Chromatin replication and epigenetic cell memory

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Chromatin replication and epigenetic cell memory"


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ABSTRACT Propagation of the chromatin landscape across cell divisions is central to epigenetic cell memory. Mechanistic analysis of the interplay between DNA replication, the cell cycle, and


the epigenome has provided insights into replication-coupled chromatin assembly and post-replicative chromatin maintenance. These breakthroughs are critical for defining how proliferation


impacts the epigenome during cell identity changes in development and disease. Here we review these findings in the broader context of epigenetic inheritance across mitotic cell division.


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OTHERS PARENTAL NUCLEOSOME SEGREGATION AND THE INHERITANCE OF CELLULAR IDENTITY Article 26 January 2021 SYMMETRIC INHERITANCE OF PARENTAL HISTONES GOVERNS EPIGENOME MAINTENANCE AND EMBRYONIC


STEM CELL IDENTITY Article Open access 04 September 2023 MITOTIC CHROMATIN MARKING GOVERNS THE SEGREGATION OF DNA DAMAGE Article Open access 16 January 2025 REFERENCES * Bannister, A. J.


& Kouzarides, T. Regulation of chromatin by histone modifications. _Cell Res._ 21, 381–395 (2011). CAS  PubMed  PubMed Central  Google Scholar  * Hauer, M. H. & Gasser, S. M.


Chromatin and nucleosome dynamics in DNA damage and repair. _Genes Dev._ 31, 2204–2221 (2017). CAS  PubMed  PubMed Central  Google Scholar  * Allshire, R. C. & Madhani, H. D. Ten


principles of heterochromatin formation and function. _Nat. Rev. Mol. Cell Biol._ 19, 229–244 (2018). CAS  PubMed  Google Scholar  * Boyle, A. P. et al. High-resolution mapping and


characterization of open chromatin across the genome. _Cell_ 132, 311–322 (2008). CAS  PubMed  PubMed Central  Google Scholar  * Mikkelsen, T. S. et al. Genome-wide maps of chromatin state


in pluripotent and lineage-committed cells. _Nature_ 448, 553–560 (2007). CAS  PubMed  PubMed Central  Google Scholar  * Kurimoto, K. & Saitou, M. Epigenome regulation during germ cell


specification and development from pluripotent stem cells. _Curr. Opin. Genet. Dev._ 52, 57–64 (2018). CAS  PubMed  Google Scholar  * Heard, E. & Martienssen, R. A. Transgenerational


epigenetic inheritance: myths and mechanisms. _Cell_ 157, 95–109 (2014). CAS  PubMed  PubMed Central  Google Scholar  * Flavahan, W. A., Gaskell, E. & Bernstein, B. E. Epigenetic


plasticity and the hallmarks of cancer. _Science_ 357, eaal2380 (2017). PubMed  PubMed Central  Google Scholar  * Kornberg, R. D. Chromatin structure: a repeating unit of histones and DNA.


_Science_ 184, 868–871 (1974). CAS  PubMed  Google Scholar  * Annunziato, A. T. The fork in the road: histone partitioning during DNA replication. _Genes (Basel)_ 6, 353–371 (2015). CAS 


Google Scholar  * Siddiqui, K., On, K. F. & Diffley, J. F. X. Regulating DNA replication in eukarya. _Cold Spring Harb. Perspect. Biol._ 5, a012930 (2013). PubMed  PubMed Central  Google


Scholar  * Marchal, C., Sima, J. & Gilbert, D. M. Control of DNA replication timing in the 3D genome. _Nat. Rev. Mol. Cell Biol._ 20, 721–737 (2019). CAS  PubMed  Google Scholar  *


Kschonsak, M. & Haering, C. H. Shaping mitotic chromosomes: from classical concepts to molecular mechanisms. _BioEssays_ 37, 755–766 (2015). CAS  PubMed  PubMed Central  Google Scholar 


* Palozola, K. C., Lerner, J. & Zaret, K. S. A changing paradigm of transcriptional memory propagation through mitosis. _Nat. Rev. Mol. Cell Biol._ 20, 55–64 (2019). CAS  PubMed  PubMed


Central  Google Scholar  * Hammond, C. M., Strømme, C. B., Huang, H., Patel, D. J. & Groth, A. Histone chaperone networks shaping chromatin function. _Nat. Rev. Mol. Cell Biol._ 18,


141–158 (2017). CAS  PubMed  PubMed Central  Google Scholar  * Grover, P., Asa, J. S. & Campos, E. I. H3-H4 histone chaperone pathways. _Annu. Rev. Genet._ 52, 109–130 (2018). CAS 


PubMed  Google Scholar  * Buschbeck, M. & Hake, S. B. Variants of core histones and their roles in cell fate decisions, development and cancer. _Nat. Rev. Mol. Cell Biol._ 18, 299–314


(2017). CAS  PubMed  Google Scholar  * Smolle, M. & Workman, J. L. Transcription-associated histone modifications and cryptic transcription. _Biochim. Biophys. Acta_ 1829, 84–97 (2013).


