Signal-dependent regulation of the sea urchin skeletogenic gene regulatory network

Sun, Zhongling; Ettensohn, Charles A.

doi:10.1016/j.gep.2014.10.002

Cited by 75 publications

(98 citation statements)

References 44 publications

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“…Sp-Krl is DL-N independent, therefore it is possible that PKS is activated by additional positive regulatory inputs. Such a GRN architecture including parallel positive regulatory inputs into differentiation genes has been also observed for the skeletogenic precursors in S. purpuratus (http://www.spbase.org/endomes/#; Sun and Ettensohn, 2014). Sp-Pks1 expression is maintained by a positive feedback loop of Sp-Gcm throughout development (Ransick et al, 2002; Ransick and Davidson, 2006), while Sp-GataE and Sp-Krl are most likely required only up to mesenchyme blastula–early gastrula stages (Calestani and Rogers, 2010).…”

Section: What Is the Major Enzymatic Activity Of Polyketide Synthases?supporting

confidence: 56%

These Colors Don’t Run: Regulation of Pigment—Biosynthesis in Echinoderms

Calestani

Wessel

2018

Results and Problems in Cell Differentiation

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Pigment production is an important biological process throughout the tree of life. Some pigments function for collecting light energy, or for visual identification, while others have dramatic antimicrobial functions, or camouflage capabilities. The functions of these pigments and their biosynthesis are of great interest if only because of their diversity. The biochemistry of echinoderm pigmentation has been intensively studied for many years, and with more recent technologies, the origin and functions of these pigments are being exposed. Here we summarize the major pigment types in biology and emphasize the status of the field in echinoderms, taking full advantage of the new genomic and technologic resources for studying these important animals and their beautiful pigmentation.

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Section: What Is the Major Enzymatic Activity Of Polyketide Synthases?supporting

confidence: 56%

These Colors Don’t Run: Regulation of Pigment—Biosynthesis in Echinoderms

Calestani

Wessel

2018

Results and Problems in Cell Differentiation

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“…In spite of its markedly reduced skeleton, the sea cucumber A . japonicus shares many components of the skeletogenic regulatory system with heavily calcified sea urchins and other echinoderms [36–38]. It has relatively intact skeletogenic signal pathways, key transcription factors, and important skeletogenesis-related genes (e.g., otx , soxB , ets1 , alx1 , dlx , runx2 , snail , and twist ) (S18 Table).…”

Section: Resultsmentioning

confidence: 99%

The sea cucumber genome provides insights into morphological evolution and visceral regeneration

et al. 2017

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Apart from sharing common ancestry with chordates, sea cucumbers exhibit a unique morphology and exceptional regenerative capacity. Here we present the complete genome sequence of an economically important sea cucumber, A. japonicus, generated using Illumina and PacBio platforms, to achieve an assembly of approximately 805 Mb (contig N50 of 190 Kb and scaffold N50 of 486 Kb), with 30,350 protein-coding genes and high continuity. We used this resource to explore key genetic mechanisms behind the unique biological characters of sea cucumbers. Phylogenetic and comparative genomic analyses revealed the presence of marker genes associated with notochord and gill slits, suggesting that these chordate features were present in ancestral echinoderms. The unique shape and weak mineralization of the sea cucumber adult body were also preliminarily explained by the contraction of biomineralization genes. Genome, transcriptome, and proteome analyses of organ regrowth after induced evisceration provided insight into the molecular underpinnings of visceral regeneration, including a specific tandem-duplicated prostatic secretory protein of 94 amino acids (PSP94)-like gene family and a significantly expanded fibrinogen-related protein (FREP) gene family. This high-quality genome resource will provide a useful framework for future research into biological processes and evolution in deuterostomes, including remarkable regenerative abilities that could have medical applications. Moreover, the multiomics data will be of prime value for commercial sea cucumber breeding programs.

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“…PMC patterning and the formation of connecting syncytia are requisite for spiculogenesis, since PMCs deposit calcite within the syncytium space that acts as a mold (Wilt, 1999(Wilt, , 2002Lyons et al, 2014;Vidavsky et al, 2014). However, other factors may control the expression of biomineralization genes needed for skeletogenesis later in development (Rafiq et al, 2012;Sun and Ettensohn, 2014). Thus, the PMC patterning defects in the miR-31 KD embryos may contribute in part to the shortening of the skeleton spicules (Fig.…”

Section: Discussionmentioning

confidence: 99%

microRNA-31 modulates skeletal patterning in the sea urchin embryos

Stepicheva

Song

2015

Development

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MicroRNAs (miRNAs) are small non-coding RNAs that repress the translation and reduce the stability of target mRNAs in animal cells. microRNA-31 (miR-31) is known to play a role in cancer, bone formation and lymphatic development. However, studies to understand the function of miR-31 in embryogenesis have been limited. We examined the regulatory role of miR-31 in early development using the sea urchin as a model. miR-31 is expressed at all stages of development and its knockdown (KD) disrupts the patterning and function of primary mesenchyme cells (PMCs), which form the embryonic skeleton spicules. We identified that miR-31 directly represses Pmar1, Alx1, Snail and VegfR7 within the PMC gene regulatory network using reporter constructs. Further, blocking the miR-31-mediated repression of Alx1 and/or VegfR7 in the developing embryo resulted in defects in PMC patterning and skeletogenesis. The majority of the mislocalized PMCs in miR-31 KD embryos did not express VegfR10, indicating that miR-31 regulates VegfR gene expression within PMCs. In addition, miR-31 indirectly suppresses Vegf3 expression in the ectoderm. These results indicate that miR-31 coordinately suppresses genes within the PMCs and in the ectoderm to impact PMC patterning and skeletogenesis. This study identifies the novel function and molecular mechanism of miR-31-mediated regulation in the developing embryo.

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Signal-dependent regulation of the sea urchin skeletogenic gene regulatory network

Cited by 75 publications

References 44 publications

These Colors Don’t Run: Regulation of Pigment—Biosynthesis in Echinoderms

These Colors Don’t Run: Regulation of Pigment—Biosynthesis in Echinoderms

The sea cucumber genome provides insights into morphological evolution and visceral regeneration

microRNA-31 modulates skeletal patterning in the sea urchin embryos

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