Breakup of a homeobox cluster after genome duplication in teleosts

Mulley, John F.; Chiu, Chi-hua; Holland, Peter W.H.

doi:10.1073/pnas.0600341103

Cited by 67 publications

(75 citation statements)

References 18 publications

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“…As reducing Cdx1a activity did not allow the pancreatic islet to shift further posterior than in the cdx4/kgg mutant, we suggest that additional mechanisms operate in the posterior of the embryo to control the location of the pancreas. Although a third Cdx gene, cdx1b (Mulley et al, 2006), has been described for zebrafish, our preliminary data show that this gene is not expressed during the first 48 hours of development (M.D.K., M.R.A. and V.E.P., unpublished), making it an unlikely candidate to modulate pancreas position.…”

Section: Cdx4 and Cdx1a Function Redundantly During Pancreas Developmentmentioning

confidence: 76%

“…In a variety of contexts, Cdx factors have been shown to function downstream of RA, FGFs and Wnts, and, in turn, to convey these signals by directly regulating Hox gene expression (Lohnes, 2003). All vertebrates have three Cdx genes: Cdx1, Cdx2 and Cdx4 in tetrapods, and cdx1a, cdx1b and cdx4 in zebrafish (Mulley et al, 2006). In the endoderm, Cdx factors are crucial for patterning the intestine along the AP axis as well as along the crypt-villus axis.…”

Section: Introductionmentioning

confidence: 99%

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Cdx4 is required in the endoderm to localize the pancreas and limitβ-cell number

et al. 2008

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Cdx transcription factors have crucial roles in anteroposterior patterning of the nervous system and mesoderm. Here we focus on the role of cdx4 in patterning the endoderm in zebrafish. We show that cdx4 has roles in determining pancreatic ␤-cell number, directing midline convergence of ␤-cells during early pancreatic islet formation, and specifying the anteroposterior location of foregut organs. Embryos deficient in cdx4 have a posteriorly shifted pancreas, liver and small intestine. The phenotype is more severe with knockdown of an additional Cdx factor, cdx1a. We show that cdx4 functions within the endoderm to localize the pancreas. Morpholino knockdown of cdx4 specifically in the endoderm recapitulates the posteriorly shifted pancreas observed in cdx4 mutants. Conversely, overexpression of cdx4 specifically in the endoderm is sufficient to shift the pancreas anteriorly. Together, these results suggest a model in which cdx4 confers posterior identity to the endoderm. Cdx4 might function to block pancreatic identity by preventing retinoic acid (RA) signal transduction in posterior endoderm. In support of this, we demonstrate that in cdx4-deficient embryos treated with RA, ectopic ␤-cells are located well posterior to the normal pancreatic domain.

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Section: Cdx4 and Cdx1a Function Redundantly During Pancreas Developmentmentioning

confidence: 76%

Section: Introductionmentioning

confidence: 99%

Cdx4 is required in the endoderm to localize the pancreas and limitβ-cell number

et al. 2008

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“…The forces acting to keep the NK genes, the Hox genes, and WNT genes together may also have kept this block of CYP genes from dispersing after their formation through cis duplication. Studies on fish ParaHox gene clusters support the existence of interdigitated control regions in the clusters that select against their loss [99]. Irimia et al proposed the existence of Genomic Regulatory Blocks, with transcriptional enhancers for developmental genes being embedded in neighbouring genes, thus keeping them together [51].…”

Section: Discussionmentioning

confidence: 99%

The cytochrome P450 genesis locus: the origin and evolution of animal cytochrome P450s

Nelson

Goldstone

Stegeman

2013

Phil. Trans. R. Soc. B

163

153

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The neighbourhoods of cytochrome P450 (CYP) genes in deuterostome genomes, as well as those of the cnidarians Nematostella vectensis and Acropora digitifera and the placozoan Trichoplax adhaerens were examined to find clues concerning the evolution of CYP genes in animals. CYP genes created by the 2R whole genome duplications in chordates have been identified. Both microsynteny and macrosynteny were used to identify genes that coexisted near CYP genes in the animal ancestor. We show that all 11 CYP clans began in a common gene environment. The evidence implies the existence of a single locus, which we term the 'cytochrome P450 genesis locus', where one progenitor CYP gene duplicated to create a tandem set of genes that were precursors of the 11 animal CYP clans: CYP Clans 2, 3,4,7,19,20,26,46,51,74 and mitochondrial. These early CYP genes existed side by side before the origin of cnidarians, possibly with a few additional genes interspersed. The Hox gene cluster, WNT genes, an NK gene cluster and at least one ARF gene were close neighbours to this original CYP locus. According to this evolutionary scenario, the CYP74 clan originated from animals and not from land plants nor from a common ancestor of plants and animals. The CYP7 and CYP19 families that are chordate-specific belong to CYP clans that seem to have originated in the CYP genesis locus as well, even though this requires many gene losses to explain their current distribution. The approach to uncovering the CYP genesis locus overcomes confounding effects because of gene conversion, sequence divergence, gene birth and death, and opens the way to understanding the biodiversity of CYP genes, families and subfamilies, which in animals has been obscured by more than 600 Myr of evolution.

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“…Although the amount of data is still limited, the pre-TSGD condition of gene repertoires or selected genomic segments haboring them has been confirmed for some more cases (e.g., Chiu et al, 2004;Hoegg and Meyer, 2007). For example, for the ParaHox gene family, Amia calva, an extant member of one of the lineages that diverged immediately before the TSGD, seems to possess a similar gene organization (Gsx, Xlox , and Cdx ) in the same transcription orientation to that of human and amphioxus (Mulley et al, 2006). The ParaHox gene repertoire of teleost fishes whose ancestor experienced the third vertebrate genome duplication is different.…”

Section: Evolution Before the Tsgdmentioning

confidence: 97%