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

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

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.
Pages305-341
Number of pages37
DOIs
StatePublished - Jan 1 2019

Publication series

NameMethods in Molecular Biology
Volume1933
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029

Fingerprint

Genome
RNA
Glyoxal
Transcriptome
Bacteria
Data Accuracy

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Ritchey, L. E., Su, Z., Assmann, S. M., & Bevilacqua, P. C. (2019). In Vivo Genome-Wide RNA Structure Probing with Structure-seq. In Methods in Molecular Biology (pp. 305-341). (Methods in Molecular Biology; Vol. 1933). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-9045-0_20
Ritchey, Laura E. ; Su, Zhao ; Assmann, Sarah Mary ; Bevilacqua, Philip C. / In Vivo Genome-Wide RNA Structure Probing with Structure-seq. Methods in Molecular Biology. Humana Press Inc., 2019. pp. 305-341 (Methods in Molecular Biology).
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Ritchey, LE, Su, Z, Assmann, SM & Bevilacqua, PC 2019, In Vivo Genome-Wide RNA Structure Probing with Structure-seq. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1933, Humana Press Inc., pp. 305-341. https://doi.org/10.1007/978-1-4939-9045-0_20

In Vivo Genome-Wide RNA Structure Probing with Structure-seq. / Ritchey, Laura E.; Su, Zhao; Assmann, Sarah Mary; Bevilacqua, Philip C.

Methods in Molecular Biology. Humana Press Inc., 2019. p. 305-341 (Methods in Molecular Biology; Vol. 1933).

Research output: Chapter in Book/Report/Conference proceedingChapter

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Ritchey LE, Su Z, Assmann SM, Bevilacqua PC. In Vivo Genome-Wide RNA Structure Probing with Structure-seq. In Methods in Molecular Biology. Humana Press Inc. 2019. p. 305-341. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-9045-0_20