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 language | English (US) |
|---|---|
| Title of host publication | Methods in Molecular Biology |
| Publisher | Humana Press Inc. |
| Pages | 305-341 |
| Number of pages | 37 |
| DOIs | |
| State | Published - Jan 1 2019 |
Publication series
| Name | Methods in Molecular Biology |
|---|---|
| Volume | 1933 |
| ISSN (Print) | 1064-3745 |
| ISSN (Electronic) | 1940-6029 |
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All Science Journal Classification (ASJC) codes
- Molecular Biology
- Genetics
Cite this
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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 proceeding › Chapter
TY - CHAP
T1 - In Vivo Genome-Wide RNA Structure Probing with Structure-seq
AU - Ritchey, Laura E.
AU - Su, Zhao
AU - Assmann, Sarah Mary
AU - Bevilacqua, Philip C.
PY - 2019/1/1
Y1 - 2019/1/1
N2 - 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.
AB - 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.
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UR - http://www.scopus.com/inward/citedby.url?scp=85064239085&partnerID=8YFLogxK
U2 - 10.1007/978-1-4939-9045-0_20
DO - 10.1007/978-1-4939-9045-0_20
M3 - Chapter
C2 - 30945195
AN - SCOPUS:85064239085
T3 - Methods in Molecular Biology
SP - 305
EP - 341
BT - Methods in Molecular Biology
PB - Humana Press Inc.
ER -