Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators.
Genome-Wide Mapping Targets of the Metazoan Chromatin Remodeling Factor NURF Reveals Nucleosome Remodeling at Enhancers, Core Promoters and Gene Insulators.
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DOI：
10.1371/journal.pgen.1005969
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发表时间：
2016-04
期刊：
影响因子：
4.5
通讯作者：
Badenhorst P
中科院分区：
文献类型：
--
作者：
Kwon SY;Grisan V;Jang B;Herbert J;Badenhorst P
CANF是一种保守的高等真核生物，含有ISWI的染色质重塑复合物，催化ATP依赖的核小体滑动。通过滑动核小体，BNF能够改变染色质动力学以控制转录和基因组组织。先前对果蝇BNF特异性亚基（Nurf 301/Enhancer of Bithorax（E（bx）的生化和遗传分析已经将BNF定义为同源异型、热休克和类固醇应答基因转录的关键调节因子。据推测，BMPF通过与序列特异性转录因子合作以在专用增强子处重塑染色质来控制途径特异性转录。然而，这是缺乏的，确切的体内证明，并精确的调控元件靶向的BMPF的定义很差。为了解决这一问题，我们已经产生了一个全面的地图，在体内BNF活性，使用MNase测序，以确定在碱基对分辨率BNF靶核小体，和ChIP测序，以确定网站的BNF招聘。我们的数据表明，除了预期的作用，在增强子中，TRF 2/DREF基础转录因子的物理和功能相互作用，组织核小体的活性启动子下游。此外，我们在远端绝缘子位点检测到BNF重塑和招募，BNF在功能上与DREF和绝缘子蛋白（包括CP 190）相互作用并共定位，以建立核小体耗尽结构域。这种绝缘子的功能是最明显的绝缘子的亚类，标记的染色质结构域的边界，其中多个绝缘子蛋白共同缔合。通过可视化的完整剧目，在体内BNF染色质的目标，我们的数据提供了新的见解，染色质重塑如何控制基因组的组织和监管的相互作用。在真核生物中，DNA被折叠并压缩成可管理的单元，通过包裹在组蛋白蛋白的蛋白质线轴上形成核小体。通过使用能量依赖性染色质重塑酶改变核小体的位置和动力学，可以选择性地关闭或打开细胞中的基因，控制发育和细胞功能。ATP依赖性染色质重塑酶的不同亚家族已被表征。然而，它们在基因组中的特定核小体靶点以及它们如何被招募到这些靶点并没有完全确定。在这里，我们已经确定了保守的高等真核细胞染色质重塑酶BNF的核小体靶点。我们的数据表明，三个不同的功能，转录过程中的转录。BNF在基因增强子元件处组织核小体位置以调节转录起始，但也需要维持活性基因转录起始位点下游的核小体位置。此外，我们还检测到在基因组功能组织所需的远端绝缘子位点处的BDNF重塑和招募。我们假设，在绝缘子以及启动子的BLOMF功能反映了远距离绝缘子和活性启动子之间的功能相互作用，与调控元件的功能聚类提供了一个解决方案，染色质重塑酶如何在基因组中参与多个目标。
NURF is a conserved higher eukaryotic ISWI-containing chromatin remodeling complex that catalyzes ATP-dependent nucleosome sliding. By sliding nucleosomes, NURF is able to alter chromatin dynamics to control transcription and genome organization. Previous biochemical and genetic analysis of the specificity-subunit of Drosophila NURF (Nurf301/Enhancer of Bithorax (E(bx)) has defined NURF as a critical regulator of homeotic, heat-shock and steroid-responsive gene transcription. It has been speculated that NURF controls pathway specific transcription by co-operating with sequence-specific transcription factors to remodel chromatin at dedicated enhancers. However, conclusive in vivo demonstration of this is lacking and precise regulatory elements targeted by NURF are poorly defined. To address this, we have generated a comprehensive map of in vivo NURF activity, using MNase-sequencing to determine at base pair resolution NURF target nucleosomes, and ChIP-sequencing to define sites of NURF recruitment. Our data show that, besides anticipated roles at enhancers, NURF interacts physically and functionally with the TRF2/DREF basal transcription factor to organize nucleosomes downstream of active promoters. Moreover, we detect NURF remodeling and recruitment at distal insulator sites, where NURF functionally interacts with and co-localizes with DREF and insulator proteins including CP190 to establish nucleosome-depleted domains. This insulator function of NURF is most apparent at subclasses of insulators that mark the boundaries of chromatin domains, where multiple insulator proteins co-associate. By visualizing the complete repertoire of in vivo NURF chromatin targets, our data provide new insights into how chromatin remodeling can control genome organization and regulatory interactions. In eukaryotes DNA is folded and compacted into manageable units by wrapping around a protein spool of histone proteins to form nucleosomes. By varying the position and dynamics of nucleosomes using energy-dependent chromatin remodeling enzymes, genes can be selectively turned off or on in cells, controlling development and cellular function. Distinct sub-families of ATP-dependent chromatin remodeling enzymes have been characterised. However, their specific nucleosome targets in the genome and how they are recruited to these are not completely defined. Here we have identified nucleosome targets of the conserved higher eukaryotic chromatin remodeling enzyme NURF. Our data indicate three distinct functions for NURF during transcription. NURF organizes nucleosome positions at gene enhancer elements to regulate transcription initiation, but is also required to maintain nucleosome position downstream of the transcription start site of active genes. In addition, we detect NURF remodeling and recruitment at distal insulator sites that are required for functional organisation of the genome. We postulate that NURF function at insulators as well as promoters reflects functional interaction between distant insulators and active promoters, with functional clustering of regulatory elements providing a solution to how chromatin remodeling enzymes engage multiple targets in the genome.