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Specificity of translational control during unfolded protein response

Final Report Summary - TRANSLATE (Specificity of translational control during unfolded protein response)

The project’s aim was to determine how RNA-binding proteins (RBPs) regulate translation of specific sets of mRNAs, and how the following factors contribute to this regulation:
1) mRNA structure,
2) low-complexity sequences in RBPs,
3) the position of protein-RNA interactions
The functions of these factors were studied during cellular differentiation, and during response to cellular stress, in particular the unfolded protein response (UPR). Here I sum up the achievements for each of these aims.

1) We have developed a method hybrid iCLIP (hiCLIP), which identified functionally important secondary mRNA structures that interact with the RBP Staufen1 in HEK293 cells, studied their impact on mRNA translation and stability, and performed computational analysis of mRNA structures, as described in our publication (Sugimoto et al, Nature 2015). This uncovered the unforeseen importance of long-range RNA structures in the 3’ UTRs. We have then using hiCLIP to produce further data for Staufen proteins (STAU1 and STAU2) in variety of systems, such as upon induction of UPR, in differentiation and in multiple regions of rodent brain across development, which greatly increased our understanding of endogenous secondary RNA structures, its variability and functions.

2. We have uncovered a new form of RNA processing that is important in mammalian long genes, called recursive splicing, and have shown that long genes are primarily expressed in the brain (Sibley et al, Nature 2015). We then described the position-dependent principles of regulating recursive splicing by the exon-junction complex (Blazquez et al, Mol Cell, 2018). We also examined position-dependent principles that explain TDP-43 regulates RNA processing, for which we established new computational tools (Rot et al, Cell rep, 2017). We then studied the role of these principles in cellular differentiation, which uncovered how a long RNA (a scaffold of paraspeckles) acts in cross-regulation with TDP-43 to regulate early cell fate transition of embryonic stem cells (Modic et al, Mol Cell, 2019). Finally, we have optimized experimental and computational tools for analysis protein-RNA regulatory networks and positional principles of regulation, as described in recent reviews (Lee et al, Mol Cell 2018, Chakrabarti et al, Annual rev data sci, 2018).

3) We have performed iCLIP and RNA-seq experiments to study the function of low-complexity sequences in the RNA assembly and function of RBPs. We have particularly focused on the regulation of RNA elements derived from retrotransposable elements, which turned out to be particularly relevant in this aspect (Attig et al, eLife 2016, Attig et al, Cell 2018, Attig and Ule, Bioessays, 2019).

While increasing our understanding of fundamental mechanisms of gene regulation, these findings also have strong biomedical implications. Our insights are of great relevance to amyotrophic lateral sclerosis (ALS), where the factors we’ve studied, such as TDP-43, MATR3, STAU1 and paraspeckles, are particularly important. By characterising the function of these factors, and cross-regulation between them, we demonstrated how an unbalance in the regulatory networks that they control may contribute to ALS.