In vivo probing of nascent RNA structures reveals principles of cotranscriptional folding

被引:35
作者
Incarnato, Danny [1 ,2 ]
Morandi, Edoardo [1 ,2 ]
Anselmi, Francesca [1 ,2 ]
Simon, Lisa M. [1 ,2 ]
Basile, Giulia [1 ,2 ]
Oliviero, Salvatore [1 ,2 ]
机构
[1] Univ Torino, Dipartimento Sci Vita & Biol Sistemi, Via Acad Albertina 13, Turin, Italy
[2] IIGM, Via Nizza 52, I-10126 Turin, Italy
关键词
SECONDARY STRUCTURES; KINETIC TRAPS; LIVING CELLS; TRANSCRIPTOME; COMPLEX;
D O I
10.1093/nar/gkx617
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Defining the in vivo folding pathway of cellular RNAs is essential to understand how they reach their final native conformation. We here introduce a novel method, named Structural Probing of Elongating Transcripts (SPET-seq), that permits single-base resolution analysis of transcription intermediates' secondary structures on a transcriptome-wide scale, enabling base-resolution analysis of the RNA folding events. Our results suggest that cotranscriptional RNA folding in vivo is a mixture of cooperative folding events, in which local RNA secondary structure elements are formed as they get transcribed, and non-cooperative events, in which 5 '-halves of long-range helices get sequestered into transient non-native interactions until their 3 ' counterparts have been transcribed. Together our work provides the first transcriptome-scale overview of RNA cotranscriptional folding in a living organism.
引用
收藏
页码:9716 / 9725
页数:10
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