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A systematic RNAi synthetic interaction screen reveals a link between p53 and snoRNP assembly

Abstract

TP53(tumour protein 53) is one of the most frequently mutated genes in human cancer and its role during cellular transformation has been studied extensively. However, the homeostatic functions of p53 are less well understood. Here, we explore the molecular dependency network of TP53 through an RNAi-mediated synthetic interaction screen employing two HCT116 isogenic cell lines and a genome-scale endoribonuclease-prepared short interfering RNA library. We identify a variety of TP53 synthetic interactions unmasking the complex connections of p53 to cellular physiology and growth control. Molecular dissection of the TP53 synthetic interaction with UNRIP indicates an enhanced dependency of TP53-negative cells on small nucleolar ribonucleoprotein (snoRNP) assembly. This dependency is mediated by the snoRNP chaperone gene NOLC1 (also known as NOPP140), which we identify as a physiological p53 target gene. This unanticipated function of TP53 in snoRNP assembly highlights the potential of RNAi-mediated synthetic interaction screens to dissect molecular pathways of tumour suppressor genes.

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Figure 1: Genome-scale TP53 synthetic interaction screen.
Figure 2: Depletion phenotypes of knockdowns increasing the wild-type/knockout ratio.
Figure 3: SMN complex localization on UNRIP depletion.
Figure 4: NOLC1 differentially associates with UNRIP in wild-type and knockout cells and NOLC1 is a p53 target gene.
Figure 5: rRNA pseudouridylation is dependent on p53 and UNRIP.

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Acknowledgements

We would like to thank all members of the Buchholz laboratory for discussions and sharing reagents. We thank A. K. Heninger for help with carrying out the screen, V. Surendranath for esiRNA design, M. Theis, S. Rose and A. Weise for esiRNA production and I. Poser for assistance with BAC cell line generation. This work was supported by the Max Planck Society, the German Federal Ministry of Education and Research grants Go-Bio (0315105), DiGtoP (01GS0859) and the DFG grant SFB655.

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D.B.K., M.S., N.C.H., M.J. and K.M.N. carried out experiments, M.P-R. analysed data, A.S., M.M. and F.B. planned the project and D.B.K. and F.B. wrote the manuscript.

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Correspondence to Frank Buchholz.

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Krastev, D., Slabicki, M., Paszkowski-Rogacz, M. et al. A systematic RNAi synthetic interaction screen reveals a link between p53 and snoRNP assembly. Nat Cell Biol 13, 809–818 (2011). https://doi.org/10.1038/ncb2264

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