Hybridization-proximity labeling reveals spatially ordered interactions of nuclear RNA compartments

Karen Yap, Tek Hong Chung, Eugene V. Makeyev*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

18 Citations (Scopus)


The ability of RNAs to form specific contacts with other macromolecules provides an important mechanism for subcellular compartmentalization. Here we describe a suite of hybridization-proximity (HyPro) labeling technologies for unbiased discovery of proteins (HyPro-MS) and transcripts (HyPro-seq) associated with RNAs of interest in genetically unperturbed cells. As a proof of principle, we show that HyPro-MS and HyPro-seq can identify both known and previously unexplored spatial neighbors of the noncoding RNAs 45S, NEAT1, and PNCTR expressed at markedly different levels. Notably, HyPro-seq uncovers an extensive repertoire of incompletely processed, adenosine-to-inosine-edited transcripts accumulating at the interface between their encoding chromosomal regions and the NEAT1-containing paraspeckle compartment. At least some of these targets require NEAT1 for their optimal expression. Overall, this study provides a versatile toolkit for dissecting RNA interactomes in diverse biomedical contexts and expands our understanding of the functional architecture of the mammalian nucleus.

Original languageEnglish
Pages (from-to)463-478.e11
Issue number2
Publication statusPublished - 20 Jan 2022


  • ascorbate peroxidase
  • digoxigenin-binding domain
  • higher-order nuclear organization
  • nucleolus
  • paraspeckles
  • perinucleolar compartment
  • proteome
  • proximity biotinylation
  • RNA-containing compartments
  • transcriptome


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