PHF3 regulates neuronal gene expression through the Pol II CTD reader domain SPOC

The C-terminal domain (CTD) of the largest subunit of RNA polymerase II (Pol II) is a regulatory hub for transcription and RNA processing. Here, we identify PHD-finger protein 3 (PHF3) as a regulator of transcription and mRNA stability that docks onto Pol II CTD through its SPOC domain. We characterize SPOC as a CTD reader domain that preferentially binds two phosphorylated Serine-2 marks in adjacent CTD repeats. PHF3 drives liquid-liquid phase separation of phosphorylated Pol II, colocalizes with Pol II clusters and tracks with Pol II across the length of genes. PHF3 knock-out or SPOC deletion in human cells results in increased Pol II stalling, reduced elongation rate and an increase in mRNA stability, with marked derepression of neuronal genes. Key neuronal genes are aberrantly expressed in Phf3 knock-out mouse embryonic stem cells, resulting in impaired neuronal differentiation. Our data suggest that PHF3 acts as a prominent effector of neuronal gene regulation by bridging transcription with mRNA decay

Bayes'sche Sequentielle Verfahren in Klinischen Studien

Abweichender Titel nach Übersetzung der Verfasserin/des VerfassersBayesian techniques allow the design of flexible and adaptive trials. This flexibility is given by accepting the Likelihood principle, which is presented in the first chapter, that shows equivalence to the Conditionality principle. The second chapter introduces the Bayesian foundations and finishes with an introduction into hierarchical Bayesian modeling. Latter permits inference about the efficiency of treatments on rare diseases with many subgroups and/or by including patients from multiple clinics into the study. Additionally, a coherent combination of multiple studies is possible in this framework. The third chapter covers decision theory and the intrinsically linked Bayesian hypothesis testing. It further shows some modeling tools available to the statisticians. The fourth chapter presents Bayesian sequential decision theory. Backward induction a method to find an optimal procedure is used to deduce the widely known sequential probability ratio test. This chapter concludes with the introduction of predictive probabilities and the corresponding clinical trial design. The temporal classification is used in the fifth chapter to introduce the reader into clinical trials. The work completes with exemplary clinical studies. A decision theoretical design optimize the simultaneous run of many phase \RM{2} studies in one center is presented in detail. Furthermore, a lung cancer trial designed with predictive probabilities is described. Lastly, accrual of patients for trials on the treatment of rare diseases like sarcomas is challenging. A design that uses hierarchical Bayes to analyze a treatment for twelve different sarcomas is shown.8

A novel non-canonical PIP-box mediates PARG interaction with PCNA

Poly(ADP-ribose) glycohydrolase (PARG) regulates cellular poly(ADP-ribose) (PAR) levels by rapidly cleaving glycosidic bonds between ADP-ribose units. PARG interacts with proliferating cell nuclear antigen (PCNA) and is strongly recruited to DNA damage sites in a PAR- and PCNA-dependent fashion. Here we identified PARG acetylation site K409 that is essential for its interaction with PCNA, its localization within replication foci and its recruitment to DNA damage sites. We found K409 to be part of a non-canonical PIP-box within the PARG disordered regulatory region. The previously identified putative N-terminal PIP-box does not bind PCNA directly but contributes to PARG localization within replication foci. X-ray structure and MD simulations reveal that the PARG non-canonical PIP-box binds PCNA in a manner similar to other canonical PIP-boxes and may represent a new type of PIP-box. While the binding of previously described PIP-boxes is based on hydrophobic interactions, PARG PIP-box binds PCNA via both stabilizing hydrophobic and fine-tuning electrostatic interactions. Our data explain the mechanism of PARG–PCNA interaction through a new PARG PIP-box that exhibits non-canonical sequence properties but a canonical mode of PCNA binding.© The Author(s) 201