McAninch Dale, Thomas Paul
Department of Biochemistry, School of Molecular & Biomedical Science and Robinson Research Institute, The University of Adelaide, Adelaide, Australia.
PLoS One. 2014 Nov 19;9(11):e113361. doi: 10.1371/journal.pone.0113361. eCollection 2014.
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.
转录因子SOX3在脊椎动物中枢神经系统（CNS）的大多数神经祖细胞（NP）中表达，对小鼠和人类的正常脑发育至关重要。然而，尽管Sox3广泛表达，但由于与其他SOXB1亚组成员Sox1和Sox2存在功能冗余，敲除小鼠中的CNS缺陷相对较轻。为了进一步了解SOX3的分子功能，我们使用ChIP-seq研究了NP细胞中内源性SOX3的全基因组结合图谱。在超过8000个位点鉴定到了SOX3结合，其中大多数位于内含子或基因间区域，并且与神经发育基因显著相关。大多数结合位点具有中度或高度保守性（phastCons评分分别>0.1和0.5），包括先前已表征的SOXB1结合的巢蛋白NP细胞增强子。将SOX3与已发表的胚胎脑中辅激活因子P300的ChIP-Seq数据进行比较，鉴定出数百个高度保守的假定增强子元件。此外，我们在NP细胞中鉴定出了SOXB1成员共有的CNS发育基因的一个高度保守的假定增强子子集，所有这些增强子都包含SOX共有基序（ACAAWR）。这些数据共同表明SOX3直接调控数百个NP基因，并为SOXB1蛋白在CNS发育中的重叠作用提供了分子层面的见解。
