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Subcellular spatial transcriptomics identifies three mechanistically different classes of localizing RNAs

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  • Lucia Cassella

    (European Molecular Biology Laboratory
    Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences)

  • Anne Ephrussi

    (European Molecular Biology Laboratory)

Abstract

Intracellular RNA localization is a widespread and dynamic phenomenon that compartmentalizes gene expression and contributes to the functional polarization of cells. Thus far, mechanisms of RNA localization identified in Drosophila have been based on a few RNAs in different tissues, and a comprehensive mechanistic analysis of RNA localization in a single tissue is lacking. Here, by subcellular spatial transcriptomics we identify RNAs localized in the apical and basal domains of the columnar follicular epithelium (FE) and we analyze the mechanisms mediating their localization. Whereas the dynein/BicD/Egl machinery controls apical RNA localization, basally-targeted RNAs require kinesin-1 to overcome a default dynein-mediated transport. Moreover, a non-canonical, translation- and dynein-dependent mechanism mediates apical localization of a subgroup of dynein-activating adaptor-encoding RNAs (BicD, Bsg25D, hook). Altogether, our study identifies at least three mechanisms underlying RNA localization in the FE, and suggests a possible link between RNA localization and dynein/dynactin/adaptor complex formation in vivo.

Suggested Citation

  • Lucia Cassella & Anne Ephrussi, 2022. "Subcellular spatial transcriptomics identifies three mechanistically different classes of localizing RNAs," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    • Handle: RePEc:nat:natcom:v:13:y:2022:i:1:d:10.1038_s41467-022-34004-2
    DOI: 10.1038/s41467-022-34004-2
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    References listed on IDEAS

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    1. Stavroula Mili & Konstadinos Moissoglu & Ian G. Macara, 2008. "Genome-wide screen reveals APC-associated RNAs enriched in cell protrusions," Nature, Nature, vol. 453(7191), pages 115-119, May.
    2. In-Gyun Lee & Mara A. Olenick & Malgorzata Boczkowska & Clara Franzini-Armstrong & Erika L. F. Holzbaur & Roberto Dominguez, 2018. "A conserved interaction of the dynein light intermediate chain with dynein-dynactin effectors necessary for processivity," Nature Communications, Nature, vol. 9(1), pages 1-12, December.
    3. Isabel M. Palacios & David Gatfield & Daniel St Johnston & Elisa Izaurralde, 2004. "An eIF4AIII-containing complex required for mRNA localization and nonsense-mediated mRNA decay," Nature, Nature, vol. 427(6976), pages 753-757, February.
    4. Simon L. Bullock & David Ish-Horowicz, 2001. "Conserved signals and machinery for RNA transport in Drosophila oogenesis and embryogenesis," Nature, Nature, vol. 414(6864), pages 611-616, December.
    5. Olivier Hachet & Anne Ephrussi, 2004. "Splicing of oskar RNA in the nucleus is coupled to its cytoplasmic localization," Nature, Nature, vol. 428(6986), pages 959-963, April.
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