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Series GSE74353 Query DataSets for GSE74353
Status Public on Apr 04, 2016
Title RNA duplex map in living cells reveals higher order transcriptome structure
Organisms Homo sapiens; Mus musculus
Experiment type Other
Summary RNA has the intrinsic property to base pair, forming complex structures fundamental to its diverse functions. Here we develop PARIS, a method based on reversible psoralen-crosslinking for global mapping of RNA duplexes with near base-pair resolution in living cells. PARIS analysis in three human and mouse cell types reveals frequent long-range structures, higher order architectures, and RNA:RNA interactions in trans across the transcriptome. PARIS determines base-pairing interactions on an individual-molecule level, revealing pervasive alternative conformations. We used PARIS-determined helices to guide phylogenetic analysis of RNA structures, and discovered conserved long-range and alternative structures. XIST, a lncRNA essential for X chromosome inactivation, folds into evolutionarily conserved RNA structural domains that span many kilobases. XIST A-repeat forms complex inter-repeat duplexes that nucleate higher order assembly of the key epigenetic silencing protein SPEN. PARIS is a generally applicable and versatile method that provides novel insights into the RNA structurome and interactome.
Overall design Cells are crosslinked with AMT and RNA is extracted from cells by RNase digestion. Crosslinked RNA fragments are selected from total RNA by 2D gel electrophoresis. Purified crosslinked RNA duplexes are proximity ligated and crosslinking is reversed. Then the chimeric RNA molecules are converted into cDNA libraries for high-throughput sequencing.
Contributor(s) Lu Z
Citation(s) 27180905
Submission date Oct 26, 2015
Last update date Sep 18, 2020
Contact name Zhipeng Lu
Organization name Stanford University
Department Department of Dermatology
Lab Howard Chang
Street address 269 Campus Drive
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
Platforms (3)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
GPL19057 Illumina NextSeq 500 (Mus musculus)
GPL20301 Illumina HiSeq 4000 (Homo sapiens)
Samples (14)
GSM1917753 HeLa_LowRNase
GSM1917754 HeLa_HighRNase
GSM1917755 HEK293T_1
BioProject PRJNA299809
SRA SRP065268

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE74353_HS_293T_icSHAPE_InVitro_BaseReactivities.txt.gz 7.0 Mb (ftp)(http) TXT
GSE74353_HS_293T_icSHAPE_InVivo_BaseReactivities.txt.gz 8.8 Mb (ftp)(http) TXT
GSE74353_RAW.tar 2.1 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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