体内与体外RNA-RNA相互作用的比较初探

A systematic comparison of in vivo and in vitro RNA-RNA interactions

目的通过比较in vitro与in vivo的RNA-RNA相互作用(RNA-RNA interaction,RRI),探究通过in vitroRRI推测in vivo RRI的可靠性。方法采用perl语言编写脚本分析酵母转录组水平in vitro RNA的二级结构信息,得到可能的in vitro RRI,再与酵母的in vivo小核仁RNA(snoRNA)-rRNA相互作用进行比较。结果发现in vitrosnoRNA-rRNA相互作用与in vivo snoRNA-rRNA相互作用的重叠率仅为23.42%(26/111);而in vitro测定的snoRNA双链片段与in vivo测定的参与RRI的snoRNA片段重叠率为38.78%(19/49);in vitro测定的rRNA双链片段与in vivo测定的参与RRI的rRNA片段重叠率为80.70%(46/57)。结论 in vitro和in vivo条件下snoRNA-rRNA的相互作用差异很大,提示in vitro条件下测定的snoRNA-rRNA的相互作用不能真实反映它们在in vivo的相互作用。

Objective To compare in vitro and in vivo RNA-RNA interactions （RRI） systematically in order to analyze the reliability of obtaining in vivo RRI by determining in vitro RRI. Methods Programs were written using perl language to obtain all the candidate in vitro RRIs based on transcriptome-wide in vitro RNA secondary structure profile in yeast. The in vitro RRIs were then compared with in vivo small nucleolar RNA （snoRNA）-rRNA interactions in yeast. Result Compared with in vivo snoRNA-rRNA interactions, only 23.42% （26/111 ） of in vitro snoRNA-rRNA interactions were reproduced in in vivo snoRNA-rRNA interactions, whereas 38.78% （19/49） of in vitro snoRNA double-stranded fragments overlapped with in vivo snoRNA fragments that participated in snoRNA-rRNA interactions, and 80.70% （46/57） of in vitro RDN37-1 double-stranded fragments overlapped in vivo RDN37-1 fragments that participated in snoRNA-rRNA interactions. Conclu- sion There is huge difference between in vitro and in vivo snoRNA-rRNA interactions, snoRNA-rRNA interactions deter- mined in vitro cannot really reflect in vivo interactions.