Chromatin remodeling and dna topology in transcription and genome stability

Eukaryotic DNA is wrapped around histone proteins to form nucleosomes, the fundamental repeating 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 DNA, 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 enable 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 genomewide and single-locus techniques to study the interplay between DNA topoisomerases, Snf2 family chromatin remodelers, and transcription in the fission yeast Schizosaccharomyces pombe. We find that topoisomerase activity is essential for transcription elongation 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 remodelers 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 the 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 alternative transcription start site.

List of scientific papers

I. Durand-Dubief M, Persson J, Norman U, Hartsuiker E, Ekwall K (2010). Topoisomerase I regulates open chromatin and controls gene expression in vivo. EMBO J. 29 : 2126-3 214.
https://doi.org/10.1038/emboj.2010.109

II. Durand-Dubief M, Svensson JP, Persson J, Ekwall K (2011). Topoisomerases, chromatin and transcription termination. Transcription. 2:66-70.
https://doi.org/10.4161/trns.2.2.14411

III. Pointner J, Persson J, Prasad P, Norman-Axelsson U, Strålfors A, Khorosjutina O, Krietenstein N, Svensson JP, Ekwall K, Korber P (2012). CHD1 remodelers regulate nucleosome spacing in vitro and align nucleosomal arrays over gene coding regions in S. pombe. EMBO J. 31:4388-4403.
https://doi.org/10.1038/emboj.2012.289

IV. Persson J, Steglich B, Smialowska A, Ekwall K. Controlling retrotransposons and maintaining genome integrity: Fun30 remodeler cooperation. [Manuscript]