Structural Visualization of the p53/RNA Polymerase II Assembly

Abstract

The master tumor suppressor p53 activates transcription in response to various cellular stresses in part by facilitating recruitment of the transcription machinery to DNA. Recent studies have documented a direct yet poorly characterized interaction between p53 and RNA polymerase II (Pol II). Therefore, we dissected the human p53/Pol II interaction via single-particle cryo-electron microscopy, structural docking, and biochemical analyses. This study reveals that p53 binds Pol II via the Rpb1 and Rpb2 subunits, bridging the DNA-binding cleft of Pol II proximal to the upstream DNA entry site. In addition, the key DNA-binding surface of p53, frequently disrupted in various cancers, remains exposed within the assembly. Furthermore, the p53/Pol II cocomplex displays a closed conformation as defined by the position of the Pol II clamp domain. Notably, the interaction of p53 and Pol II leads to increased Pol II elongation activity. These findings indicate that p53 may structurally regulate DNA-binding functions of Pol II via the clamp domain, thereby providing insights into p53-regulated Pol II transcription.

Nuclear myosin 1 activates p21 gene transcription in response to DNA damage through a chromatin-based mechanism

“…Upon DNA damage, NM1 binds to both the promoter and TSS of the p21 gene, and is necessary for deposition of the active epigenetic marks H3K9ac and H3K4me3. p53 binds to nucleosomes within the p21 promoter, leading to nucleosome loss, and regulates transcription by regulating Pol II DNA-binding functions 44,45 . This suggests that at the p21 promoter there is no pre-requirement for NM1 to open the chromatin and facilitate p53 binding itself, although we cannot exclude that NM1 may facilitate p53 posttranslational modifications.…”

Structural Assessment of the Full-Length Wild-Type Tumor Suppressor Protein p53 by Mass Spectrometry-Guided Computational Modeling

“…Recently, a cryo-electron microscopy (cryo-EM) structure of p53 with the nucleosome, H2A, H2B, H3.1, and H4 plus DNA fragment containing the p53 binding site was proposed, but the low resolution obtained for p53 did not allow resolving its structure in the cryo-EM map (18). Different models have been proposed for the topology and overall conformation of the p53 tetramer in the absence and presence of DNA (19)(20)(21)(22)(23)(24)(25)(26). Those models were generated using both experimental as well as computational approaches and differ substantially in their domain organization (Supporting Information, Figure S1).…”