In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation

Mol Cell. 2016 May 19;62(4):603-17. doi: 10.1016/j.molcel.2016.04.028. Epub 2016 May 12.


Identifying pairwise RNA-RNA interactions is key to understanding how RNAs fold and interact with other RNAs inside the cell. We present a high-throughput approach, sequencing of psoralen crosslinked, ligated, and selected hybrids (SPLASH), that maps pairwise RNA interactions in vivo with high sensitivity and specificity, genome-wide. Applying SPLASH to human and yeast transcriptomes revealed the diversity and dynamics of thousands of long-range intra- and intermolecular RNA-RNA interactions. Our analysis highlighted key structural features of RNA classes, including the modular organization of mRNAs, its impact on translation and decay, and the enrichment of long-range interactions in noncoding RNAs. Additionally, intermolecular mRNA interactions were organized into network clusters and were remodeled during cellular differentiation. We also identified hundreds of known and new snoRNA-rRNA binding sites, expanding our knowledge of rRNA biogenesis. These results highlight the underexplored complexity of RNA interactomes and pave the way to better understanding how RNA organization impacts biology.

MeSH terms

  • Binding Sites
  • Cell Differentiation
  • Computational Biology
  • Cross-Linking Reagents / chemistry
  • Databases, Genetic
  • Embryonic Stem Cells / metabolism
  • Ficusin / chemistry
  • Gene Expression Regulation, Fungal
  • Gene Expression Regulation, Neoplastic
  • Genome-Wide Association Study
  • HeLa Cells
  • High-Throughput Nucleotide Sequencing / methods*
  • Humans
  • Nucleic Acid Conformation
  • RNA Stability
  • RNA, Fungal / chemistry
  • RNA, Fungal / genetics*
  • RNA, Fungal / metabolism
  • RNA, Messenger / chemistry
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism
  • RNA, Neoplasm / chemistry
  • RNA, Neoplasm / genetics*
  • RNA, Neoplasm / metabolism
  • RNA, Ribosomal / chemistry
  • RNA, Ribosomal / genetics*
  • RNA, Ribosomal / metabolism
  • RNA, Small Nucleolar / chemistry
  • RNA, Small Nucleolar / genetics*
  • RNA, Small Nucleolar / metabolism
  • Ribosomes / genetics
  • Ribosomes / metabolism
  • Saccharomyces cerevisiae / genetics*
  • Saccharomyces cerevisiae / metabolism
  • Transcriptome*


  • Cross-Linking Reagents
  • RNA, Fungal
  • RNA, Messenger
  • RNA, Neoplasm
  • RNA, Ribosomal
  • RNA, Small Nucleolar
  • Ficusin