Molecular mechanisms and functions of global chromatin control

Project Summary/Abstract The long term goal of the proposed study is to determine, at the molecular level, mechanisms and functions of chromatin regulation at a global level. Chromatin regulation profoundly affects a wide variety of DNA-dependent processes, including transcription, DNA replication, recombination, DNA repair, and DNA damage response. Therefore, elucidating the mechanisms of chromatin regulation is a necessary prerequisite for understanding how these essential processes are controlled. One of the major challenges the chromatin field is to elucidate how chromatin is globally reprogrammed during processes like cell fate determination, development and cell-cycle control. This is a particularly important challenge, because it was recently determined that mutations in chromatin regulators represent one major class of so called cancer driver mutations, yet how these mutations drive cancer remains unknown. Therefore, elucidating the mechanisms of chromatin regulation impacts not only the researchers who study fundamental principles of DNA-dependent processes, but also cancer biologists. We have previously elucidated how chromatin regulation affects transcription, DNA replication, S phase checkpoint and recombination using budding yeast as a model organism. Like most studies in the field, we did our work during the mitotic cell-cycle. However, yeast cells in the wild, like other eukaryotic cells, spend most of their time in quiescence. Quiescence is associated with massive chromatin reprogramming for global condensation. Because the vast majority of work on chromatin regulation has been done during mitotic cell-cycle, we have little idea of how chromatin is regulated during the time cells spend most of their time. In order to understand the whole picture of chromatin regulation in vivo, it is essential to understand mechanisms and functions of chromatin regulation during quiescence. In the next funding period, we will ask the following questions in quiescent state: 1) How is chromatin globally reprogrammed by ATP-dependent chromatin remodeling factors? 2) How are chromatin domains and nucleosome array folding regulated? 3) How is gene expression regulated post-transcriptionally at a global scale? We will use the combination of genomics, molecular genetics, EM, modeling and biochemistry to identify novel mechanisms by which highly conserved chromatin regulators function to massively reprogram chromatin in a genome-wide scale. In the long run, these studies will allow us to compare and integrate the principles of chromatin regulation throughout the mitotic cell-cycle and quiescence, such that we can obtain the full picture of chromatin regulation.