Developmental changes of rRNA ribose methylations in the mouse

A sequencing-based profiling method (RiboMeth-seq) for ribose methylations was used to study methylation patterns in mouse adult tissues and during development. In contrast to previous reports based on studies of human cancer cell lines, almost all methylation sites were close to fully methylated in adult tissues. A subset of sites was differentially modified in developing tissues compared to their adult counterparts and showed clear developmental dynamics. This provides the first evidence for ribosome heterogeneity at the level of rRNA modifications during mouse development. In a prominent example, the expression levels of SNORD78 during development appeared to be regulated by alternative splicing of the Gas5 host-gene and to correlate with the methylation level of its target site at LSU-G4593. The results are discussed in the context of the specialized ribosome hypothesis. Overall design: 11 samples analyzed in biological triplicates, in total 33 samples本研究采用基于测序的核糖甲基化分析方法（RiboMeth-seq），对小鼠成年组织及发育进程中的甲基化模式展开探究。与此前基于人类癌细胞系的相关研究报道不同，成年小鼠组织内几乎所有甲基化位点均接近完全甲基化状态。部分位点在发育中的组织与成年对应组织中存在修饰差异，并呈现出清晰的发育动态变化特征。该发现首次为小鼠发育过程中核糖体RNA（ribosomal RNA, rRNA）修饰层面的核糖体异质性提供了实验证据。在一个典型案例中，SNORD78在发育过程中的表达水平似乎受其宿主基因Gas5的可变剪接调控，且与其靶位点LSU-G4593的甲基化水平显著相关。本研究结果结合特化核糖体假说展开讨论。实验整体设计：共11份样本，每份样本设置生物学重复3次，总计33份样本。