A06: Regulation of alternative polyadenylation by RNA-binding proteins in senescence

Cellular senescence is one of the hallmarks of biological ageing and refers to the process by which cells cease proliferation and enter a state of growth arrest without undergoing cell death. Severe alterations of the transcriptome and proteome accompany the phenotypic changes of senescent cells (reviewed in López-Otín et al. 2023). These systemic changes can be attributed—in one part—to active regulation and—in another part—to a decline in transcriptional and splicing fidelity (Debès…Müller…Papantonis, Beyer, 2023) leading to the occurrence of erroneous RNA sequences, incorrect RNA folding and localisation. The general consequence is that RNA maturation and quality control processes are impacted including but not limited to 3′ end processing, RNA localization, nonsense-mediated decay and ribosome-associated degradation.

Alternative polyadenylation (APA) denominates an important regulatory step in mammalian RNA processing generating distinct mRNA 3′ ends through the action of the cleavage and polyadenylation-ribonucleoprotein (CPA-RNP) machinery (reviewed in (Tian & Manley, 2017)). APA can impact mRNA stability (Sandberg et al. 2008; Spies et al. 2013; Thivierge et al. 2018) (relevant for Gehring, A08), nuclear export (Djebali et al. 2012; Neve et al. 2016) (relevant for Tresch/ Mayer, A07), translation (Irier et al. 2009; Trentini et al. 2020) (relevant for Trentini, B01, Ignatova/ Tresch, B04), and cellular localisation (Böckers et al. 2004; An et al. 2008; Berkovits & Mayr, 2015) (relevant for Vilchez, B06, Riemer, B03) due to the occurrence of cis-regulatory elements in the 3′ untranslated region (UTR) of mRNAs or the binding of trans-acting factors (Smibert et al. 2012). The preferential usage of the proximal or distal poly(A) site (PAS) can result in UTR shortening or lengthening, respectively. In the context of senescence, a global lengthening of the 3′ UTR due to favouring of the distal PAS has been described (Chen et al. 2018; Wang et al. 2020). It remains elusive whether the global change in PAS usage in senescence is connected to changes in fidelity of the transcription and splicing machineries or a result of fidelity loss of APA itself.

To this end, we will explore how a decline in transcriptional and splicing fidelity in senescent cells affects APA (Aim 1), whether and how senescence impacts the fidelity of the CPA-RNP machinery (Aim 2), and ultimately how interference with APA can have pro- or anti-senescence effects (Aim 3). To achieve this, we will compare replicative and irradiation-induced senescence in IMR90 cells, as these cells are an established system for cellular senescence and are shared with the project on transcriptional fidelity under genotoxic stress (Beli/Papantonis, A02). These two causes of senescence will provide insights on convergent and stressor-specific effects.