CAS  PubMed  Google Scholar  * Greenberg, M. V. C. & Bourc’his, D. The diverse roles of DNA methylation in mammalian development and disease. _Nat. Rev. Mol. Cell Biol._ 20, 590–607


(2019). CAS  PubMed  Google Scholar  * Alabert, C. & Groth, A. Chromatin replication and epigenome maintenance. _Nat. Rev. Mol. Cell Biol._ 13, 153–167 (2012). CAS  PubMed  Google


Scholar  * Luger, K., Dechassa, M. L. & Tremethick, D. J. New insights into nucleosome and chromatin structure: an ordered state or a disordered affair? _Nat. Rev. Mol. Cell Biol._ 13,


436–447 (2012). CAS  PubMed  PubMed Central  Google Scholar  * Stillman, B. Histone modifications: insights into their influence on gene expression. _Cell_ 175, 6–9 (2018). CAS  PubMed 


Google Scholar  * Alabert, C. et al. Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components. _Nat. Cell Biol._ 16,


281–293 (2014). CAS  PubMed  PubMed Central  Google Scholar  * Sirbu, B. M. et al. Identification of proteins at active, stalled, and collapsed replication forks using isolation of proteins


on nascent DNA (iPOND) coupled with mass spectrometry. _J. Biol. Chem._ 288, 31458–31467 (2013). CAS  PubMed  PubMed Central  Google Scholar  * Li, H. & O’Donnell, M. E. The eukaryotic


CMG helicase at the replication fork: emerging architecture reveals an unexpected mechanism. _BioEssays_ 40, 1700208 (2018). Google Scholar  * Burgers, P. M. J. & Kunkel, T. A.


Eukaryotic DNA replication fork. _Annu. Rev. Biochem._ 86, 417–438 (2017). CAS  PubMed  PubMed Central  Google Scholar  * Alabert, C. et al. Two distinct modes for propagation of histone


PTMs across the cell cycle. _Genes Dev._ 29, 585–590 (2015). CAS  PubMed  PubMed Central  Google Scholar  * Loyola, A., Bonaldi, T., Roche, D., Imhof, A. & Almouzni, G. PTMs on H3


variants before chromatin assembly potentiate their final epigenetic state. _Mol. Cell_ 24, 309–316 (2006). CAS  PubMed  Google Scholar  * Scharf, A. N. D. et al. Monomethylation of lysine


20 on histone H4 facilitates chromatin maturation. _Mol. Cell. Biol._ 29, 57–67 (2009). CAS  PubMed  Google Scholar  * Burgess, R. J. & Zhang, Z. Histone chaperones in nucleosome


assembly and human disease. _Nat. Struct. Mol. Biol._ 20, 14–22 (2013). CAS  PubMed  PubMed Central  Google Scholar  * Nagarajan, P. et al. Histone acetyl transferase 1 is essential for


mammalian development, genome stability, and the processing of newly synthesized histones H3 and H4. _PLoS Genet._ 9, e1003518 (2013). CAS  PubMed  PubMed Central  Google Scholar  * Xu, M.,


Wang, W., Chen, S. & Zhu, B. A model for mitotic inheritance of histone lysine methylation. _EMBO Rep._ 13, 60–67 (2011). PubMed  PubMed Central  Google Scholar  * Zee, B. M., Levin, R.


S., DiMaggio, P. A. & Garcia, B. A. Global turnover of histone post-translational modifications and variants in human cells. _Epigenetics Chromatin_ 3, 22 (2010). CAS  PubMed  PubMed


Central  Google Scholar  * Probst, A. V., Dunleavy, E. & Almouzni, G. Epigenetic inheritance during the cell cycle. _Nat. Rev. Mol. Cell Biol._ 10, 192–206 (2009). CAS  PubMed  Google


Scholar  * Tagami, H., Ray-Gallet, D., Almouzni, G. & Nakatani, Y. Histone H3.1 and H3.3 complexes mediate nucleosome assembly pathways dependent or independent of DNA synthesis. _Cell_


116, 51–61 (2004). CAS  PubMed  Google Scholar  * Xu, M. et al. Partitioning of histone H3-H4 tetramers during DNA replication-dependent chromatin assembly. _Science_ 328, 94–98 (2010). CAS


  PubMed  Google Scholar  * Saredi, G. et al. H4K20me0 marks post-replicative chromatin and recruits the TONSL–MMS22L DNA repair complex. _Nature_ 534, 714–718 (2016). CAS  PubMed  PubMed


Central  Google Scholar  * Nakamura, K. et al. H4K20me0 recognition by BRCA1-BARD1 directs homologous recombination to sister chromatids. _Nat. Cell Biol._ 21, 311–318 (2019). CAS  PubMed 


PubMed Central  Google Scholar  * Pellegrino, S., Michelena, J., Teloni, F., Imhof, R. & Altmeyer, M. Replication-coupled dilution of H4K20me2 guides 53BP1 to pre-replicative chromatin.


