Nanodynamo quantifies subcellular RNA dynamics revealing extensive coupling between steps of the RNA life cycle

Lucia Coscujuela Tarrero, Valeria Famà, Giacomo D’Andrea, Simone Maestri, Anna Polo, Stefano Biffo, Mattia Furlan () and Mattia Pelizzola ()
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Lucia Coscujuela Tarrero: Istituto Italiano di Tecnologia (IIT)
Valeria Famà: Istituto Italiano di Tecnologia (IIT)
Giacomo D’Andrea: Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”
Simone Maestri: Istituto Italiano di Tecnologia (IIT)
Anna Polo: Istituto Italiano di Tecnologia (IIT)
Stefano Biffo: Istituto Nazionale Genetica Molecolare “Romeo ed Enrica Invernizzi”
Mattia Furlan: Istituto Italiano di Tecnologia (IIT)
Mattia Pelizzola: Istituto Italiano di Tecnologia (IIT)

Nature Communications, 2024, vol. 15, issue 1, 1-19

Abstract: Abstract The coordinated action of transcriptional and post-transcriptional machineries shapes gene expression programs at steady state and determines their concerted response to perturbations. We have developed Nanodynamo, an experimental and computational workflow for quantifying the kinetic rates of nuclear and cytoplasmic steps of the RNA life cycle. Nanodynamo is based on mathematical modelling following sequencing of native RNA from cellular fractions and polysomes. We have applied this workflow to triple-negative breast cancer cells, revealing widespread post-transcriptional RNA processing that is mutually exclusive with its co-transcriptional counterpart. We used Nanodynamo to unravel the coupling between transcription, processing, export, decay and translation machineries. We have identified a number of coupling interactions within and between the nucleus and cytoplasm that largely contribute to coordinating how cells respond to perturbations that affect gene expression programs. Nanodynamo will be instrumental in unravelling the determinants and regulatory processes involved in the coordination of gene expression responses.

Date: 2024
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DOI: 10.1038/s41467-024-51917-2

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