Phylogenetic footprinting and genome scanning identify vertebrate BMP response elements and new target genes
Phylogenetic footprinting and genome scanning identify vertebrate BMP response elements and new target genes
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DOI：
10.1016/j.ydbio.2005.02.014
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发表时间：
2005-05-15
影响因子：
2.7
通讯作者：
Cho, KWY
中科院分区：
文献类型：
--
作者：
von Bubnoff, A;Peiffer, DA;Cho, KWY
The complex gene regulatory networks governed by growth factor signaling are still poorly understood. In order to accelerate the rate of progress in uncovering these networks, we explored the usefulness of interspecies sequence comparison (phylogenetic footprinting) to identify conserved growth factor response elements. The promoter regions of two direct target genes of Bone Morphogenetic Protein (BMP) signaling in Xenopus, Xvent2 and Xld3, were compared with the corresponding human and/or mouse counterparts to identify conserved sequences. A comparison between the Xenopus and human Vent2 promoter sequences revealed a highly conserved 21 by sequence that overlaps the previously reported Xvent2 BMP response element (BRE). Reporter gene assays using Xenopus animal pole ectodermal explants (animal caps) revealed that this conserved 21 by BRE is both necessary and sufficient for BMP responsiveness. We combine the same phylogenetic footprinting approach with luciferase assays to identify a highly conserved 49 by BMP responsive region in the Xenopus ld3 promoter. GFP reporters containing multimers of either the Xvent2 or Xld3 BREs appear to recapitulate endogenous BMP signaling activity in transgenic Xenopus embryos. Comparison of the Xvent2 and the Xld3 BRE revealed core sequence features that are both necessary and sufficient for BMP responsiveness: a Smad binding element (SBE) and a GC-rich element resembling an OAZ binding site. Based on these findings, we have implemented genome scanning to identify over 100 additional putative target genes containing 2 or more BRE-like sequences which are conserved between human and mouse. RT-PCR and in situ analyses revealed that this in silico approach can effectively be used to identify potential BMP target genes. (C) 2005 Elsevier Inc. All rights reserved.
