A massively parallel reporter assay reveals focused and broadly encoded RNA localization signals in neurons

Martin Mikl, Davide Eletto, Malak Nijim, Minkyoung Lee, Atefeh Lafzi, Farah Mhamedi, Orit David, Simona Baghai Sain, Kristina Handler, Andreas E. Moor

Research output: Contribution to journalArticlepeer-review


Asymmetric subcellular mRNA localization allows spatial regulation of gene expression and functional compartmentalization. In neurons, localization of specific mRNAs to neurites is essential for cellular functioning. However, it is largely unknown how transcript sorting works in a sequence-specific manner. Here, we combined subcellular transcriptomics and massively parallel reporter assays and tested ∼50 000 sequences for their ability to localize to neurites. Mapping the localization potential of >300 genes revealed two ways neurite targeting can be achieved: focused localization motifs and broadly encoded localization potential. We characterized the interplay between RNA stability and localization and identified motifs able to bias localization towards neurite or soma as well as the trans-acting factors required for their action. Based on our data, we devised machine learning models that were able to predict the localization behavior of novel reporter sequences. Testing this predictor on native mRNA sequencing data showed good agreement between predicted and observed localization potential, suggesting that the rules uncovered by our MPRA also apply to the localization of native full-length transcripts.

Original languageEnglish
Pages (from-to)10643-10664
Number of pages22
JournalNucleic Acids Research
Issue number18
StatePublished - 14 Oct 2022

Bibliographical note

Publisher Copyright:
© 2022 The Author(s). Published by Oxford University Press on behalf of Nucleic Acids Research.


  • Neurites/metabolism
  • Neurons/metabolism
  • RNA Stability
  • RNA, Messenger/genetics
  • Trans-Activators/metabolism


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