Chromatin remodeling and dna topology in transcription and genome stability

Abstract: Eukaryotic DNA is wrapped around histone proteins to form nucleosomes, the fundamental repeati ng unit of chromatin. DNA packaging into chromatin both solves and creates problems. It allows the centimeters, or even meters, of DNA that constitute a eukaryotic genome to fit inside a micrometer - scale cell nucleus. Nucleosomes also block access to the D NA, necessitating complex rearrangements to allow for transcription, replication, recombination, or repair, while also providing a way to regulate these processes. ATP - dependent chromatin remodelers slide, assemble, disassemble, and alter nucleosomes to en able and regulate DNA - dependent processes. In parallel, topoisomerases relieve the tangles, torsional stress, and supercoils generated when DNA is exposed and unwound. Topoisomerases also enable efficient nucleosome remodeling. In this thesis, we use genom ewide and single - locus techniques to study the interplay between DNA topoisomerases, Snf2 family chromati n remodelers, and transcription in the fission yeast Schizosaccharomyces pombe. We find that topoisomerase activity is essential for transcription elon gation and for proper chromatin structure at genes, which in turn are required for efficient transcription initiation and termination. This is partially mediated by cooperation with chromatin remodelers. We also find that the fission yeast Chd1 subfamily r emodelers maintain correct gene body nucleosome positioning, which inhibits cryptic transcription initiation. Finally, we show that the Fun30 subfamily chromatin remodeler Fft2 is involved in centromere function and heterochromatic silencing, as well as th e full transcription of highly transcribed genes. Fft2 and its paralog Fft3 also regulate the transcriptional response to stress. As a part of this function, Fft2 and Fft3 repress retrotransposons by a novel mechanism, in which they enforce the use of an a lternative transcription start site.