_Cell Rep._ 19, 1819–1831 (2017). CAS  PubMed  PubMed Central  Google Scholar  * Stillman, B. Chromatin assembly during SV40 DNA replication in vitro. _Cell_ 45, 555–565 (1986). CAS  PubMed


  Google Scholar  * Smith, S. & Stillman, B. Purification and characterization of CAF-I, a human cell factor required for chromatin assembly during DNA replication in vitro. _Cell_ 58,


15–25 (1989). CAS  PubMed  Google Scholar  * Shibahara, K. & Stillman, B. Replication-dependent marking of DNA by PCNA facilitates CAF-1-coupled inheritance of chromatin. _Cell_ 96,


575–585 (1999). CAS  PubMed  Google Scholar  * Petryk, N. et al. MCM2 promotes symmetric inheritance of modified histones during DNA replication. _Science_ 361, 1389–1392 (2018). CAS  PubMed


  Google Scholar  * Yu, C. et al. A mechanism for preventing asymmetric histone segregation onto replicating DNA strands. _Science_ 361, 1386–1389 (2018). CAS  PubMed  PubMed Central  Google


Scholar  * Gan, H. et al. The Mcm2-Ctf4-Polα axis facilitates parental histone H3-H4 transfer to lagging strands. _Mol. Cell_ 72, 140–151.e3 (2018). CAS  PubMed  PubMed Central  Google


Scholar  * Pospelov, V., Russev, G., Vassilev, L. & Tsanev, R. Nucleosome segregation in chromatin replicated in the presence of cycloheximide. _J. Mol. Biol._ 156, 79–91 (1982). CAS 


PubMed  Google Scholar  * Jackson, V. & Chalkley, R. Histone segregation on replicating chromatin. _Biochemistry_ 24, 6930–6938 (1985). CAS  PubMed  Google Scholar  * Cusick, M. E.,


DePamphilis, M. L. & Wassarman, P. M. Dispersive segregation of nucleosomes during replication of simian virus 40 chromosomes. _J. Mol. Biol._ 178, 249–271 (1984). CAS  PubMed  Google


Scholar  * Jackson, V., Granner, D. K. & Chalkley, R. Deposition of histones onto replicating chromosomes. _Proc. Natl Acad. Sci. USA_ 72, 4440–4444 (1975). CAS  PubMed  PubMed Central 


Google Scholar  * Russev, G. & Hancock, R. Assembly of new histones into nucleosomes and their distribution in replicating chromatin. _Proc. Natl Acad. Sci. USA_ 79, 3143–3147 (1982).


CAS  PubMed  PubMed Central  Google Scholar  * Crémisi, C., Chestier, A. & Yaniv, M. Assembly of SV40 and polyoma minichromosomes during replication. _Cold Spring Harb. Symp. Quant.


Biol._ 42, 409–416 (1978). PubMed  Google Scholar  * Ishimi, Y., Komamura-Kohno, Y., Arai, K. & Masai, H. Biochemical activities associated with mouse Mcm2 protein. _J. Biol. Chem._ 276,


42744–42752 (2001). CAS  PubMed  Google Scholar  * Groth, A. et al. Regulation of replication fork progression through histone supply and demand. _Science_ 318, 1928–1931 (2007). CAS 


PubMed  Google Scholar  * Huang, H. et al. A unique binding mode enables MCM2 to chaperone histones H3-H4 at replication forks. _Nat. Struct. Mol. Biol._ 22, 618–626 (2015). CAS  PubMed 


PubMed Central  Google Scholar  * Richet, N. et al. Structural insight into how the human helicase subunit MCM2 may act as a histone chaperone together with ASF1 at the replication fork.


