REVIEWS Fork direction ork direction Lagging DNM O General O DNA methylation dependen Domain HPL-SUV39HI O DNA methylation independent specific New nucleosomes Figure 1 Asymmetric DNA replication and coupling of inheritance of DNA and histone marks a An intrinsic strand bias at DNA replication. DNA replication occurs in the 5 to 3 direction. One strand is replicated as the leading strand and the other as the lagging strand is b Proliferating cell nuclear antigen(PCNA) molecules associate with the 3'end of newly synthesized DNA. This results in the loading of PCNA on to the two strands. c Maintenance of dNa and specific histone modifications at the replication fork Homotrimeric PCNA recruits general factors that function at all PR-SET7 and SETD8)y8-75, chromatin remodellers(Williams syndrome transcription factor(STF-SNF2H (als ko,, forks, such as histone modifiers(histone deacetylases(HDACs) and the Lys methyltransferase SET8(also known as SMARCAS)) and chromatin assembly factor 1(CAF1; also known as CHAF1) Depending on the presence of DNA methylation, PCNA together with NP95(also called UHRF1 and ICBP90)recruits DNA methyltransferase 1(DNMT1). which methylates hemimethylated CpG n daughter strands 32.33. Certain histone modifiers use the dNA methylation machinery as a template-for example, HDAC activity is recruited by DNMTl and NP95(REFS 81, 82), and DNMT1 interacts with the Lys methyltransferase G9a(also known as KMT1C)In DNA methylation-rich regions, CAF1 forms a complex with methyl CpG-binding protein 1(MBD1)and the Lys methyltransferase SETDB1(also known as KMT1E), thereby coupling histone deposition with histone methylation CAFl also contributes to the maintenance of heterochromatin protein 1(HP1)in a DNA-methylation-independent process 10.HPl, in turn, interacts with the histone methyltransferase SUV39H1(also known as KMT1A ith high fidelity. The maintenance of DNA methyl- NP95 binds preferentially to hemimethylated DNA-36 ation at the fork is ensured by DNA methyltransferase 1 interacts with DNMTI and is required for its localization (NMTI), owing to its affinity for hemimethylated dNA to replicating heterochromatic regions(FIG. 1c). Indeed, in vitro242 and its interaction with PCNA". However, the deletion of NP95 results in methylation defectsthat mechanism by which methylation maintenance is ensured resemble those that are observed following the loss of in a faithful manner was unclear, as DNMTI also shows DNMTI(REF. 37), which suggests that NP95 has a domi de novo methylation activity and its ability to bind nant role in tethering maintenance methyltransferase PCNA is not absolutely required for DNA methylation activity to newly replicated DNA. The maintenance of maintenance. Recent evidence now suggests that the DNA methylation further requires the ATP-dependent DNA methyltransferase SET-and RING-associated(SRA)-domain-containing chromatin-remodelling factor decreased DNA methy ne that transfers proteins variant in methylation 1(VIMI)in Arabidopsis ation 1 (DDMI)in A thaliana and LSH (also known ethyl groups fro thaliana and NP95(also called UHRFI and ICBP90) as HELLS)in mice, which have been suggested specific adenines or cytosines in mammals constitute an additional mechanistic link provide access of the methylation machinery to newly between hemimethylated DNA and DNMTI (REFS 30-33). replicated DNA NATURE REVIEWS MOLECULAR CELL BIOLOGY 22009 Macmillan Publishers Limited All rights reservedDNMT1 NP95 Nature Reviews | Molecular Cell Biology 5′ 5′ 3′ 5′ 3′ 5′ 3′ 5′ 3′ 3′ 5′ 3′ a b Leading c Lagging Leading Lagging PCNA PCNA Fork direction Fork direction HDAC SET8 HDAC WSTF– SNF2H MBD1–SETDB1 HP1–SUV39H1 HDAC G9a CAF1 General DNA methylation dependent DNA methylation independent DNA methylation Domain specific Parental nucleosomes New nucleosomes Replication machinery DNA methyltransferase An enzyme that transfers methyl groups from S-adenosylmethionine to specific adenines or cytosines in DNA. with high fidelity. The maintenance of DNA methyl￾ation at the fork is ensured by DNA methyltransferase 1 (DNmT1), owing to its affinity for hemimethylated DNA in vitro24,25 and its interaction with PcNA26. However, the mechanism by which methylation maintenance is ensured in a faithful manner was unclear, as DNmT1 also shows de novo methylation activity27 and its ability to bind PcNA is not absolutely required for DNA methylation maintenance28,29. Recent evidence now suggests that the SeT­ and RING­associated (SRA)­domain­containing proteins variant in methylation 1 (VIm1) in Arabidopsis thaliana and NP95 (also called uHRF1 and IcBP90) in mammals constitute an additional mechanistic link between hemimethylated DNA and DNmT1 (ReFs 30–33). NP95 binds preferentially to hemimethylated DNA34–36, interacts with DNmT1 and is required for its localization to replicating heterochromatic regions32 (FIG. 1c). Indeed, deletion of NP95 results in methylation defects33 that resemble those that are observed following the loss of DNmT1 (ReF. 37), which suggests that NP95 has a domi￾nant role in tethering maintenance methyltransferase activity to newly replicated DNA. The maintenance of DNA methylation further requires the ATP­dependent chromatin­remodelling factor decreased DNA methyl￾ation 1 (DDm1) in A. thaliana38,39 and lSH (also known as HellS) in mice40, which have been suggested to provide access of the methylation machinery to newly replicated DNA38. Figure 1 | asymmetric DNa replication and coupling of inheritance of DNa and histone marks. a | An intrinsic strand bias at DNA replication. DNA replication occurs in the 5′ to 3′ direction. One strand is replicated as the leading strand and the other as the lagging strand18. b | Proliferating cell nuclear antigen (PCNA) molecules associate with the 3′ end of newly synthesized DNA. This results in the loading of PCNA on to the two strands. c | Maintenance of DNA and specific histone modifications at the replication fork. Homotrimeric PCNA recruits general factors that function at all forks, such as histone modifiers (histone deacetylases (HDACs) and the Lys methyltransferase SET8 (also known as KMT5A, PR-SET7 and SETD8))73–75, chromatin remodellers (Williams syndrome transcription factor (WSTF)–SNF2H (also known as SMARCA5))76 and chromatin assembly factor 1 (CAF1; also known as CHAF1)21. Depending on the presence of DNA methylation, PCNA together with NP95 (also called UHRF1 and ICBP90) recruits DNA methyltransferase 1 (DNMT1), which methylates hemimethylated CpG sites on daughter strands26,32,33. Certain histone modifiers use the DNA methylation machinery as a template — for example, HDAC activity is recruited by DNMT1 and NP95 (ReFs 81,82), and DNMT1 interacts with the Lys methyltransferase G9a (also known as KMT1C)83. In DNA methylation-rich regions, CAF1 forms a complex with methyl CpG-binding protein 1 (MBD1) and the Lys methyltransferase SETDB1 (also known as KMT1E), thereby coupling histone deposition with histone methylation79,80. CAF1 also contributes to the maintenance of heterochromatin protein 1 (HP1) in a DNA-methylation-independent process128,130. HP1, in turn, interacts with the histone methyltransferase SUV39H1 (also known as KMT1A)68. REVIEWS NATuRe ReVIeWS | Molecular cell Biology VOlume 10 | mARcH 2009 | 195 © 2009 Macmillan Publishers Limited. All rights reserved