TIRR regulates 53BP1 by masking its histone methyl-lysine binding function

53BP1 is a multi-functional double-strand break (DSB) repair protein that is essential for class switch recombination in B lymphocytes and for sensitizing BRCA1-deficient tumors to PARP inhibitors. Central to all 53BP1 activities is its recruitment to DSBs via the interaction of the tandem Tudor domain with dimethylated lysine 20 of histone H4 (H4K20me2). Here we identify an uncharacterized protein, TIRR (Tudor Interacting Repair Regulator) that directly binds the tandem Tudor domain and masks its H4K20me2 binding motif. Upon DNA damage, ATM phosphorylates 53BP1 and recruits RIF1 to dissociate the 53BP1–TIRR complex. However, overexpression of TIRR impedes 53BP1 function by blocking its localization to DSBs. Depletion of TIRR destabilizes 53BP1 in the nuclear soluble fraction and also alters the DSB-induced protein complex centering 53BP1. These findings identify TIRR as a new factor that influences DSB repair utilizing a unique mechanism of masking the histone methyl-lysine binding function of 53BP1

The importance of phosphate ester backbone flexibility in protein-DNA recognition

The N-terminal 56 amino acid headpieces of the wild-type and mutant Y7I lac repressors and the 14-22 base pair DNAs containing the symmetric lac operator sequences can be used to study protein-DNA interaction. Phosphorus-31 NMR gives direct information as to the type of phosphate conformations present in the DNA. Thus, it can potentially provide information about protein-DNA phosphate backbone interaction. The alkaline phosphatase assay can be used to measure the dissociation constants of the headpiece:operator complexes. The wild-type operator forms the strongest complex with the wild-type headpiece while the mutant operators form weaker complexes. Relative to the wild-type headpiece, the Y7I headpiece forms weaker complexes with the operators. Although the recognition helix of this mutant headpiece is partially destroyed, its overall folding is still comparable to that of the wild-type headpiece. Most of the tertiary structure crosspeaks in the wild-type headpiece are still found in the Y7I headpiece. Results from the phosphorus-31 titrations and binding studies suggest that specific, strongly bound complexes retain the inherent conformational flexibility of the operator itself, whereas more weakly bound, but still specific, operator:protein complexes restrict the phosphate ester conformational freedom in the complex relative to the free DNA. NMR and molecular dynamics methodologies can be successfully applied to structure refinement of macromolecules. Using these methods, the 14-mer 7G 434 operator has been found to have both A- and B-like DNA conformations

Solution conformation of an essential region of the p53 transactivation domain

Background:The peptide segment surrounding residues Leu22 and Trp23 of the p53 transactivation domain plays a critical role in the transactivation activity of p53. This region binds basal transcriptional components such as the TATA-box binding protein associated factors TAFII40 and TAFII60 as well as the mdm-2 and adenovirus type 5 E1B 55 kDa oncoproteins.Results:The structure of residues 14–28 of p53 was studied by nuclear magnetic resonance spectroscopy and found to prefer a two-β-turn structure stabilized by a hydrophobic cluster consisting of residues known to be important for transactivation and binding to p53-binding proteins. A peptide segment in which Leu22 and Trp23 were replaced by Gln and Ser displays a random structure.Conclusions:This structural propensity observed in the wild-type p53 peptide is important for understanding the mechanism of transcriptional activation, because very few structural data are available on transactivation domains to date. These results should aid in the design of therapeutics that could competitively inhibit binding of p53 to the oncogene product mdm-2

TIRR inhibits the 53BP1-p53 complex to alter cell-fate programs

53BP1 influences genome stability via two independent mechanisms: (1) regulating DNA double-strand break (DSB) repair and (2) enhancing p53 activity. We discovered a protein, Tudor-interacting repair regulator (TIRR), that associates with the 53BP1 Tudor domain and prevents its recruitment to DSBs. Here, we elucidate how TIRR affects 53BP1 function beyond its recruitment to DSBs and biochemically links the two distinct roles of 53BP1. Loss of TIRR causes an aberrant increase in the gene transactivation function of p53, affecting several p53-mediated cell-fate programs. TIRR inhibits the complex formation between the Tudor domain of 53BP1 and a dimethylated form of p53 (K382me2) that is poised for transcriptional activation of its target genes. TIRR mRNA expression levels negatively correlate with the expression of key p53 target genes in breast and prostate cancers. Further, TIRR loss is selectively not tolerated in p53-proficient tumors. Therefore, we establish that TIRR is an important inhibitor of the 53BP1-p53 complex

Stabilization of Nucleosomes by Histone Tails and by FACT Revealed by spFRET Microscopy

A correct chromatin structure is important for cell viability and is tightly regulated by numerous factors. Human protein complex FACT (facilitates chromatin transcription) is an essential factor involved in chromatin transcription and cancer development. Here FACT-dependent changes in the structure of single nucleosomes were studied with single-particle Förster resonance energy transfer (spFRET) microscopy using nucleosomes labeled with a donor-acceptor pair of fluorophores, which were attached to the adjacent gyres of DNA near the contact between H2A-H2B dimers. Human FACT and its version without the C-terminal domain (CTD) and the high mobility group (HMG) domain of the structure-specific recognition protein 1 (SSRP1) subunit did not change the structure of the nucleosomes, while FACT without the acidic C-terminal domains of the suppressor of Ty 16 (Spt16) and the SSRP1 subunits caused nucleosome aggregation. Proteolytic removal of histone tails significantly disturbed the nucleosome structure, inducing partial unwrapping of nucleosomal DNA. Human FACT reduced DNA unwrapping and stabilized the structure of tailless nucleosomes. CTD and/or HMG domains of SSRP1 are required for this FACT activity. In contrast, previously it has been shown that yeast FACT unfolds (reorganizes) nucleosomes using the CTD domain of SSRP1-like Pol I-binding protein 3 subunit (Pob3). Thus, yeast and human FACT complexes likely utilize the same domains for nucleosome reorganization and stabilization, respectively, and these processes are mechanistically similar