Effect of top2 and hmo1 on chromatin architecture and transcription in yeast

DNA topoisomerase-2 and high mobility group protein Hmo1 are known to regulate chromatin architecture by regulating gene boundaries. Here we report how these proteins affect global RNA level after inactivation of Top2 and Hmo1. Our data indicate that inactivating Hmo1 has a drastic effect on transcription levels of 20% yeast genes, however, this phenomenon can slightly be rescued by inactivating Top2 functions. Also, we study the Top2 and Top1 role in nucleosome architecture with and without expressing E.coli TopA. In top2-1;top1∆ condition with TopA expressed, it affects the nucleosome occupancy at the global level compared with top2-1;top1∆-Control plasmid. The ChIA-PET (Chromatin interaction analysis by paired-end tag sequencing) method is used to address whether a specific protein is engaged in the chromosomal interactions. Epitope tagged Top2 protein is used as probe in ChIA-PET experiments to map Top2 mediated chromatin-chromatin interactions. RNA-seq for yeast strains: wildtype, top2-1, hmo1∆, and hmo1∆;top2-1. ChIP-seq for Hmo1 Protein: Hmo1tag-ControlPlasmid, Hmo1tag-top2-1;top1∆-TopAPlasmid. Histone H3 ChIP-seq: wildtype-ControlPlasmid, wildtype-TopAPlasmid, top2-1;top1∆-ControlPlasmid, top2-1;top1∆-TopAPlasmid.