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ERC

DECOR Report Summary

Project ID: 649030
Funded under: H2020-EU.1.1.

Periodic Reporting for period 1 - DECOR (Dynamic assembly and exchange of RNA polymerase II CTD factors)

Reporting period: 2015-08-01 to 2017-01-31

Summary of the context and overall objectives of the project

The C-terminal domain (CTD) of the RNA polymerase II (RNAPII) largest subunit coordinates co-transcriptional processing and it is decorated by many processing factors throughout the transcription cycle. To determine how these accessory factors assemble and exchange on the CTD of RNAPII has remained a major challenge. In this project, we aim to unravel the structural and mechanistic bases for the dynamic assembly of RNAPII CTD with its transcription and processing factors.
The architecture and dynamics of CTDsome are not only important for a general understanding of transcription regulation and co-transcriptional processing, but also have implications for the design of novel therapies. For example, viral RNA polymerase of influenza binds the CTD in order to replicate viral RNAs. The detailed knowledge of interactions in the CTDsome will be critical for the future development of new anti-viral agents.
Our study will answer the long-standing questions of how the overall CTD structure is modulated on binding to processing factors, and whether these factors cross-talk and compete with each other.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

In the first period of the project we reached several important milestones: (i) we prepared and biochemically characterized the studied proteins and their fragments, (ii) we prepared stable protein-peptide complexes and performed their characterization, (iii) we carried out NMR data acquisition and resonance assignments of the studied complexes, (iv) we performed SAXS and X-ray data measurement and data analyses (v) We determined the first structures of the studied complexes, (vi) we started with functional analyses of the studied systems. Altogether, this is in accord with the proposed plan and it will enable us to probe the structural basis of the CTD code and CTDsome assembly in the next years of the project.
We wish to highlight that the first structural and biochemical data from this project were just accepted for publication in EMBO reports. In this paper in press, we reported the structural and functional characterization of Thr4 phosphorylated CTD-- Rtt103 complex. Our data reveal a direct recognition of phosphorylated Thr4 by Rtt103p, the phosphorylation mark previously thought to be incompatible with recruitment of CTD reader factors. Based on our data, we proposed that the CTD code of RNAP II is degenerated, a feature which is similar to the codon degeneracy.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The CTDsome assembly/disassembly is encoded by the so called CTD code. This concept which was proposed almost a decade ago considers that the association of specific factors with the CTD is dictated by different post-translational modification patterns and conformational changes in the CTD. Within this project, we found that the CTD code of RNAP II is degenerated, that is the recruitment of a single CTD binding factor may be coded for by more than one letter of the CTD code. This is conceptually new consideration in the field of transcription regulation and has a number of practical consequences. For example, it explains how CTD binding factors can be recruited to the poorly conserved heptad repeats, which are frequently present in all eukaryotes It also explains how the CTD-binding factors can tolerate some errors or imperfections in phosphorylation of the CTD.
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