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 longrange helices get sequestered into transient nonnative 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.

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

Incarnato D.;Morandi E.;Anselmi F.;SIMON, LISA MARIE;Basile G.;Oliviero S.
Last
2017

Abstract

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 longrange helices get sequestered into transient nonnative 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.
45
16
9716
9725
http://nar.oxfordjournals.org/
Biochemistry; Escherichia coli; Nucleic Acid Conformation; RNA; Ribonuclease P; Sulfuric Acid Esters; Transcription, Genetic; RNA Folding
Incarnato D.; Morandi E.; Anselmi F.; Simon L.M.; Basile G.; Oliviero S.
File in questo prodotto:
File Dimensione Formato  
2017 Incarnato NARin vivo probing nascent.pdf

Accesso aperto

Descrizione: Articolo principale
Tipo di file: PDF EDITORIALE
Dimensione 1.78 MB
Formato Adobe PDF
1.78 MB Adobe PDF Visualizza/Apri

I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.

Utilizza questo identificativo per citare o creare un link a questo documento: http://hdl.handle.net/2318/1706468
Citazioni
  • ???jsp.display-item.citation.pmc??? 17
  • Scopus 27
  • ???jsp.display-item.citation.isi??? 26
social impact