STOP-OR-GO · Unraveling the network that controls the fate of RNA Polymerase II during early elongation.

The repertoire of messenger RNAs (mRNAs) in a cell dictates cell identity and function. Therefore, mRNA expression is tightly controlled. A previously underappreciated regulatory step is early transcription termination, which can abort the synthesis of full-length mRNAs. The early termination of many non-coding RNAs prevents transcriptional interference and genomic instability. Thus, cells need to correctly balance early termination and productive elongation at both coding and non-coding loci. Why elongation is favoured at some loci, and termination at others, is poorly understood.To understand how the balance between elongation and termination is achieved, we need to know what sequence elements and proteins are involved, and how they work together. These regulatory sequences and proteins have not been systematically identified. Using INSERT-seq, I have identified novel candidate regulators that I will study here in more detail. The same reporter setup will be adapted to identify novel trans-acting regulators of the elongation/termination balance. These approaches act synergistically to uncover the network of regulators. I will then apply a combination of unbiased and hypothesis-driven experiments to understand the mechanisms of regulation. We will also focus on understanding how early termination is promoted by ZC3H4 (Restrictor), a recently identified suppressor of non-coding RNAs. The work proposed here will uncover the principles that decide if transcription of a locus will terminate early, an essential step towards fully understanding transcription regulation. Knowing the sequence and protein regulators that determine the fate of early elongating RNAPII will open opportunities to study how disease mutations affect their function. Moreover, understanding the control of this elongation/termination balance will also provide us with tools to manipulate this balance. This will improve our ability to design sequences for optimal transgene expression in gene therapy.