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Published December 1, 2009 | Supplemental Material
Journal Article Open

Flexibility of transcription factor target site position in conserved cis-regulatory modules

Abstract

Eight Strongylocentrotus purpuratus cis-regulatory modules, in each of which up to three different transcription factor target sites had been previously authenticated in gene transfer and mutagenesis studies, were compared to the orthologous modules in the genome of Lytechinus variegatus. These species diverged about 50 million years ago. The orthologous modules were identified in sequenced Lytechinus BACs, as conserved sequence patches in similar regions of the respective genes. The similar functionality of several of these control modules in the two species was confirmed by cross-species gene transfer experiments. In each case the repertoire of transcription factor target sites was the same in the orthologous modules, but the positions of the individual sites with respect to one another was evolutionarily flexible, even though the intervening sequence was often strongly conserved. The most invariably conserved features, as seen also in other systems, were pairs of target sites that are immediately adjacent to one another. Their conservation is probably due to the necessity for interaction of proximally bound transcription factors, while a facilitated form of sequence conversion might be the mechanism of site position change.

Additional Information

© 2009 Elsevier Inc. All rights reserved. Received 7 July 2009; revised 9 September 2009; accepted 10 September 2009. Available online 18 September 2009. We gratefully acknowledge the patience of the investigators in the Davidson laboratory who lent sequences, intermediate analyses and explanations about the functions of the cis-regulatory modules discussed in the paper. We thank Rachel Gray and William Chu for expert technical assistance with the BAC transgene injections . Julie Hahn made the recombineered BACs used in this study. This research was supported by NSF IOS-0517316.

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