_Nucleic Acids Res._ 43, 1905–1917 (2015). CAS  PubMed  PubMed Central  Google Scholar  * Foltman, M. et al. Eukaryotic replisome components cooperate to process histones during chromosome


replication. _Cell Rep._ 3, 892–904 (2013). CAS  PubMed  Google Scholar  * Jasencakova, Z. et al. Replication stress interferes with histone recycling and predeposition marking of new


histones. _Mol. Cell_ 37, 736–743 (2010). CAS  PubMed  Google Scholar  * Wang, H., Wang, M., Yang, N. & Xu, R.-M. Structure of the quaternary complex of histone H3-H4 heterodimer with


chaperone ASF1 and the replicative helicase subunit MCM2. _Protein Cell_ 6, 693–697 (2015). CAS  PubMed  PubMed Central  Google Scholar  * Zasadzińska, E. et al. Inheritance of CENP-A


nucleosomes during DNA replication requires HJURP. _Dev. Cell_ 47, 348–362.e7 (2018). PubMed  PubMed Central  Google Scholar  * Douglas, M. E., Ali, F. A., Costa, A. & Diffley, J. F. X.


The mechanism of eukaryotic CMG helicase activation. _Nature_ 555, 265–268 (2018). CAS  PubMed  PubMed Central  Google Scholar  * Georgescu, R. et al. Structure of eukaryotic CMG helicase at


a replication fork and implications to replisome architecture and origin initiation. _Proc. Natl Acad. Sci. USA_ 114, E697–E706 (2017). CAS  PubMed  PubMed Central  Google Scholar  *


Saxton, D. S. & Rine, J. Epigenetic memory independent of symmetric histone inheritance. _eLife_ 8, e51421 (2019). PubMed  PubMed Central  Google Scholar  * Simon, A. C. et al. A Ctf4


trimer couples the CMG helicase to DNA polymerase α in the eukaryotic replisome. _Nature_ 510, 293–297 (2014). CAS  PubMed  PubMed Central  Google Scholar  * He, H. et al. Coordinated


regulation of heterochromatin inheritance by Dpb3-Dpb4 complex. _Proc. Natl Acad. Sci. USA_ 114, 12524–12529 (2017). CAS  PubMed  PubMed Central  Google Scholar  * Bellelli, R. et al.


POLE3-POLE4 is a histone H3-H4 chaperone that maintains chromatin integrity during DNA replication. _Mol. Cell_ 72, 112–126.e5 (2018). CAS  PubMed  PubMed Central  Google Scholar  * Iida, T.


& Araki, H. Noncompetitive counteractions of DNA polymerase and ISW2/yCHRAC for epigenetic inheritance of telomere position effect in _Saccharomyces cerevisiae_. _Mol. Cell. Biol._ 24,


217–227 (2004). CAS  PubMed  PubMed Central  Google Scholar  * Bellelli, R. et al. Polε instability drives replication stress, abnormal development, and tumorigenesis. _Mol. Cell_ 70,


707–721.e7 (2018). CAS  PubMed  PubMed Central  Google Scholar  * Mejlvang, J. et al. New histone supply regulates replication fork speed and PCNA unloading. _J. Cell Biol._ 204, 29–43


(2014). CAS  PubMed  PubMed Central  Google Scholar  * Liu, S. et al. RPA binds histone H3-H4 and functions in DNA replication-coupled nucleosome assembly. _Science_ 355, 415–420 (2017). CAS


  PubMed  Google Scholar  * Evrin, C., Maman, J. D., Diamante, A., Pellegrini, L. & Labib, K. Histone H2A-H2B binding by Pol α in the eukaryotic replisome contributes to the maintenance


of repressive chromatin. _EMBO J._ 37, e99021 (2018). PubMed  PubMed Central  Google Scholar  * Clément, C. et al. High-resolution visualization of H3 variants during replication reveals


their controlled recycling. _Nat. Commun._ 9, 3181 (2018). PubMed  PubMed Central  Google Scholar  * Gurova, K., Chang, H.-W., Valieva, M. E., Sandlesh, P. & Studitsky, V. M. Structure


and function of the histone chaperone FACT - resolving FACTual issues. _Biochim. Biophys. Acta. Gene Regul. Mech._ 1861, 892–904 (2018). CAS  Google Scholar  * Kurat, C. F., Yeeles, J. T.


P., Patel, H., Early, A. & Diffley, J. F. X. Chromatin controls DNA replication origin selection, lagging-strand synthesis, and replication fork rates. _Mol. Cell_ 65, 117–130 (2017).


CAS  PubMed  PubMed Central  Google Scholar  * Abe, T. et al. The histone chaperone facilitates chromatin transcription (FACT) protein maintains normal replication fork rates. _J. Biol.


