ABSTRACT
Intrinsically disordered proteins can phase separate from the soluble intracellular space, and tend to aggregate under pathological conditions. The physiological functions and molecular triggers of liquid demixing by phase separation are not well understood. Here we show in vitro and in vivo that the nucleic acid-mimicking biopolymer poly(ADP-ribose) (PAR) nucleates intracellular liquid demixing. PAR levels are markedly induced at sites of DNA damage, and we provide evidence that PAR-seeded liquid demixing results in rapid, yet transient and fully reversible assembly of various intrinsically disordered proteins at DNA break sites. Demixing, which relies on electrostatic interactions between positively charged RGG repeats and negatively charged PAR, is amplified by aggregation-prone prion-like domains, and orchestrates the earliest cellular responses to DNA breakage. We propose that PAR-seeded liquid demixing is a general mechanism to dynamically reorganize the soluble nuclear space with implications for pathological protein aggregation caused by derailed phase separation.
Subject(s)
Poly Adenosine Diphosphate Ribose/chemistry , Proteins/chemistry , Proteins/metabolism , Cell Line, Tumor , Cloning, Molecular , DNA Damage , Gene Expression Regulation/physiology , Humans , Protein Conformation , Protein Structure, Tertiary , Proteins/geneticsABSTRACT
Chromosome breakage elicits transient silencing of ribosomal RNA synthesis, but the mechanisms involved remained elusive. Here we discover an in trans signalling mechanism that triggers pan-nuclear silencing of rRNA transcription in response to DNA damage. This is associated with transient recruitment of the Nijmegen breakage syndrome protein 1 (NBS1), a central regulator of DNA damage responses, into the nucleoli. We further identify TCOF1 (also known as Treacle), a nucleolar factor implicated in ribosome biogenesis and mutated in Treacher Collins syndrome, as an interaction partner of NBS1, and demonstrate that NBS1 translocation and accumulation in the nucleoli is Treacle dependent. Finally, we provide evidence that Treacle-mediated NBS1 recruitment into the nucleoli regulates rRNA silencing in trans in the presence of distant chromosome breaks.
Subject(s)
Cell Cycle Proteins/metabolism , DNA Damage/genetics , DNA Damage/physiology , Nuclear Proteins/metabolism , RNA, Ribosomal/genetics , Amino Acid Sequence , Cell Cycle Proteins/chemistry , Cell Cycle Proteins/genetics , Cell Line , Cell Nucleolus/metabolism , Conserved Sequence , DNA Breaks, Double-Stranded , Gene Silencing , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , HEK293 Cells , HeLa Cells , Humans , Models, Biological , Molecular Sequence Data , Multiprotein Complexes/chemistry , Multiprotein Complexes/metabolism , Nuclear Proteins/chemistry , Nuclear Proteins/genetics , Phosphoproteins/chemistry , Phosphoproteins/metabolism , Phosphorylation , Protein Interaction Domains and Motifs , RNA Polymerase I/metabolism , Recombinant Fusion Proteins/genetics , Recombinant Fusion Proteins/metabolism , Transcription, GeneticABSTRACT
Although the general relevance of chromatin modifications for genotoxic stress signaling, cell-cycle checkpoint activation, and DNA repair is well established, how these modifications reach initial thresholds in order to trigger robust responses remains largely unexplored. Here, we identify the chromatin-associated scaffold attachment factor SAFB1 as a component of the DNA damage response and show that SAFB1 cooperates with histone acetylation to allow for efficient γH2AX spreading and genotoxic stress signaling. SAFB1 undergoes a highly dynamic exchange at damaged chromatin in a poly(ADP-ribose)-polymerase 1- and poly(ADP-ribose)-dependent manner and is required for unperturbed cell-cycle checkpoint activation and guarding cells against replicative stress. Altogether, our data reveal that transient recruitment of an architectural chromatin component is required in order to overcome physiological barriers by making chromatin permissive for DNA damage signaling, whereas the ensuing exclusion of SAFB1 may help prevent excessive signaling.
Subject(s)
Chromatin/genetics , DNA Damage , Matrix Attachment Region Binding Proteins/genetics , Nuclear Matrix-Associated Proteins/genetics , Receptors, Estrogen/genetics , Signal Transduction/genetics , Acetylation , Blotting, Western , Cell Cycle Checkpoints/genetics , Cell Line, Tumor , Chromatin/metabolism , DNA Breaks, Double-Stranded/drug effects , DNA Breaks, Double-Stranded/radiation effects , DNA Repair , Green Fluorescent Proteins/genetics , Green Fluorescent Proteins/metabolism , Histones/metabolism , Humans , Matrix Attachment Region Binding Proteins/metabolism , Microscopy, Fluorescence , Models, Genetic , Mutagenicity Tests , Nuclear Matrix-Associated Proteins/metabolism , Phosphorylation , Poly Adenosine Diphosphate Ribose/metabolism , Poly(ADP-ribose) Polymerases/metabolism , RNA Interference , Receptors, Estrogen/metabolism , Reverse Transcriptase Polymerase Chain ReactionABSTRACT
Histone ubiquitylation is a prominent response to DNA double-strand breaks (DSBs), but how these modifications are confined to DNA lesions is not understood. Here, we show that TRIP12 and UBR5, two HECT domain ubiquitin E3 ligases, control accumulation of RNF168, a rate-limiting component of a pathway that ubiquitylates histones after DNA breakage. We find that RNF168 can be saturated by increasing amounts of DSBs. Depletion of TRIP12 and UBR5 allows accumulation of RNF168 to supraphysiological levels, followed by massive spreading of ubiquitin conjugates and hyperaccumulation of ubiquitin-regulated genome caretakers such as 53BP1 and BRCA1. Thus, regulatory and proteolytic ubiquitylations are wired in a self-limiting circuit that promotes histone ubiquitylation near the DNA lesions but at the same time counteracts its excessive spreading to undamaged chromosomes. We provide evidence that this mechanism is vital for the homeostasis of ubiquitin-controlled events after DNA breakage and can be subverted during tumorigenesis.
Subject(s)
Carrier Proteins/metabolism , Chromatin/metabolism , DNA Breaks, Double-Stranded , DNA Repair , Ubiquitin-Protein Ligases/metabolism , Alphapapillomavirus , Cell Line , Cell Line, Tumor , Gene Silencing , Humans , Intracellular Signaling Peptides and Proteins/metabolism , Neoplasms/metabolism , Neoplasms/pathology , Neoplasms/virology , Papillomavirus Infections/metabolism , Papillomavirus Infections/pathology , Transcription, Genetic , Tumor Suppressor p53-Binding Protein 1 , UbiquitinationABSTRACT
Completion of genome duplication is challenged by structural and topological barriers that impede progression of replication forks. Although this can seriously undermine genome integrity, the fate of DNA with unresolved replication intermediates is not known. Here, we show that mild replication stress increases the frequency of chromosomal lesions that are transmitted to daughter cells. Throughout G1, these lesions are sequestered in nuclear compartments marked by p53-binding protein 1 (53BP1) and other chromatin-associated genome caretakers. We show that the number of such 53BP1 nuclear bodies increases after genetic ablation of BLM, a DNA helicase associated with dissolution of entangled DNA. Conversely, 53BP1 nuclear bodies are partially suppressed by knocking down SMC2, a condensin subunit required for mechanical stability of mitotic chromosomes. Finally, we provide evidence that 53BP1 nuclear bodies shield chromosomal fragile sites sequestered in these compartments against erosion. Together, these data indicate that restoration of DNA or chromatin integrity at loci prone to replication problems requires mitotic transmission to the next cell generations.
