ABSTRACT

Epitranscriptomic modifications of stable RNAs are dynamically regulated and specific profiles of 2ʹ-O-methylation in rRNA have been associated with distinct cancer types. However, these observations pointed out the existence of at least two distinct groups: a rather large group with constitutive rRNA Nm residues exhibiting a stable level of methylation and a more restricted set of variable modifications, giving rise to the concept of ‘specialized ribosomes’. These heterogeneous ribosomes can modulate their translational properties and be key regulatory players, depending on the physiological state of the cell. However, these conclusions were drawn from a limited set of explored human cell lines or tissues, mostly related to cancer cells of the same type. Here, we report a comprehensive analysis of human rRNA Nm modification variability observed for >15 human cell lines grown in different media and conditions. Our data demonstrate that human Nm sites can be classified into four groups, depending on their observed variability. About ⅓ of rRNA 2ʹ-O-methylations are almost invariably modified at the same level in all tested samples (stable modifications), the second group of relatively invariant modifications (another ½ of the total) showing a slightly higher variance (low variable group) and two variable groups, showing an important heterogeneity. Mapping of these four classes on the human ribosome 3D structure shows that stably modified positions are preferentially located in the important ribosome functional sites, while variable and highly variable residues are mostly distributed to the ribosome periphery. Possible relationships of such stable and variable modifications to the ribosome functions are discussed.

 抽象的

稳定 RNA 的表观转录修饰是动态调节的，rRNA 中 2ʹ-O-甲基化的特定特征与不同的癌症类型相关。然而，这些观察指出至少存在两个不同的组：一个相当大的组，其组成性 rRNA Nm 残基表现出稳定的甲基化水平，以及一组更受限制的可变修饰，从而产生了“特殊核糖体”的概念。这些异质核糖体可以调节其翻译特性并成为关键的调节因子，具体取决于细胞的生理状态。然而，这些结论是从有限的一组已探索的人类细胞系或组织中得出的，大部分与同一类型的癌细胞有关。在此，我们报告了对在不同培养基和条件下生长的 >15 人类细胞系观察到的人类 rRNA Nm 修饰变异性的全面分析。我们的数据表明，人类 Nm 位点可以根据观察到的变异性分为四组。在所有测试样本中，大约 1/3 的 rRNA 2ʹ-O-甲基化几乎总是以相同水平进行修饰（稳定修饰），第二组相对不变的修饰（总数的另外 1/2）显示出稍高的方差（低变量组）和两个变量组，显示出重要的异质性。这四类在人类核糖体3D结构上的映射表明，稳定修饰的位置优先位于重要的核糖体功能位点，而可变和高度可变的残基主要分布在核糖体外围。讨论了这种稳定和可变修饰与核糖体功能的可能关系。