Genome-wide identification of calcium-response factor (CaRF) binding sites predicts a role in regulation of neuronal signaling pathways
Abstract
Calcium-Response Factor (CaRF) was first identified as a transcription factor based
on its affinity for a neuronal-selective calcium-response element (CaRE1) in the gene
encoding Brain-Derived Neurotrophic Factor (BDNF). However, because CaRF shares no
homology with other transcription factors, its properties and gene targets have remained
unknown. Here we show that the DNA binding domain of CaRF has been highly conserved
across evolution and that CaRF binds DNA directly in a sequence-specific manner in
the absence of other eukaryotic cofactors. Using a binding site selection screen we
identify a high-affinity consensus CaRF response element (cCaRE) that shares significant
homology with the CaRE1 element of Bdnf. In a genome-wide chromatin immunoprecipitation
analysis (ChIP-Seq), we identified 176 sites of CaRF-specific binding (peaks) in neuronal
genomic DNA. 128 of these peaks are within 10kB of an annotated gene, and 60 are within
1kB of an annotated transcriptional start site. At least 138 of the CaRF peaks contain
a common 10-bp motif with strong statistical similarity to the cCaRE, and we provide
evidence predicting that CaRF can bind independently to at least 64.5% of these motifs
in vitro. Analysis of this set of putative CaRF targets suggests the enrichment of
genes that regulate intracellular signaling cascades. Finally we demonstrate that
expression of a subset of these target genes is altered in the cortex of Carf knockout
(KO) mice. Together these data strongly support the characterization of CaRF as a
unique transcription factor and provide the first insight into the program of CaRF-regulated
transcription in neurons. © 2010 Pfenning et al.
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Journal articlePermalink
https://hdl.handle.net/10161/4544Published Version (Please cite this version)
10.1371/journal.pone.0010870Publication Info
Pfenning, Andreas R; Kim, Tae-Kyung; Spotts, James M; Hemberg, Martin; Su, Dan; &
West, Anne E (2010). Genome-wide identification of calcium-response factor (CaRF) binding sites predicts
a role in regulation of neuronal signaling pathways. PLoS ONE, 5(5). pp. e10870. 10.1371/journal.pone.0010870. Retrieved from https://hdl.handle.net/10161/4544.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
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Show full item recordScholars@Duke
Anne Elizabeth West
Professor of Neurobiology
The long term goal of our laboratory is to understand at a cellular/molecular level
how neuronal activity regulates the formation and maturation of synapses during brain
development, and ultimately to use genetic model systems to understand how defects
in this developmental process lead to cognitive dysfunction.

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