression (Fig. 2c) and the stage when Hox genes, known targets of Cdx, are activated. Replicate sets of embryos were injected with a standard control morpholino or MOs targeted against the Cdx1, Cdx2, and Cdx4 mRNAs, either individually or in combination (Fig. 1b). After culturing to stage 14, injected and uninjected control embryos were collected [23] and Illumina RNA-seq used to profile gene expression. As previously reported [23], no large scale disruption of anteroposterior organisation is apparent by this stage.Fig. 2


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)

Cdx expression, cross-regulation, and pair-wise comparison. a Normalized expression of three Cdx paralogues at stage 14 derived from the control uninjected embryos. b Fold-change effect of alternative Cdx MOs on Cdx expression. Error bars indicate standard error; significance level noted as (**) and (*) for Benjamini-Hochberg-adjusted P <0.005 and <0.05, respectively. c Temporal expression profile of Cdx paralogues recovered from data of [25]. d–g Pairwise comparison of gene-specific fold-change triggered by distinct Cdx MOs. Genes with expression affected by both Cdx MOs are plotted as red dots, other genes plotted as grey dots
© Copyright Policy - open-access
Related In: Results  -  Collection

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getmorefigures.php?uid=PMC4522105&req=5

Fig2: Cdx expression, cross-regulation, and pair-wise comparison. a Normalized expression of three Cdx paralogues at stage 14 derived from the control uninjected embryos. b Fold-change effect of alternative Cdx MOs on Cdx expression. Error bars indicate standard error; significance level noted as (**) and (*) for Benjamini-Hochberg-adjusted P <0.005 and <0.05, respectively. c Temporal expression profile of Cdx paralogues recovered from data of [25]. d–g Pairwise comparison of gene-specific fold-change triggered by distinct Cdx MOs. Genes with expression affected by both Cdx MOs are plotted as red dots, other genes plotted as grey dots
Mentions: We used injection of translation-blocking morpholino oligonucleotides (MOs) in X. tropicalis to investigate whether, or to what extent, duplicate genes of the Cdx homeobox gene family have distinct effects on developmental pathways in the embryo, assessed through alterations to transcriptional profiles (Fig. 1b). In X. tropicalis, all three Cdx genes are initially expressed in the early mesoderm at the start of gastrulation (stage 10) [22]. Following the end of gastrulation, the Cdx genes are expressed in both the ectoderm and mesoderm in the posterior of the neurula stage embryo (stage 14). We chose the early neurula stage, 6 hours after the initiation of Cdx expression, for transcriptomic analyses because it represents the peak of Cdx expression (Fig. 2c) and the stage when Hox genes, known targets of Cdx, are activated. Replicate sets of embryos were injected with a standard control morpholino or MOs targeted against the Cdx1, Cdx2, and Cdx4 mRNAs, either individually or in combination (Fig. 1b). After culturing to stage 14, injected and uninjected control embryos were collected [23] and Illumina RNA-seq used to profile gene expression. As previously reported [23], no large scale disruption of anteroposterior organisation is apparent by this stage.Fig. 2

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.