Xrn1 activates transcription, translation and decay of mRNAs encoding membrane proteins

To study the role of the exonuclease Xrn1 in translational control, we performed ribosome profiling and RNA-seq in Xrn1-depleted cells. By using an auxin-inducible degron, we were able to study immediate effects of Xrn1 depletion in translational control. Therefore, we could overcome experimental limitations associated to stable deletion mutants. Overall design: mRNA and ribosome footprints were obtained as described in (Ingolia, 2009) from BY25598 cells (Nishimura and Kanemaki, 2014) modified to express an Xrn1 protein tagged with an auxin inducible degron (AID). Libraries were obtained from cells treated with auxin for 30 minutes (t30) and compared from libraries from untreated controls (t0). After 30 minutes of treatment, Xrn1 protein was reduced to less than 10%. For the Xrn1-D208A mutant, a BY4741 background was used. Wild-type and mutant strains were grown to logarithmic phase and collected at approximately 0.5 OD.

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Blasco-Moreno B, de Campos-Mata L, Böttcher R, García-Martínez J, Jungfleisch J, Nedialkova DD, Chattopadhyay S, Gas ME, Oliva B, Pérez-Ortín JE, Leidel SA, Choder M, Díez J