Genome-wide promotor binding profiling of Protein phosphatase 1 and its major nuclear targeting subunits

Protein phosphatase-1 (PP1) is a key regulator of transcription and is targeted to promoter regions via associated proteins. However, the chromatin binding sites of PP1 have never been studied in a systematic and genome-wide manner. Methylation-based DamID profiling in HeLa cells has enabled us to map hundreds of promoter binding sites of PP1 and three of its major nuclear interactors, i.e. RepoMan, NIPP1 and PNUTS.  In the first part of the thesis, we show that the α, β and γ isoforms of PP1 largely bind to distinct subsets of promoters and can also be differentiated by their promoter-binding pattern. PP1β emerged as the major promoter-associated isoform and shows an overlapping binding profile with PNUTS at dozens of active promoters. Surprisingly, most promoter binding sites of PP1 are not shared with RepoMan, NIPP1 or PNUTS, hinting at the existence of additional, largely unidentified chromatin-targeting subunits. In the second part of the thesis, we further found that PP1 does not affect the promoter-targeting of RepoMan, but enhances the binding affinity of PNUTS and alters the binding specificity of NIPP1. Our data disclose an unexpected specificity and complexity in the promoter binding of PP1 isoforms, and reveal that PP1 guides the chromatin targeting of some of its own interactors. In the third part of the thesis we identified the PP1β-PNUTS holoenzyme as overlapping with the elongating Pol II-pS2 complex both bioinformatically andin vivo, and further link this complex to two major gene clusters, namely histone and small nucleolar RNA genes. This revealed a potential linkbetween the PP1β-PNUTS holoenzyme and the 3 end processing of these two gene clusters.

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Keywords:cancer, treatment

Disciplines:Biochemistry and metabolism, Medical biochemistry and metabolism

Project type:PhD project