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Published May 15, 2004 | public
Journal Article

An otx cis-regulatory module: a key node in the sea urchin endomesoderm gene regulatory network

Abstract

An essential node in the gene regulatory network (GRN) for endomesoderm specification in the sea urchin embryo lies within the regulatory system of the otx gene. According to the predictions of the GRN, based on perturbation analysis and expression data, the β1/2 transcription unit of this gene is engaged during specification in interactions with two other regulatory genes, krox and gatae. It is predicted to be driven into activity by the krox gene, to form a positively reinforcing functional loop with the gatae gene, and to respond to its own output as well. Here we isolate the relevant otx cis-regulatory element, and examine the specific input predictions of the GRN at the level of its genomic DNA sequence. This β1/2-otx regulatory module performs the necessary functions, as shown by use of expression constructs. It requires gatae, otx, and krox inputs, as predicted, and it operates as an "AND" logic processor in that removal of any one of these inputs essentially destroys activity. The necessary target sites were identified in the module sequence, and mutation of these sites was demonstrated to produce the same respective effects on construct expression as does blocking its regulatory inputs by treatment with morpholino antisense oligonucleotides. For spatial expression in the endoderm, one particular pair of Gata sites is essential and these function synergistically with an adjacent Otx site. We thus demonstrate directly the structure/function relationships of the genomic regulatory code, at this key node of the endomesoderm GRN.

Additional Information

© 2004 Elsevier Inc. Received for publication 20 February 2004, accepted 26 February 2004. Available online 23 April 2004. The authors are grateful to Dr. Paola Oliveri and Prof. Ellen Rothenberg for extremely useful critical reviews of a draft of the manuscript. This research was supported by NIH grants HD-37105 and GM-61005 and by the Office of Science (BER), U.S. Department of Energy, Grant No. DEFG02-03ER63584.

Additional details

Created:
August 22, 2023
Modified:
October 17, 2023