Department of Biochemistry, UCB 596, University of Colorado Boulder, Boulder, Colorado, United States of America.
PLoS One. 2021 Feb 19;16(2):e0237956. doi: 10.1371/journal.pone.0237956. eCollection 2021.
Cyp33 is an essential human cyclophilin prolyl isomerase that plays myriad roles in splicing and chromatin remodeling. In addition to a canonical cyclophilin (Cyp) domain, Cyp33 contains an RNA-recognition motif (RRM) domain, and RNA-binding triggers proline isomerase activity. One prominent role for Cyp33 is through a direct interaction with the mixed lineage leukemia protein 1 (MLL1, also known as KMT2A) complex, which is a histone methyltransferase that serves as a global regulator of human transcription. MLL activity is regulated by Cyp33, which isomerizes a key proline in the linker between the PHD3 and Bromo domains of MLL1, acting as a switch between gene activation and repression. The direct interaction between MLL1 and Cyp33 is critical, as deletion of the MLL1-PHD3 domain responsible for this interaction results in oncogenesis. The Cyp33 RRM is central to these activities, as it binds both the PHD3 domain and RNA. To better understand how RNA binding drives the action of Cyp33, we performed RNA-SELEX against full-length Cyp33 accompanied by deep sequencing. We have identified an enriched Cyp33 binding motif (AAUAAUAA) broadly represented in the cellular RNA pool as well as tightly binding RNA aptamers with affinities comparable and competitive with the Cyp33 MLL1-PHD3 interaction. RNA binding extends beyond the canonical RRM domain, but not to the Cyp domain, suggesting an indirect mechanism of interaction. NMR chemical shift mapping confirms an overlapping, but not identical, interface on Cyp33 for RNA and PHD3 binding. This finding suggests RNA can disrupt the gene repressive Cyp33-MLL1 complex providing another layer of regulation for chromatin remodeling by MLL1.
Cyp33 是一种必需的人类亲环素脯氨酰基异构酶，在剪接和染色质重塑中发挥着多种作用。除了经典的亲环素（Cyp）结构域外，Cyp33 还包含一个 RNA 识别基序（RRM）结构域，并且 RNA 结合可触发脯氨酰基异构酶活性。Cyp33 的一个突出作用是通过与混合谱系白血病蛋白 1（MLL1，也称为 KMT2A）复合物的直接相互作用来实现的，该复合物是一种组蛋白甲基转移酶，作为人类转录的全局调节剂。Cyp33 调节 MLL1 的活性，其使 MLL1 的 PHD3 和溴结构域之间的连接中的关键脯氨酸异构化，充当基因激活和抑制之间的开关。MLL1 和 Cyp33 之间的直接相互作用至关重要，因为删除负责这种相互作用的 MLL1-PHD3 结构域会导致致癌。Cyp33 的 RRM 是这些活性的核心，因为它结合了 PHD3 结构域和 RNA。为了更好地理解 RNA 结合如何驱动 Cyp33 的作用，我们对全长 Cyp33 进行了 RNA-SELEX 实验，同时进行了深度测序。我们已经鉴定出一个富含 Cyp33 结合基序（AAUAAUAA）的基序，该基序广泛存在于细胞 RNA 库中，并且与 Cyp33 MLL1-PHD3 相互作用具有可比性和竞争性的紧密结合 RNA 适体。RNA 结合不仅延伸到经典的 RRM 结构域，而且延伸到 Cyp 结构域，这表明存在间接相互作用机制。NMR 化学位移映射证实 Cyp33 上存在用于 RNA 和 PHD3 结合的重叠但不相同的界面。这一发现表明，RNA 可以破坏基因抑制性 Cyp33-MLL1 复合物，为 MLL1 介导的染色质重塑提供了另一层调节。