Chem._ 286, 30504–30512 (2011). CAS  PubMed  PubMed Central  Google Scholar  * Tsunaka, Y., Fujiwara, Y., Oyama, T., Hirose, S. & Morikawa, K. Integrated molecular mechanism directing


nucleosome reorganization by human FACT. _Genes Dev._ 30, 673–686 (2016). CAS  PubMed  PubMed Central  Google Scholar  * Wang, T. et al. The histone chaperone FACT modulates nucleosome


structure by tethering its components. _Life Sci. Alliance_ 1, e201800107 (2018). PubMed  PubMed Central  Google Scholar  * Mayanagi, K. et al. Structural visualization of key steps in


nucleosome reorganization by human FACT. _Sci. Rep._ 9, 10183 (2019). PubMed  PubMed Central  Google Scholar  * Liu, Y. et al. FACT caught in the act of manipulating the nucleosome. _Nature_


577, 426–431 (2020). CAS  PubMed  Google Scholar  * Chereji, R. V. & Clark, D. J. Major determinants of nucleosome positioning. _Biophys. J._ 114, 2279–2289 (2018). CAS  PubMed  PubMed


Central  Google Scholar  * Meyer, C. A. & Liu, X. S. Identifying and mitigating bias in next-generation sequencing methods for chromatin biology. _Nat. Rev. Genet._ 15, 709–721 (2014).


CAS  PubMed  PubMed Central  Google Scholar  * Ramachandran, S. & Henikoff, S. Transcriptional regulators compete with nucleosomes post-replication. _Cell_ 165, 580–592 (2016). CAS 


PubMed  PubMed Central  Google Scholar  * Vasseur, P. et al. Dynamics of nucleosome positioning maturation following genomic replication. _Cell Rep._ 16, 2651–2665 (2016). CAS  PubMed 


PubMed Central  Google Scholar  * Fennessy, R. T. & Owen-Hughes, T. Establishment of a promoter-based chromatin architecture on recently replicated DNA can accommodate variable


inter-nucleosome spacing. _Nucleic Acids Res._ 44, 7189–7203 (2016). CAS  PubMed  PubMed Central  Google Scholar  * Gutiérrez, M. P., MacAlpine, H. K. & MacAlpine, D. M. Nascent


chromatin occupancy profiling reveals locus- and factor-specific chromatin maturation dynamics behind the DNA replication fork. _Genome Res._ 29, 1123–1133 (2019). PubMed  PubMed Central 


Google Scholar  * Stewart-Morgan, K. R., Reverón-Gómez, N. & Groth, A. Transcription restart establishes chromatin accessibility after DNA replication. _Mol. Cell_ 75, 284–297.e6 (2019).


CAS  PubMed  Google Scholar  * Smith, D. J. & Whitehouse, I. Intrinsic coupling of lagging-strand synthesis to chromatin assembly. _Nature_ 483, 434–438 (2012). CAS  PubMed  PubMed


Central  Google Scholar  * Yadav, T. & Whitehouse, I. Replication-coupled nucleosome assembly and positioning by ATP-dependent chromatin-remodeling enzymes. _Cell Rep._ 15, 715–723


(2016). CAS  PubMed  PubMed Central  Google Scholar  * Kaplan, N. et al. The DNA-encoded nucleosome organization of a eukaryotic genome. _Nature_ 458, 362–366 (2009). CAS  PubMed  Google


Scholar  * Anderson, J. D. & Widom, J. Poly(dA-dT) promoter elements increase the equilibrium accessibility of nucleosomal DNA target sites. _Mol. Cell. Biol._ 21, 3830–3839 (2001). CAS


  PubMed  PubMed Central  Google Scholar  * Ramachandran, S., Ahmad, K. & Henikoff, S. Capitalizing on disaster: establishing chromatin specificity behind the replication fork.


_BioEssays_ 39, 1600150 (2017). Google Scholar  * Petruk, S. et al. Delayed accumulation of H3K27me3 on nascent DNA is essential for recruitment of transcription factors at early stages of


stem cell differentiation. _Mol. Cell_ 66, 247–257.e5 (2017). CAS  PubMed  PubMed Central  Google Scholar  * Petruk, S. et al. Structure of nascent chromatin is essential for hematopoietic


lineage Specification. _Cell Rep._ 19, 295–306 (2017). CAS  PubMed  PubMed Central  Google Scholar  * Iwafuchi-Doi, M. & Zaret, K. S. Pioneer transcription factors in cell reprogramming.


