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Series GSE61489 Query DataSets for GSE61489
Status Public on Jun 23, 2016
Title Mapping RNA-RNA interactome and RNA structures in vivo with MARIO
Organism Mus musculus
Experiment type Other
Summary Many biological processes are regulated by RNA-RNA interactions 1, nonetheless it remains formidable to analyze the entire RNA interactome. We developed a method, MARIO (MApping Rna-rna Interactions in vivO), to map protein-assisted RNA-RNA interactions in vivo. By circumventing the selection for a specific RNA-binding protein 2-5, our approach vastly expands the identifiable portion of the RNA interactome. Using this technology, we mapped the RNA interactome in mouse embryonic stem cells, which was composed of 46,780 RNA-RNA interactions. The RNA interactome was a scale-free network, with several lincRNAs and mRNAs emerging as hubs. We validated an interaction between two hubs, Malat1 and Slc2a3 using single molecule RNA fluorescence in situ hybridization. Base pairing was observed at the interaction sites of long RNAs, and was particularly strong in transposonRNA-mRNA and lincRNA-mRNA interactions. This reveals a new type of regulatory sequences acting in trans. Consistent with their hypothesized roles, the RNA interaction sites were more evolutionarily conserved than other regions of the transcripts. MARIO also provided new information on RNA structures, by simultaneously revealing the footprint of single stranded regions and the spatially proximal sites of each RNA. The unbiased mapping of the protein-assisted RNA interactome with minimum perturbation of cell physiology will greatly expand our capacity to investigate RNA functions.
Overall design Three (3) ESC samples with different treatment (different digestion size and/or crosslinking method) and one (1) MEF sample were included to test our new approach for RNA-interactome mapping and the different samples were analyzed to show RNA interactome differences between them.
Contributor(s) Nguyen TC, Yu P, Cao X, Xiao S, Lu J, Biase FH, Sridhar B, Huang N, Zhang K, Zhong S
Citation(s) 27338251
Submission date Sep 17, 2014
Last update date May 15, 2019
Contact name Sheng Zhong
Organization name University of California, San Diego
Department Bioengineering Department
Street address 9500 Gilman Drive, Mail Code 0412
City La Jolla
State/province California
ZIP/Postal code 92093-0412
Country USA
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (6)
GSM1506092 ES cell sample 1
GSM1506093 ES cell sample 2
GSM1506094 ES cell indirect crosslinking
This SubSeries is part of SuperSeries:
GSE81388 Mapping RNA-RNA interactome and RNA structures in vivo
BioProject PRJNA261375
SRA SRP047277

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Supplementary file Size Download File type/resource
GSE61489_RAW.tar 698.9 Mb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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