Alternative gene ends: the crosstalk of RNA cleavage and transcription termination

Project Information

AlternativeEnds

Grant agreement ID: 101042642

DOI

10.3030/101042642

EC signature date 31 July 2022

Start date 1 October 2022

End date 30 September 2027

Funded under

• European Research Council (ERC)

Total cost

€ 1 493 850,00

EU contribution

€ 1 493 850,00

Coordinated by

UNIWERSYTET IM. ADAMA MICKIEWICZA WPOZNANIU
Poland

Periodic Reporting for period 1 - AlternativeEnds (Alternative gene ends: the crosstalk of RNA cleavage and transcription termination)

Reporting period: 2022-10-01 to 2025-03-31

Summary of the context and overall objectives of the project

The human genome contains only ~20.000 genes, however, most of them encode multiple transcripts resulting from alternative promoter usage, splicing, and 3’ end selection. Gene 3’ ends can be defined by the positions of RNA 3’ cleavage, or the location where RNA polymerase II terminates transcription. Alternative 3’ ends determine the properties of the encoded protein: typically its abundance, but sometimes also domain structure – as for immunoglobulin M heavy chain which is membrane-bound or secreted depending on the 3’ cleavage site. Widespread changes in 3’ end usage are characteristic of many processes e.g. differentiation and cancer like neuroblastoma. We do not understand what drives this selectivity. This research projects tackles the relationship of RNA polymerase II entering into termination mode with RNA 3’ cleavage. Ultimately, understanding the complex crosstalk between RNA cleavage and transcription termination in alternative 3’ end selection will enable the manipulation of this process e.g. to alleviate diseases such as neuroblastoma.

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

This research project has allowed our lab to complement our previous genomics and nascent transcriptomics based approaches with biochemical and high-throughput microscopy methodologies.
We have performed a number of nascent and steady-state transcriptomics experiments on neuroblastoma and iPSC differentiation systems to find out about the timing of gene end changes.
We have set up a biochemistry in vitro system, that allows us to test our hypotheses related to factors influencing 3’ RNA cleavage directly in the test tube.
A novel microscopy-based methodology for direct detection of transcription termination windows allowed us to perform a screening of 5000 compounds with respect to their ability to influence alternative transcription termination.
Combining those unique integrative and separation-of-function approaches will yield a comprehensive view of alternative gene end regulation.

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)

Our novel methodology for directly measuring alterations in transcription termination is not only valuable in basic research, but could be of use for pharmaceutical purposes. Therefore we have recently applied for a Proof of Concept funding.
Our value proposition is improving cancer therapy by identification of novel anti-cancer candidate drug leads modulating transcription termination, bridging molecular cancer biology and therapeutic applications. We have developed a methodology to directly measure alterations in transcription termination and successfully subjected it to miniaturization and automatization processes. We are applying for funding to validate a screening service platform to identify small molecule inhibitors of transcription termination.