H4 K20me0 marks post-replicative chromatin and recruits the TONSL-MMS22L DNA repair complex

After DNA replication, chromosomal processes including DNA repair and transcription take place in the context of sister chromatids. While cell cycle regulation can guide these processes globally, mechanisms to distinguish pre- and post-replicative states locally remain unknown. Here we reveal that new histones incorporated during DNA replication provide a signature of post-replicative chromatin, read by the human TONSL–MMS22L homologous recombination complex. We identify the TONSL ankyrin repeat domain (ARD) as a reader of histone H4 tails unmethylated at K20 (H4K20me0), which are specific to new histones incorporated during DNA replication and mark post-replicative chromatin until the G2/M phase of the cell cycle. Accordingly, TONSL–MMS22L binds new histones H3–H4 both before and after incorporation into nucleosomes, remaining on replicated chromatin until late G2/M. H4K20me0 recognition is required for TONSL–MMS22L binding to chromatin and accumulation at challenged replication forks and DNA lesions. Consequently, TONSL ARD mutants are toxic, compromising genome stability, cell viability and resistance to replication stress. Together, these data reveal a histone-reader-based mechanism for recognizing the post-replicative state, offering a new angle to understand DNA repair with the potential for targeted cancer therapy.

[1]  S. Robson,et al.  Nucleosome-Interacting Proteins Regulated by DNA and Histone Methylation , 2010, Cell.

[2]  B. Stillman,et al.  Dynamics of pre-replication complex proteins during the cell division cycle. , 2004, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[3]  K. Helin,et al.  The histone methyltransferase SET8 is required for S-phase progression , 2007, The Journal of cell biology.

[4]  Grant W. Brown,et al.  The MMS22L-TONSL complex mediates recovery from replication stress and homologous recombination. , 2010, Molecular cell.

[5]  Imen Lassadi,et al.  High‐resolution profiling of γH2AX around DNA double strand breaks in the mammalian genome , 2010, The EMBO journal.

[6]  D. Wigley,et al.  Pumps, paradoxes and ploughshares: mechanism of the MCM2-7 DNA helicase. , 2005, Trends in biochemical sciences.

[7]  J. Bartek,et al.  Regulation of Replication Fork Progression Through Histone Supply and Demand , 2007, Science.

[8]  C. Ponting,et al.  Identification of the MMS22L-TONSL complex that promotes homologous recombination. , 2010, Molecular cell.

[9]  Uma M. Muthurajan,et al.  The role of the nucleosome acidic patch in modulating higher order chromatin structure , 2013, Journal of The Royal Society Interface.

[10]  M. Monden,et al.  Mutational analysis of BARD1 in familial breast cancer patients in Japan. , 2003, Cancer letters.

[11]  Kevin Cowtan,et al.  research papers Acta Crystallographica Section D Biological , 2005 .

[12]  Danny Reinberg,et al.  PR-Set7 and H4K20me1: at the crossroads of genome integrity, cell cycle, chromosome condensation, and transcription. , 2012, Genes & development.

[13]  J Wade Harper,et al.  A genome-wide camptothecin sensitivity screen identifies a mammalian MMS22L-NFKBIL2 complex required for genomic stability. , 2010, Molecular cell.

[14]  D. Patel,et al.  A unique binding mode enables MCM2 to chaperone histones H3–H4 at replication forks , 2015, Nature Structural &Molecular Biology.

[15]  P. Lichter,et al.  hMOF Histone Acetyltransferase Is Required for Histone H4 Lysine 16 Acetylation in Mammalian Cells , 2005, Molecular and Cellular Biology.

[16]  Patrick G. A. Pedrioli,et al.  RNAi‐based screening identifies the Mms22L–Nfkbil2 complex as a novel regulator of DNA replication in human cells , 2010, The EMBO journal.

[17]  Axel Imhof,et al.  PTMs on H3 variants before chromatin assembly potentiate their final epigenetic state. , 2006, Molecular cell.