_Genes Dev._ 28, 2679–2692 (2014). PubMed  PubMed Central  Google Scholar  * Owens, N. et al. CTCF confers local nucleosome resiliency after DNA replication and during mitosis. _eLife_ 8,


e47898 (2019). PubMed  PubMed Central  Google Scholar  * Reverón-Gómez, N. et al. Accurate recycling of parental histones reproduces the histone modification landscape during DNA


replication. _Mol. Cell_ 72, 239–249.e5 (2018). PubMed  PubMed Central  Google Scholar  * Madamba, E. V., Berthet, E. B. & Francis, N. J. Inheritance of histones H3 and H4 during DNA


Replication In Vitro. _Cell Rep._ 21, 1361–1374 (2017). CAS  PubMed  Google Scholar  * Schlissel, G. & Rine, J. The nucleosome core particle remembers its position through DNA


replication and RNA transcription. _Proc. Natl Acad. Sci. USA_ 116, 20605–20611 (2019). CAS  PubMed  PubMed Central  Google Scholar  * Escobar, T. M. et al. Active and repressed chromatin


domains exhibit distinct nucleosome segregation during DNA replication. _Cell_ 179, 953–963.e11 (2019). CAS  PubMed  PubMed Central  Google Scholar  * Hansen, K. H. et al. A model for


transmission of the H3K27me3 epigenetic mark. _Nat. Cell Biol._ 10, 1291–1300 (2008). CAS  PubMed  Google Scholar  * Hathaway, N. A. et al. Dynamics and memory of heterochromatin in living


cells. _Cell_ 149, 1447–1460 (2012). CAS  PubMed  PubMed Central  Google Scholar  * Coleman, R. T. & Struhl, G. Causal role for inheritance of H3K27me3 in maintaining the OFF state of a


_Drosophila HOX_ gene. _Science_ 356, eaai8236 (2017). PubMed  PubMed Central  Google Scholar  * Laprell, F., Finkl, K. & Müller, J. Propagation of Polycomb-repressed chromatin requires


sequence-specific recruitment to DNA. _Science_ 356, eaai8266 (2017). Google Scholar  * Gaydos, L. J., Wang, W. & Strome, S. Gene repression. H3K27me and PRC2 transmit a memory of


repression across generations and during development. _Science_ 345, 1515–1518 (2014). CAS  PubMed  PubMed Central  Google Scholar  * Audergon, P. N. C. B. et al. Epigenetics. Restricted


epigenetic inheritance of H3K9 methylation. _Science_ 348, 132–135 (2015). CAS  PubMed  PubMed Central  Google Scholar  * Ragunathan, K., Jih, G. & Moazed, D. Epigenetics. Epigenetic


inheritance uncoupled from sequence-specific recruitment. _Science_ 348, 1258699 (2015). PubMed  Google Scholar  * Aygün, O., Mehta, S. & Grewal, S. I. S. HDAC-mediated suppression of


histone turnover promotes epigenetic stability of heterochromatin. _Nat. Struct. Mol. Biol._ 20, 547–554 (2013). PubMed  PubMed Central  Google Scholar  * Zentner, G. E. & Henikoff, S.


Regulation of nucleosome dynamics by histone modifications. _Nat. Struct. Mol. Biol._ 20, 259–266 (2013). CAS  PubMed  Google Scholar  * Dodd, I. B., Micheelsen, M. A., Sneppen, K. &


Thon, G. Theoretical analysis of epigenetic cell memory by nucleosome modification. _Cell_ 129, 813–822 (2007). CAS  PubMed  Google Scholar  * Pesavento, J. J., Yang, H., Kelleher, N. L.


& Mizzen, C. A. Certain and progressive methylation of histone H4 at lysine 20 during the cell cycle. _Mol. Cell. Biol._ 28, 468–486 (2008). CAS  PubMed  Google Scholar  * Sweet, S. M.


M., Li, M., Thomas, P. M., Durbin, K. R. & Kelleher, N. L. Kinetics of re-establishing H3K79 methylation marks in global human chromatin. _J. Biol. Chem._ 285, 32778–32786 (2010). CAS 


PubMed  PubMed Central  Google Scholar  * Alabert, C. et al. Domain model explains propagation dynamics and stability of histone H3K27 and H3K36 methylation landscapes. _Cell Rep._ 30,


1223–1234.e8 (2020). PubMed  Google Scholar  * Bonnet, J. et al. Quantification of proteins and histone marks in _Drosophila_ embryos reveals stoichiometric relationships impacting chromatin


regulation. _Dev. Cell_ 51, 632–644.e6 (2019). CAS  PubMed  Google Scholar  * Reinberg, D. & Vales, L. D. Chromatin domains rich in inheritance. _Science_ 361, 33–34 (2018). CAS  PubMed


  Google Scholar  * Laugesen, A., Højfeldt, J. W. & Helin, K. Molecular mechanisms directing PRC2 recruitment and H3K27 methylation. _Mol. Cell_ 74, 8–18 (2019). CAS  PubMed  PubMed


Central  Google Scholar  * Oksuz, O. et al. Capturing the onset of PRC2-mediated repressive domain formation. _Mol. Cell_ 70, 1149–1162.e5 (2018). CAS  PubMed  PubMed Central  Google Scholar


  * Poepsel, S., Kasinath, V. & Nogales, E. Cryo-EM structures of PRC2 simultaneously engaged with two functionally distinct nucleosomes. _Nat. Struct. Mol. Biol._ 25, 154–162 (2018).


