The role of mRNA 5' end capping in the transcriptional regulation of gene expression in eukaryotic cells.

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The 5' RNA m7G cap is an essential modification of the RNA Polymerase II-dependent (Pol II) transcripts. An efficient mRNA capping is crucial for mRNA stability as it protects the RNA from 5'-3' degradation. The cap functions also as a platform for the Cap Binding Complex (CBC) which is essential for cellular RNA metabolism including nuclear export, degradation, and translation. Although the m7G cap has a crucial function in the mRNA biogenesis, very little is known about its direct role in transcription and ultimately, in gene expression. Previous reports indicate that defects in mRNA capping may affect the transition from transcription initiation to elongation or trigger premature transcription termination. Thus, the project will investigate in the model organism Saccharomyces cerevisiae how the mRNA cap, the capping enzymes and the capping process regulate transcription and RNA synthesis in eukaryotic cells. The student will employ chromatin immunoprecipitation (ChIP-seq) analysis to test genomic positions of Pol II phosphoisoforms as well as RNA analyses of steady-state (RNA-seq and direct RNA-seq) and nascent RNA (4tU RNA-seq) in cap-deficient cells. These approaches will provide a comprehensive analysis of how m7G cap and the capping impact nuclear RNA biology in eukaryotic cells. The outcomes of this project will reveal if and how RNA cap is related to 5'-3' co-transcriptional degradation and will define a correlation between capping, transcription progression and transcription termination of Pol II-transcribed genes.