SUMMARYA central challenge of developmental and evolutionary biology is to understand how anatomy is encoded in the genome. Elucidating the genetic mechanisms that control the development of specific anatomical features will require the analysis of model morphogenetic processes and an integration of biological information at genomic, cellular and tissue levels. The formation of the endoskeleton of the sea urchin embryo is a powerful experimental system for developing such an integrated view of the genomic regulatory control of morphogenesis. The dynamic cellular behaviors that underlie skeletogenesis are well understood and a complex transcriptional gene regulatory network (GRN) that underlies the specification of embryonic skeletogenic cells (primary mesenchyme cells, PMCs) has recently been elucidated. Here, we link the PMC specification GRN to genes that directly control skeletal morphogenesis. We identify new gene products that play a proximate role in skeletal morphogenesis and uncover transcriptional regulatory inputs into many of these genes. Our work extends the importance of the PMC GRN as a model developmental GRN and establishes a unique picture of the genomic regulatory control of a major morphogenetic process. Furthermore, because echinoderms exhibit diverse programs of skeletal development, the newly expanded sea urchin skeletogenic GRN will provide a foundation for comparative studies that explore the relationship between GRN evolution and morphological evolution.
KEY WORDS: Gene regulatory network, Primary mesenchyme, Sea urchin, Skeletal morphogenesis, SkeletonThe genomic regulatory control of skeletal morphogenesis in the sea urchin Kiran Rafiq, Melani S. Cheers and Charles A. Ettensohn* DEVELOPMENT 580 this library allowed us to identify several components of the PMC GRN, including delta (Sweet et al., 2002), the transcription factors alx1 and erg (Zhu et al., 2001; Ettensohn et al., 2003), and several biomineralization-related genes (Illies et al., 2002; Cheers and Ettensohn, 2005;Livingston et al., 2006). In the present study, we greatly expand the current PMC GRN model by identifying many additional morphoregulatory genes and by uncovering regulatory inputs into these genes. Our work extends the value of the PMC GRN as a model developmental GRN and establishes a framework for understanding the genomic circuitry that encodes a major anatomical feature.
MATERIALS AND METHODS
Embryo cultureStrongylocentrotus purpuratus embryos were obtained and cultured at 15°C as described previously (Zhu et al., 2001).
The PMC cDNA library and expressed sequence tag (EST) collectionThe construction and arraying of the PMC cDNA library has been described (Zhu et al., 2001;Livingston et al., 2006). Briefly, the library was generated from polyA(+) RNA that was isolated from micromeres (presumptive PMCs) that were cultured until sibling control embryos reached the mid-gastrula stage, ~36 hours post-fertilization. The cDNA library was not normalized or subtracted in any way. Reverse transcription was primed usin...