Leone Sergio, Bär Dominik, Slabber Coenraad Frederik, Dalcher Damian, Santoro Raffaella
Department of Molecular Mechanisms of Disease, University of Zurich, Zurich, Switzerland.
Molecular Life Science Program, Life Science Zurich Graduate School, University of Zurich, Zurich, Switzerland.
EMBO Rep. 2017 Jul;18(7):1248-1262. doi: 10.15252/embr.201744330. Epub 2017 Jun 6.
Long non-coding RNAs (lncRNAs) have been implicated in the regulation of chromatin conformation and epigenetic patterns. lncRNA expression levels are widely taken as an indicator for functional properties. However, the role of RNA processing in modulating distinct features of the same lncRNA is less understood. The establishment of heterochromatin at rRNA genes depends on the processing of IGS-rRNA into pRNA, a reaction that is impaired in embryonic stem cells (ESCs) and activated only upon differentiation. The production of mature pRNA is essential since it guides the repressor TIP5 to rRNA genes, and IGS-rRNA abolishes this process. Through screening for IGS-rRNA-binding proteins, we here identify the RNA helicase DHX9 as a regulator of pRNA processing. DHX9 binds to rRNA genes only upon ESC differentiation and its activity guides TIP5 to rRNA genes and establishes heterochromatin. Remarkably, ESCs depleted of DHX9 are unable to differentiate and this phenotype is reverted by the addition of pRNA, whereas providing IGS-rRNA and pRNA mutants deficient for TIP5 binding are not sufficient. Our results reveal insights into lncRNA biogenesis during development and support a model in which the state of rRNA gene chromatin is part of the regulatory network that controls exit from pluripotency and initiation of differentiation pathways.
长链非编码RNA（lncRNAs）已被证明参与染色质构象和表观遗传模式的调控。lncRNA表达水平被广泛用作功能特性的指标。然而，RNA加工在调节同一lncRNA的不同特征方面所起的作用却鲜为人知。rRNA基因处异染色质的建立取决于IGS-rRNA加工成pRNA，这一反应在胚胎干细胞（ESCs）中受损，仅在分化时被激活。成熟pRNA的产生至关重要，因为它将阻遏物TIP5引导至rRNA基因，而IGS-rRNA会消除这一过程。通过筛选与IGS-rRNA结合的蛋白质，我们在此鉴定出RNA解旋酶DHX9是pRNA加工的调节因子。DHX9仅在ESC分化时与rRNA基因结合，其活性将TIP5引导至rRNA基因并建立异染色质。值得注意的是，缺失DHX9的ESCs无法分化，而添加pRNA可逆转这一表型，而提供IGS-rRNA和缺乏TIP5结合能力的pRNA突变体则不足以实现这一点。我们的研究结果揭示了发育过程中lncRNA生物发生的见解，并支持一种模型，即rRNA基因染色质的状态是控制多能性退出和分化途径启动的调控网络的一部分。
