Frank Christopher L, Liu Fang, Wijayatunge Ranjula, Song Lingyun, Biegler Matthew T, Yang Marty G, Vockley Christopher M, Safi Alexias, Gersbach Charles A, Crawford Gregory E, West Anne E
1] Department of Molecular Genetics and Microbiology, Duke University Medical Center, Durham, North Carolina, USA. [2] Center for Genomic and Computational Biology, Duke University Medical Center, Durham, North Carolina, USA.
Department of Neurobiology, Duke University Medical Center, Durham, North Carolina, USA.
Nat Neurosci. 2015 May;18(5):647-56. doi: 10.1038/nn.3995. Epub 2015 Apr 6.
To identify chromatin mechanisms of neuronal differentiation, we characterized chromatin accessibility and gene expression in cerebellar granule neurons (CGNs) of the developing mouse. We used DNase-seq to map accessibility of cis-regulatory elements and RNA-seq to profile transcript abundance across postnatal stages of neuronal differentiation in vivo and in culture. We observed thousands of chromatin accessibility changes as CGNs differentiated, and verified, using H3K27ac ChIP-seq, reporter gene assays and CRISPR-mediated activation, that many of these regions function as neuronal enhancers. Motif discovery in differentially accessible chromatin regions suggested a previously unknown role for the Zic family of transcription factors in CGN maturation. We confirmed the association of Zic with these elements by ChIP-seq and found, using knockdown, that Zic1 and Zic2 are required for coordinating mature neuronal gene expression patterns. Together, our data reveal chromatin dynamics at thousands of gene regulatory elements that facilitate the gene expression patterns necessary for neuronal differentiation and function.
为了确定神经元分化的染色质机制，我们对发育中小鼠的小脑颗粒神经元（CGN）的染色质可及性和基因表达进行了表征。我们使用DNase-seq绘制顺式调控元件的可及性图谱，并使用RNA-seq分析体内和体外神经元分化产后阶段的转录本丰度。我们观察到随着CGN的分化，数千个染色质可及性发生变化，并使用H3K27ac ChIP-seq、报告基因检测和CRISPR介导的激活方法进行验证，发现其中许多区域作为神经元增强子发挥作用。差异可及染色质区域的基序发现表明，锌指转录因子家族在CGN成熟中具有先前未知的作用。我们通过ChIP-seq证实了锌指与这些元件的关联，并通过敲低发现，Zic1和Zic2是协调成熟神经元基因表达模式所必需的。总之，我们的数据揭示了数千个基因调控元件处的染色质动态变化，这些变化促进了神经元分化和功能所需的基因表达模式。
