Telorac Jonas, Prykhozhij Sergey V, Schöne Stefanie, Meierhofer David, Sauer Sascha, Thomas-Chollier Morgane, Meijsing Sebastiaan H
Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany.
Max Planck Institute for Molecular Genetics, Ihnestrasse 63-73, D-14195 Berlin, Germany Dalhousie University, Halifax, NS B3K 6R8, Canada.
Nucleic Acids Res. 2016 Jul 27;44(13):6142-56. doi: 10.1093/nar/gkw203. Epub 2016 Mar 25.
Out of the myriad of potential DNA binding sites of the glucocorticoid receptor (GR) found in the human genome, only a cell-type specific minority is actually bound, indicating that the presence of a recognition sequence alone is insufficient to specify where GR binds. Cooperative interactions with other transcription factors (TFs) are known to contribute to binding specificity. Here, we reasoned that sequence signals preventing GR recruitment to certain loci provide an alternative means to confer specificity. Motif analyses uncovered candidate Negative Regulatory Sequences (NRSs) that interfere with genomic GR binding. Subsequent functional analyses demonstrated that NRSs indeed prevent GR binding to nearby response elements. We show that NRS activity is conserved across species, found in most tissues and that they also interfere with the genomic binding of other TFs. Interestingly, the effects of NRSs appear not to be a simple consequence of changes in chromatin accessibility. Instead, we find that NRSs interact with proteins found at sub-nuclear structures called paraspeckles and that these proteins might mediate the repressive effects of NRSs. Together, our studies suggest that the joint influence of positive and negative sequence signals partition the genome into regions where GR can bind and those where it cannot.
在人类基因组中发现的糖皮质激素受体（GR）众多潜在的DNA结合位点中，实际上只有少数细胞类型特异性位点会被结合，这表明仅存在识别序列不足以确定GR的结合位置。已知与其他转录因子（TFs）的协同相互作用有助于结合特异性。在此，我们推断阻止GR募集到某些基因座的序列信号提供了一种赋予特异性的替代方式。基序分析发现了干扰基因组GR结合的候选负调控序列（NRSs）。随后的功能分析表明，NRSs确实能阻止GR与附近的反应元件结合。我们表明，NRS活性在物种间是保守的，存在于大多数组织中，并且它们也会干扰其他TFs的基因组结合。有趣的是，NRSs的作用似乎不是染色质可及性变化的简单结果。相反，我们发现NRSs与在称为副斑点的亚核结构中发现的蛋白质相互作用，并且这些蛋白质可能介导NRSs的抑制作用。总之，我们的研究表明，正负序列信号的共同影响将基因组划分为GR可以结合和不能结合的区域。