CAS  PubMed  PubMed Central  Google Scholar  * Højfeldt, J. W. et al. Accurate H3K27 methylation can be established de novo by SUZ12-directed PRC2. _Nat. Struct. Mol. Biol._ 25, 225–232


(2018). PubMed  PubMed Central  Google Scholar  * Wang, X. & Moazed, D. DNA sequence-dependent epigenetic inheritance of gene silencing and histone H3K9 methylation. _Science_ 356, 88–91


(2017). CAS  PubMed  PubMed Central  Google Scholar  * Yu, R., Wang, X. & Moazed, D. Epigenetic inheritance mediated by coupling of RNAi and histone H3K9 methylation. _Nature_ 558,


615–619 (2018). CAS  PubMed  PubMed Central  Google Scholar  * Howe, F. S., Fischl, H., Murray, S. C. & Mellor, J. Is H3K4me3 instructive for transcription activation? _BioEssays_ 39,


1–12 (2017). CAS  PubMed  Google Scholar  * Hörmanseder, E. et al. H3K4 methylation-dependent memory of somatic cell identity inhibits reprogramming and development of nuclear transfer


embryos. _Cell Stem Cell_ 21, 135–143.e6 (2017). PubMed  PubMed Central  Google Scholar  * Lauberth, S. M. et al. H3K4me3 interactions with TAF3 regulate preinitiation complex assembly and


selective gene activation. _Cell_ 152, 1021–1036 (2013). CAS  PubMed  PubMed Central  Google Scholar  * Thomas, L. R. et al. Interaction with WDR5 promotes target gene recognition and


tumorigenesis by MYC. _Mol. Cell_ 58, 440–452 (2015). CAS  PubMed  PubMed Central  Google Scholar  * Cano-Rodriguez, D. et al. Writing of H3K4Me3 overcomes epigenetic silencing in a


sustained but context-dependent manner. _Nat. Commun._ 7, 12284 (2016). CAS  PubMed  PubMed Central  Google Scholar  * Flury, V. et al. The histone acetyltransferase Mst2 protects active


chromatin from epigenetic silencing by acetylating the ubiquitin ligase Brl1. _Mol. Cell_ 67, 294–307.e9 (2017). CAS  PubMed  PubMed Central  Google Scholar  * Bernstein, B. E. et al. A


bivalent chromatin structure marks key developmental genes in embryonic stem cells. _Cell_ 125, 315–326 (2006). CAS  PubMed  Google Scholar  * Liu, L., Michowski, W., Kolodziejczyk, A. &


Sicinski, P. The cell cycle in stem cell proliferation, pluripotency and differentiation. _Nat. Cell Biol._ 21, 1060–1067 (2019). CAS  PubMed  PubMed Central  Google Scholar  * Larson, A.


G. & Narlikar, G. J. The role of phase separation in heterochromatin formation, function, and regulation. _Biochemistry_ 57, 2540–2548 (2018). CAS  PubMed  Google Scholar  * Rowley, M.


J. & Corces, V. G. Organizational principles of 3D genome architecture. _Nat. Rev. Genet._ 19, 789–800 (2018). CAS  PubMed  Google Scholar  * Nagano, T. et al. Cell-cycle dynamics of


chromosomal organization at single-cell resolution. _Nature_ 547, 61–67 (2017). CAS  PubMed  PubMed Central  Google Scholar  * Wooten, M. et al. Asymmetric histone inheritance via


strand-specific incorporation and biased replication fork movement. _Nat. Struct. Mol. Biol._ 26, 732–743 (2019). CAS  PubMed  PubMed Central  Google Scholar  * Ishiuchi, T. et al. Early


embryonic-like cells are induced by downregulating replication-dependent chromatin assembly. _Nat. Struct. Mol. Biol._ 22, 662–671 (2015). CAS  PubMed  Google Scholar  * Cheloufi, S. et al.


The histone chaperone CAF-1 safeguards somatic cell identity. _Nature_ 528, 218–224 (2015). CAS  PubMed  PubMed Central  Google Scholar  * Song, Y. et al. CAF-1 is essential for _Drosophila_


development and involved in the maintenance of epigenetic memory. _Dev. Biol._ 311, 213–222 (2007). CAS  PubMed  Google Scholar  * Nakano, S., Stillman, B. & Horvitz, H. R.