[18]  Stéphanie Panier,et al.  Double-strand break repair: 53BP1 comes into focus , 2013, Nature Reviews Molecular Cell Biology.

[19]  Thomas Ludwig,et al.  Structural Requirements for the BARD1 Tumor Suppressor in Chromosomal Stability and Homology-directed DNA Repair* , 2007, Journal of Biological Chemistry.

[20]  Randy J Read,et al.  Electronic Reprint Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination Biological Crystallography Phenix: Building New Software for Automated Crystallographic Structure Determination , 2022 .

[21]  P. Brzovic,et al.  Crystal Structure of the BARD1 Ankyrin Repeat Domain and Its Functional Consequences*♦ , 2008, Journal of Biological Chemistry.

[22]  Xing Zhang,et al.  The ankyrin repeats of G9a and GLP histone methyltransferases are mono- and dimethyllysine binding modules , 2008, Nature Structural &Molecular Biology.

[23]  B. E. Black,et al.  Assembly in G1 phase and long-term stability are unique intrinsic features of CENP-A nucleosomes , 2013, Molecular biology of the cell.

[24]  D. Reinberg,et al.  Analysis of the Histone H3.1 Interactome: A Suitable Chaperone for the Right Event. , 2015, Molecular cell.

[25]  P. Ménard,et al.  Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components , 2014, Nature Cell Biology.

[26]  G. Schotta,et al.  Histone H4 Lysine 20 methylation: key player in epigenetic regulation of genomic integrity , 2013, Nucleic acids research.

[27]  S. Jackson,et al.  Transcriptionally active chromatin recruits homologous recombination at DNA double-strand breaks , 2014, Nature Structural &Molecular Biology.

[28]  Georges Mer,et al.  Structural Basis for the Methylation State-Specific Recognition of Histone H4-K20 by 53BP1 and Crb2 in DNA Repair , 2006, Cell.

[29]  N. Mailand,et al.  The Deubiquitylating Enzyme USP44 Counteracts the DNA Double-strand Break Response Mediated by the RNF8 and RNF168 Ubiquitin Ligases* , 2013, Journal of Biological Chemistry.

[30]  D. Reinberg,et al.  Mitotic-specific methylation of histone H4 Lys 20 follows increased PR-Set7 expression and its localization to mitotic chromosomes. , 2002, Genes & development.

[31]  B. Porse,et al.  Temporal mapping of CEBPA and CEBPB binding during liver regeneration reveals dynamic occupancy and specific regulatory codes for homeostatic and cell cycle gene batteries , 2013, Genome research.

[32]  Ole N Jensen,et al.  Two distinct modes for propagation of histone PTMs across the cell cycle , 2015, Genes & development.

[33]  Zhiguo Zhang,et al.  Histone chaperones in nucleosome assembly and human disease , 2013, Nature Structural &Molecular Biology.

[34]  N. Kelleher,et al.  Certain and Progressive Methylation of Histone H4 at Lysine 20 during the Cell Cycle , 2007, Molecular and Cellular Biology.

[35]  S. Gasser,et al.  Nucleosome remodelers in double-strand break repair. , 2013, Current opinion in genetics & development.

[36]  E. S,et al.  Reconstitution of Nucleosome Core Particles from Recombinant Histones and DNA , 2003 .

[37]  Randy J. Read,et al.  Phaser crystallographic software , 2007, Journal of applied crystallography.

[38]  S. Kowalczykowski,et al.  The Full-length Saccharomyces cerevisiae Sgs1 Protein Is a Vigorous DNA Helicase That Preferentially Unwinds Holliday Junctions* , 2010, The Journal of Biological Chemistry.

[39]  G. Almouzni,et al.  Replication stress interferes with histone recycling and predeposition marking of new histones. , 2010, Molecular cell.

[40]  R. Guérois,et al.  Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork , 2015, Nucleic acids research.

[41]  H. Tauchi,et al.  Regulation of homologous recombination by RNF20-dependent H2B ubiquitination. , 2011, Molecular cell.