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Despite remarkable advances in PPI analysis technologies, the development of tools for RPI analysis has lagged behind. To address this challenge, we integrated three established PPI technologies\u2014bimolecular fluorescence complementation (BiFC), NanoBiT, and split-TurboID\u2014with RNA-targeting CRISPR\/dCas13. We applied these platforms to paraspeckles, a representative MLO formed through interactions between the long non-coding RNA NEAT1 and the RNA-binding protein NONO. BiFC-dCas13 functions as a fluorescence-based recorder that enables quantitative detection of NEAT1\u2013NONO interaction events. NanoBiT-dCas13 precisely monitors dynamic changes in the NEAT1\u2013NONO interaction through a reversible luminescence readout. Split-TurboID-dCas13 induces proximity-dependent biotinylation of proteins surrounding paraspeckles, identifying the N6-methyladenosine reader YTHDC1 as a paraspeckle-associated protein. Furthermore, BiFC-dCas13 was readily reconfigured to detect additional RPI pairs, demonstrating the modularity of the platform. Together, these complementary systems provide versatile approaches for recording, monitoring, and discovering RPI-associated biology and molecular environments.<\/jats:p>","DOI":"10.1093\/nar\/gkag928","type":"journal-article","created":{"date-parts":[[2026,9,15]],"date-time":"2026-09-15T12:00:22Z","timestamp":1789473622000},"source":"Crossref","is-referenced-by-count":0,"title":["Development of CRISPR\/Cas13-based analytical tools to study RNA\u2013protein interactions"],"prefix":"10.1093","volume":"54","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-0225-9525","authenticated-orcid":false,"given":"Keita","family":"Yamamoto","sequence":"first","affiliation":[{"name":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo , Tokyo, 108-8639,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shiori","family":"Shikata","sequence":"additional","affiliation":[{"name":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo , Tokyo, 108-8639,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yangying","family":"Hao","sequence":"additional","affiliation":[{"name":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo , Tokyo, 108-8639,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4568-9940","authenticated-orcid":false,"given":"Takuya","family":"Tomita","sequence":"additional","affiliation":[{"name":"Division of Protein Metabolism, The Institute of Medical Science, The University of Tokyo , Tokyo, 108-8639,","place":["Japan"]},{"name":"Protein Metabolism Project, Tokyo Metropolitan Institute of Medical Science , Tokyo, 156-8506,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rina","family":"Kanai","sequence":"additional","affiliation":[{"name":"Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo , Tokyo, 108-8639,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Els","family":"Verhoeyen","sequence":"additional","affiliation":[{"name":"CIRI-International Center for Infectiology Research, Inserm, U1111, Universit\u00e9 Claude Bernard Lyon 1, CNRS, UMR5308, Ecole Normale Sup\u00e9rieure de Lyon, Universit\u00e9 Lyon , 69007,Lyon ,","place":["France"]},{"name":"Universit\u00e9 C\u00f4te d\u2019Azur, INSERM, C3M , 06204 Nice ,","place":["France"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yasushi","family":"Saeki","sequence":"additional","affiliation":[{"name":"Division of Protein Metabolism, The Institute of Medical Science, The University of Tokyo 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