Crosstalk between chromatin factors & RNA pol II pausing
RNA pol II pausing is a dynamic process regulated during development, which suggests that both epigenetic and genetic factors influence pausing. Conversely, paused RNA pol II complex itself can be instructive in shaping the chromatin around promoters. We aim to carefully dissect the crosstalk between core transcriptional machinery and chromatin modifying systems. In particular we will take a systems biology approach to decipher how DNA sequences and chromatin factors function in concert to regulate pol II pausing.
DNA sequences at promoters are thought to influence pol II pausing, and also to recruit chromatin modifying machinery. The quantitative principles of this are yet to be learnt and we will approach this issue by integrating chromatin profiles with sequence- and pausing information. By systematically changing DNA sequences in vivo, we will identify motifs that regulate chromatin modification and RNA pol II pausing.
Most studies rely on knock-down of chromatin modifying proteins to study how they influence pol II activity in cell populations. Given the dynamic nature of the pausing process, the slow depletion of factors by the knock-down approach is unlikely to lend itself for precise analyses. We will develop new genetic tools that rapidly degrade proteins in vivo such that pausing analyses can be performed in single or groups of cells. In combination with global transcriptome and chromatin profiling, such a method will answer fundamental questions relating chromatin and transcription.