In Vivo Genome-Wide RNA Structure Probing with Structure-seq

Laura E. Ritchey, Zhao Su, Sarah M. Assmann, Philip C. Bevilacqua

Research output: Chapter in Book/Report/Conference proceedingChapter

7 Scopus citations


In vivo genome-wide RNA structure probing provides a global view of RNA structure as it occurs in the cell and can assist in elucidating important functional aspects of RNA structure. Structure-seq2 provides high-quality data on transcriptome-wide RNA structure in vivo but contains numerous steps that require technical precision. In this chapter we present the steps needed to produce high-quality structural data with a focus on controls and troubleshooting. Structure-seq2 can be applied to numerous organisms including plants, humans, and bacteria and is amenable to a wide variety of RNA-modifying chemicals including DMS, glyoxal, and SHAPE reagents. Notably, the data generated by the method highlighted here can be readily analyzed using our StructureFold2 computational pipeline.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Number of pages37
StatePublished - 2019

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics


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