Runge John S, Raab Jesse R, Magnuson Terry
Curriculum for Genetics and Molecular Biology.
Lineberger Comprehensive Cancer Center.
G3 (Bethesda). 2018 Mar 28;8(4):1095-1102. doi: 10.1534/g3.117.300504.
Chromatin remodeling and histone modifying enzymes play a critical role in shaping the regulatory output of a cell. Although much is known about these classes of proteins, identifying the mechanisms by which they coordinate gene expression programs remains an exciting topic of investigation. One factor that may contribute to the targeting and activity of chromatin regulators is local chromatin landscape. We leveraged genomic approaches and publically-available datasets to characterize the chromatin landscape at targets of the human INO80 chromatin remodeling complex (INO80-C). Our data revealed two classes of INO80-C targets with distinct chromatin signatures. The predominant INO80-C class was enriched for open chromatin, H3K27ac, and representative subunits from each of the three INO80-C modules (RUVBL1, RUVBL2, MCRS1, YY1). We named this class Canonical INO80. Notably, we identified an unexpected class of INO80-C targets that contained only the INO80 ATPase and harbored a repressive chromatin signature characterized by inaccessible chromatin, H3K27me3, and the methyltransferase EZH2. We named this class Non-Canonical INO80 (NC-INO80). Biochemical approaches indicated that INO80-C and the H3K27 acetyltransferase P300 physically interact, suggesting INO80-C and P300 may jointly coordinate chromatin accessibility at Canonical INO80 sites. No interaction was detected between INO80-C and EZH2, indicating INO80-C and EZH2 may engage in a separate form of regulatory crosstalk at NC-INO80 targets. Our data indicate that INO80-C is more compositionally heterogenous at its genomic targets than anticipated. Moreover, our data suggest there is an important link between INO80-C and histone modifying enzymes that may have consequences in developmental and pathological contexts.
染色质重塑和组蛋白修饰酶在塑造细胞的调控输出中起着关键作用。尽管对这些蛋白质类别已经了解很多，但确定它们协调基因表达程序的机制仍然是一个令人兴奋的研究课题。可能有助于染色质调节因子靶向和活性的一个因素是局部染色质景观。我们利用基因组方法和公开可用的数据集来表征人类INO80染色质重塑复合物（INO80-C）靶点处的染色质景观。我们的数据揭示了两类具有不同染色质特征的INO80-C靶点。主要的INO80-C类别富含开放染色质、H3K27ac以及来自三个INO80-C模块（RUVBL1、RUVBL2、MCRS1、YY1）中每个模块的代表性亚基。我们将这一类命名为经典INO80。值得注意的是，我们鉴定出一类意想不到的INO80-C靶点，它们仅包含INO80 ATP酶，并具有以难以接近的染色质、H3K27me3和甲基转移酶EZH2为特征的抑制性染色质特征。我们将这一类命名为非经典INO80（NC-INO80）。生化方法表明INO80-C与H3K27乙酰转移酶P300发生物理相互作用，这表明INO80-C和P300可能在经典INO80位点共同协调染色质可及性。未检测到INO80-C与EZH2之间的相互作用，这表明INO80-C和EZH2可能在NC-INO80靶点处进行一种单独形式的调控串扰。我们的数据表明，INO80-C在其基因组靶点处的组成比预期的更加异质。此外，我们的数据表明INO80-C与组蛋白修饰酶之间存在重要联系，这可能在发育和病理背景下产生影响。
