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Series GSE60034 Query DataSets for GSE60034
Status Public on Mar 18, 2015
Title Dynamic landscape of RNA structures in vivo reveals principles of post-transcriptional regulation [icSHAPE]
Organism Mus musculus
Experiment type Other
Summary Visualizing the physical basis for molecular behavior inside living cells is a grand challenge in biology. RNAs are central to biological regulation, and RNA’s ability to adopt specific structures intimately controls every step of the gene expression program.1 However, our understanding of physiological RNA structures is limited; current in vivo RNA structure profiles predominantly viewed only two of four nucleotides that make up RNA.2,3 Here we present a novel biochemical approach, In Vivo Click SHAPE (icSHAPE), that enables the first global view of RNA secondary structures of all four bases in living cells. icSHAPE of embryonic stem cell transcriptome versus purified RNA folded in vitro shows that the structural dynamics of RNA in the cellular environment distinguishes different classes of RNAs and regulatory elements. Structural signatures at translational start sites and ribosome pause sites are conserved in vitro, suggesting that these RNA elements are programmed by sequence. In contrast, focal structural rearrangements in vivo reveal precise interfaces of RNA with RNA binding or modification proteins that are consistent with atomic-resolution structural data. Such dynamic structural footprints enable accurate prediction of RNA-protein interactions and N6-methyladenosine (m6A) modification genome-wide. These results open the door for structural genomics of RNA in living cells and reveal key physiological structures controlling gene expression.
Overall design Development and implementation of a chemoaffinity method to study the in vivo secondary structure of the transcriptome
Contributor(s) Spitale RC, Flynn RA, Zhang QC, Kuchelmeister HY, Crisalli P, Torre EA, Batista PJ, Kool ET, Chang HY
Citation(s) 25799993
Submission date Aug 01, 2014
Last update date May 15, 2019
Contact name Ryan Alexander Flynn
Organization name Stanford University
Street address 380 Roth Way, Room 265
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platforms (2)
GPL13112 Illumina HiSeq 2000 (Mus musculus)
GPL19057 Illumina NextSeq 500 (Mus musculus)
Samples (10)
GSM1464037 v65 polyA(+) icSHAPE DMSO Biological Replicate 1
GSM1464038 v65 polyA(+) icSHAPE DMSO Biological Replicate 2
GSM1464039 v65 polyA(+) icSHAPE in vitro NAI-N3 Biological Replicate 1
This SubSeries is part of SuperSeries:
GSE64169 Dynamic landscape of RNA structures in vivo reveals principles of post-transcriptional regulation
BioProject PRJNA257310
SRA SRP045191

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Supplementary file Size Download File type/resource 18.9 Mb (ftp)(http) BW 105.0 Mb (ftp)(http) BW 144.4 Mb (ftp)(http) BW 121.0 Mb (ftp)(http) BW
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