title: Mapping RNA-RNA interactome and RNA structure in vivo by MARIO.
abstract: The pervasive transcription of our genome presents a possibility of revealing new genomic functions by investigating RNA interactions. Current methods for mapping RNA-RNA interactions have to rely on an 'anchor' protein or RNA and often require molecular perturbations. Here we present the MARIO (Mapping RNA interactome in vivo) technology to massively reveal RNA-RNA interactions from unperturbed cells. We mapped tens of thousands of endogenous RNA-RNA interactions from mouse embryonic stem cells and brain. We validated seven interactions by RNA antisense purification and one interaction using single-molecule RNA-FISH. The experimentally derived RNA interactome is a scale-free network, which is not expected from currently perceived promiscuity in RNA-RNA interactions. Base pairing is observed at the interacting regions between long RNAs, including transposon transcripts, suggesting a class of regulatory sequences acting in trans. In addition, MARIO data reveal thousands of intra-molecule interactions, providing in vivo data on high-order RNA structures.
authors.affiliation: Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA.
authors.forename: Tri C
authors.initials: TC
authors.lastname: Nguyen
authors.affiliation: Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA.
authors.forename: Xiaoyi
authors.initials: X
authors.lastname: Cao
authors.affiliation: Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA.
authors.forename: Pengfei
authors.initials: P
authors.lastname: Yu
authors.affiliation: Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA.
authors.forename: Shu
authors.initials: S
authors.lastname: Xiao
authors.affiliation: Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA.
authors.forename: Jia
authors.initials: J
authors.lastname: Lu
authors.affiliation: Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA.
authors.forename: Fernando H
authors.initials: FH
authors.lastname: Biase
authors.affiliation: Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA.
authors.forename: Bharat
authors.initials: B
authors.lastname: Sridhar
authors.affiliation: Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA.
authors.forename: Norman
authors.initials: N
authors.lastname: Huang
authors.affiliation: Department of Ophthalmology, University of California, San Diego, La Jolla, California 92093, USA.
authors.forename: Kang
authors.initials: K
authors.lastname: Zhang
authors.affiliation: Department of Bioengineering, University of California, San Diego, Powell-Focht Bioengineering Hall 384, 9500 Gilman Drive, MC 0412, La Jolla, California 92093, USA.
authors.forename: Sheng
authors.initials: S
authors.lastname: Zhong
mesh_terms: D000818:Animals; D005075:Biological Evolution; D001921:Brain / Q000378:metabolism*; D017124:Conserved Sequence; D053595:Embryonic Stem Cells / Q000378:metabolism*; D005786:Gene Expression Regulation; D017404:In Situ Hybridization, Fluorescence; D051379:Mice; D009690:Nucleic Acid Conformation; D012313:RNA / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism*; D015203:Reproducibility of Results; D017423:Sequence Analysis, RNA / Q000379:methods*
chemical_list: D012313:RNA