An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions

Rajagopal, V.; Seiler, J.; Nasa, I.; Cantarella, S.; Theiss, J.; Herget, F.; Kaifer, B.; Schneider, M.; Helm, D.; Koenig, J.; Zarnack, K.; Diederichs, S.; Kettenbach, A. N.; Caudron-Herger, M.

doi:10.1101/2024.09.25.614981

bioRxiv · 10.1101/2024.09.25.614981

An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions

Rajagopal, V.·Seiler, J.·Nasa, I.·Cantarella, S.·Theiss, J.·Herget, F.·Kaifer, B.·Schneider, M.·Helm, D.·Koenig, J.·Zarnack, K.·Diederichs, S.·Kettenbach, A. N.·Caudron-Herger, M.

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Abstract

Ribonucleoprotein complexes are dynamic assemblies of RNA with RNA-binding proteins (RBPs), which can modulate the fate of the RNA molecules from transcription to degradation. Vice versa, RNA can regulate the interactions and functions of the associated proteins. Dysregulation of RBPs is linked to diseases such as cancer and neurological disorders. RNA and RBPs are present in mitotic structures like the centrosomes and spindle microtubules, but their influence on mitotic spindle integrity remains unknown. Thus, we applied the R-DeeP strategy for the proteome-wide identification of RNA-dependent proteins and complexes to cells synchronized in mitosis versus interphase. The resulting atlas of RNA-dependent proteins in cell division can be accessed through the R-DeeP 3.0 database (R-DeeP3.dkfz.de). It revealed key mitotic factors as RNA-dependent such as AURKA, KIFC1 and TPX2 that were linked to RNA despite their lack of canonical RNA-binding domains. KIFC1 was identified as a new interaction partner and phosphorylation substrate of AURKA at S349 and T359. In addition, KIFC1 interacted with both, AURKA and TPX2, in an RNA-dependent manner. Our data suggest a riboregulation of mitotic protein-protein interactions during spindle assembly, offering new perspectives on the control of cell division processes by RNA-protein complexes. HighlightsO_LIDifferential R-DeeP screens in mitosis and interphase are provided as a resource in a user-friendly database at R-DeeP3.dkfz.de C_LIO_LIAn atlas of RNA-dependent proteins in cell division identifies a substantial number of unconventional RNA-binding proteins among mitotic factors C_LIO_LIInvestigation of protein-protein interactions reveals KIFC1 as a new AURKA and TPX2 interaction partner during spindle assembly C_LIO_LIKIFC1, AURKA and TPX2 interact with each other in an RNA-dependent manner and directly bind to RNA C_LIO_LIAURKA phosphorylates KIFC1 at residues S349 and T359 C_LI

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Rajagopal, V., Seiler, J., Nasa, I., Cantarella, S., Theiss, J., Herget, F., Kaifer, B., Schneider, M., Helm, D., Koenig, J., Zarnack, K., Diederichs, S., Kettenbach, A. N., Caudron-Herger, M.. 2024-09-26. An atlas of RNA-dependent proteins in cell division reveals the riboregulation of mitotic protein-protein interactions. https://doi.org/10.1101/2024.09.25.614981

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