A compendium of Caenorhabditis elegans regulatory transcription factors: a resource for mapping transcription regulatory networks

Background Transcription regulatory networks are composed of interactions between transcription factors and their target genes. Whereas unicellular networks have been studied extensively, metazoan transcription regulatory networks remain largely unexplored. Caenorhabditis elegans provides a powerful model to study such metazoan networks because its genome is completely sequenced and many functional genomic tools are available. While C. elegans gene predictions have undergone continuous refinement, this is not true for the annotation of functional transcription factors. The comprehensive identification of transcription factors is essential for the systematic mapping of transcription regulatory networks because it enables the creation of physical transcription factor resources that can be used in assays to map interactions between transcription factors and their target genes. Results By computational searches and extensive manual curation, we have identified a compendium of 934 transcription factor genes (referred to as wTF2.0). We find that manual curation drastically reduces the number of both false positive and false negative transcription factor predictions. We discuss how transcription factor splice variants and dimer formation may affect the total number of functional transcription factors. In contrast to mouse transcription factor genes, we find that C. elegans transcription factor genes do not undergo significantly more splicing than other genes. This difference may contribute to differences in organism complexity. We identify candidate redundant worm transcription factor genes and orthologous worm and human transcription factor pairs. Finally, we discuss how wTF2.0 can be used together with physical transcription factor clone resources to facilitate the systematic mapping of C. elegans transcription regulatory networks. Conclusion wTF2.0 provides a starting point to decipher the transcription regulatory networks that control metazoan development and function

Molecular control of development in the reef coral, Acropora millepora

A brief overview of the embryonic and larval development of Acropora, including some previously unpublished data, provides the background for this review of our rapidly expanding knowledge of the genes that control early development in corals, with particular emphasis on Hox and Hox-like genes. Since the Phylum Cnidaria is widely accepted to be an ancient group of organisms, genes, and motifs within genes, that are shared by corals and higher metazoans are presumably ancient. Thus, shared genes allow us to study how gene structure and function have changed with time, while genes specific to higher metazoans have, presumably, evolved more recently. Anatomically, corals have many fewer cell types than higher metazoans, but it is not clear that this apparent simplicity will be reflected at the molecular level. We have already found Acropora representatives of structural genes, housekeeping genes, nuclear receptors, Hox-like genes, Pax genes and components of the dpp signalling pathway. However, thus far there is no unequivocal evidence for the cluster of Hox genes, known as the zootype genes, that is otherwise widespread among the Metazoa. As more data become available, the Cnidaria are making an increasing contribution to our knowledge of the evolution of gene structure, function, and regulation. We here illustrate the evolutionary approach that we are taking to the characterisation of coral genes with a review of our work on the Acropora Hox- like gene, cnox2-Am

Molecular control of development in the reef coral, Acropora millepora

A brief overview of the embryonic and larval development of Acropora, including some previously unpublished data, provides the background for this review of our rapidly expanding knowledge of the genes that control early development in corals, with particular emphasis on Hox and Hox-like genes. Since the Phylum Cnidaria is widely accepted to be an ancient group of organisms, genes, and motifs within genes, that are shared by corals and higher metazoans are presumably ancient. Thus, shared genes allow us to study how gene structure and function have changed with time, while genes specific to higher metazoans have, presumably, evolved more recently. Anatomically, corals have many fewer cell types than higher metazoans, but it is not clear that this apparent simplicity will be reflected at the molecular level. We have already found Acropora representatives of structural genes, housekeeping genes, nuclear receptors, Hox-like genes, Pax genes and components of the dpp signalling pathway. However, thus far there is no unequivocal evidence for the cluster of Hox genes, known as the zootype genes, that is otherwise widespread among the Metazoa. As more data become available, the Cnidaria are making an increasing contribution to our knowledge of the evolution of gene structure, function, and regulation. We here illustrate the evolutionary approach that we are taking to the characterisation of coral genes with a review of our work on the Acropora Hox- like gene, cnox2-Am