Please use this identifier to cite or link to this item: https://hdl.handle.net/2440/95045
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Type: Journal article
Title: Identification of highly conserved putative developmental enhancers bound by SOX3 in neural progenitors using ChIP-Seq
Author: McAninch, D.
Thomas, P.
Citation: PLoS One, 2014; 9(11):e113361-1-e113361-9
Publisher: Public Library of Science
Issue Date: 2014
ISSN: 1932-6203
1932-6203
Statement of
Responsibility: 
Dale McAninch, Paul Thomas
Abstract: The transcription factor SOX3 is expressed within most neural progenitor (NP) cells of the vertebrate central nervous system (CNS) and is essential for normal brain development in mice and humans. However, despite the widespread expression of Sox3, CNS defects in null mice are relatively mild due to functional redundancy with the other SOXB1 sub-group members Sox1 and Sox2. To further understand the molecular function of SOX3, we investigated the genome-wide binding profile of endogenous SOX3 in NP cells using ChIP-seq. SOX3 binding was identified at over 8,000 sites, most of which were intronic or intergeneic and were significantly associated with neurodevelopmental genes. The majority of binding sites were moderately or highly conserved (phastCons scores .0.1 and 0.5, respectively) and included the previously characterised, SOXB1-binding Nestin NP cell enhancer. Comparison of SOX3 and published ChIP-Seq data for the co-activator P300 in embryonic brain identified hundreds of highly conserved putative enhancer elements. In addition, we identified a subset of highly conserved putative enhancers for CNS development genes common to SOXB1 members in NP cells, all of which contained the SOX consensus motif (ACAAWR). Together these data implicate SOX3 in the direct regulation of hundreds of NP genes and provide molecular insight into the overlapping roles of SOXB1 proteins in CNS development.
Keywords: Cells, Cultured
Animals
Mice
Chromatin Immunoprecipitation
Sequence Analysis, DNA
Binding Sites
Base Sequence
Gene Regulatory Networks
Enhancer Elements, Genetic
SOXB1 Transcription Factors
Neural Stem Cells
Rights: © 2014 McAninch, Thomas. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
DOI: 10.1371/journal.pone.0113361
Grant ID: http://purl.org/au-research/grants/arc/DP140103965
Appears in Collections:Aurora harvest 3
Molecular and Biomedical Science publications

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