Replication-coupled chromatin assembly generates a neuronal bilateral asymmetry in _C. elegans_. _Cell_ 147, 1525–1536 (2011). CAS  PubMed  PubMed Central  Google Scholar  * Volk, A. et al.


A CHAF1B-dependent molecular switch in hematopoiesis and leukemia pathogenesis. _Cancer Cell_ 34, 707–723.e7 (2018). CAS  PubMed  PubMed Central  Google Scholar  * Cheng, L. et al. Chromatin


assembly factor 1 (CAF-1) facilitates the establishment of facultative heterochromatin during pluripotency exit. _Nucleic Acids Res._ 47, 11114–11131 (2019). PubMed  PubMed Central  Google


Scholar  * Yadav, T., Quivy, J.-P. & Almouzni, G. Chromatin plasticity: a versatile landscape that underlies cell fate and identity. _Science_ 361, 1332–1336 (2018). CAS  PubMed  Google


Scholar  * Yu, C. et al. Strand-specific analysis shows protein binding at replication forks and PCNA unloading from lagging strands when forks stall. _Mol. Cell_ 56, 551–563 (2014). CAS 


PubMed  PubMed Central  Google Scholar  * Xu, C. & Corces, V. G. Nascent DNA methylome mapping reveals inheritance of hemimethylation at CTCF/cohesin sites. _Science_ 359, 1166–1170


(2018). CAS  PubMed  PubMed Central  Google Scholar  * Xu, C. & Corces, V. G. Genome-wide mapping of protein-DNA interactions on nascent chromatin. _Methods Mol. Biol._ 1766, 231–238


(2018). CAS  PubMed  PubMed Central  Google Scholar  * Charlton, J. et al. Global delay in nascent strand DNA methylation. _Nat. Struct. Mol. Biol._ 25, 327–332 (2018). CAS  PubMed  PubMed


Central  Google Scholar  * Smith, D. J., Yadav, T. & Whitehouse, I. Detection and sequencing of Okazaki fragments in _S. cerevisiae_. _Methods Mol. Biol._ 1300, 141–153 (2015). CAS 


PubMed  PubMed Central  Google Scholar  Download references ACKNOWLEDGEMENTS K.R.S.-M. is supported by a postdoctoral fellowship from the Lundbeck Foundation and a Marie Curie Individual


Fellowship (MSCA-IF-2016 no. 747332). Research in the Groth laboratory is supported by the Lundbeck Foundation (R198-2015-269), the European Research Council (ERC CoG no. 724436),


Independent Research Fund Denmark (7016-00042B; 4092-00404B), the Novo Nordisk Foundation (NNF14CC0001; NNF14OC0012839), the NEYE foundation and the Danish Cancer Society. AUTHOR INFORMATION


Author notes * Nataliya Petryk Present address: Epigenetics and Cell Fate, UMR7216 CNRS, University of Paris, Paris, France AUTHORS AND AFFILIATIONS * The Novo Nordisk Foundation Center for


Protein Research (CPR), University of Copenhagen, Copenhagen, Denmark Kathleen R. Stewart-Morgan & Anja Groth * Biotech Research and Innovation Centre (BRIC), University of Copenhagen,


Copenhagen, Denmark Kathleen R. Stewart-Morgan, Nataliya Petryk & Anja Groth Authors * Kathleen R. Stewart-Morgan View author publications You can also search for this author inPubMed 


Google Scholar * Nataliya Petryk View author publications You can also search for this author inPubMed Google Scholar * Anja Groth View author publications You can also search for this


author inPubMed Google Scholar CONTRIBUTIONS K.R.S.-M., N.P. and A.G. conceived, prepared figures for and wrote the manuscript. CORRESPONDING AUTHOR Correspondence to Anja Groth. ETHICS


DECLARATIONS COMPETING INTERESTS A.G. is CSO and co-founder of Ankrin Therapeutics. ADDITIONAL INFORMATION PUBLISHER’S NOTE Springer Nature remains neutral with regard to jurisdictional


claims in published maps and institutional affiliations. RIGHTS AND PERMISSIONS Reprints and permissions ABOUT THIS ARTICLE CITE THIS ARTICLE Stewart-Morgan, K.R., Petryk, N. & Groth, A.


Chromatin replication and epigenetic cell memory. _Nat Cell Biol_ 22, 361–371 (2020). https://doi.org/10.1038/s41556-020-0487-y Download citation * Received: 12 September 2019 * Accepted:


18 February 2020 * Published: 30 March 2020 * Issue Date: April 2020 * DOI: https://doi.org/10.1038/s41556-020-0487-y SHARE THIS ARTICLE Anyone you share the following link with will be able


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