Modulating chromatin by transcription and nucleosome turnover : a genome-wide study in fission yeast

Eukaryotic DNA is wrapped around histone proteins to form a nucleosome, the basic structural unit of chromatin. Multiple levels of chromatin organization are required to compact DNA into chromosomes, to ensure an accurate cell division. The dynamic organization of chromatin modulates nuclear processes including transcription, replication and DNA repair, through altering the accessibility of DNA to regulatory proteins. Changes in chromatin structure are mediated by modification of histone proteins, remodeling of nucleosomes, incorporation of histone variants, histone turnover, noncoding RNAs and nonhistone DNA-binding proteins. Chromatin is organized into active and repressed domains separated by chromatin boundaries. The establishment and maintenance of distinct chromatin domains has important implications in regulation of gene expression. In this thesis we have used fission yeast, Schizosaccharomyces pombe as a model organism to study the interplay between histone modifications, transcription and histone turnover in modulating chromatin.

One of our main findings is that histone H2B is monoubiquitinated (H2Bub1) at centromeric chromatin. H2Bub1 dependent transcription of centromeric chromatin is required for establishment of active centromeric chromatin to ensure accurate chromosomal segregation during cell division. In this thesis we also showed that the Paf1/Leo1 heterodimer is involved in transcription dependent histone turnover to maintain active chromatin states. Loss of Paf1/Leo1 prevents histone turnover, which in turn leads to heterochromatin stabilization. In addition, by using Podbat, an in-house tool developed to visualize and analyze genome-wide data, we suggested a role for histone variant H2A.Z in DNA damage responses. We further proposed that H2A.Z is incorporated into nucleosomes in an Swr1-independent manner following genotoxic stress.

List of scientific papers

I. Sadeghi L, Bonilla C, Strålfors A, Ekwall K, Svensson JP. Podbat: a novel genomic tool reveals Swr1-independent H2A.Z incorporation at gene coding sequences through epigenetic meta-analysis. PLoS Comput Biol. 2011 Aug; 7(8): e1002163
https://doi.org/10.1371/journal.pcbi.1002163

II. Sadeghi L, Siggens L, Svensson JP, Ekwall K. Centromeric histone H2B monoubiquitination promotes noncoding transcription and chromatin integrity. Nat Struct Mol Biol. 2014 Mar; 21(3): 236-43
https://doi.org/10.1038/nsmb.2776

III. Sadeghi L, Prasad P, Ekwall K, Cohen A, Svensson JP. The Paf1 complex factors Leo1 and Paf1 promote local histone turnover to modulate chromatin states in fission yeast. EMBO Rep. 2015 Oct 29. pii: e201541214
https://doi.org/10.15252/embr.201541214