Functional Coupling in Gene Expression and Gene Regulation

There is extensive functional crosstalk among the molecular machinery responsible for genome replication/maintenance, gene expression and gene regulation. An active area of molecular biological research is concerned with the question of how genome organization, transcription, pre-mRNA processing as well as nuclear export, cytoplasmic localization, translation and degradation of mRNAs are functionally coupled via non-coding RNAs, RNA-binding proteins and RNA-modifying enzymes, and how such coupling is influenced by environmental cues.

• Explain with which methods you can selectively control histone modifications at a particular locus.
• Using electrophoretic mobility shift assays, you observed that protein X binds RNA Y in vitro. How could you test whether this binding event also occurs in vivo? How can you test which other RNAs protein X associates with transcriptome-wide?
• Explain the role of the C-terminal domain (CTD) of RNA polymerase II for the transcription process. How can you experimentally test presumed functions of the CTD?
• Design an experiment to analyze which macromolecules are involved in the process of pre-mRNA 5’-capping. What is the function of the 5’-cap and why do bacteria not process their mRNAs? To which other gene expression/regulation processes is 5'-capping coupled and how?
• How can you use the CRISPR/Cas9 technology in a transcriptome-wide manner to identify RNA-binding proteins that control a particular transcription event? How can you apply CRISPR/Cas9 technology to investigate further processing of individual transcripts in vivo?