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Structural Basis of DNMT1 and DNMT3A-Mediated DNA Methylation

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Structural Basis of DNMT1 and DNMT3A-Mediated DNA Methylation G C A T T A C G G C A T genes Review Structural Basis of DNMT1 and DNMT3A-Mediated DNA Methylation Wendan Ren 1,†, Linfeng Gao 2,† and Jikui Song 1,2,* 1 Department of Biochemistry, University of California, Riverside, CA 92521, USA; [email protected] 2 Environmental Toxicology Program, University of California, Riverside, CA 92521, USA; [email protected] * Correspondence: [email protected]; Tel.: +1-951-827-4221 † These authors contributed equally to this work. Received: 7 November 2018; Accepted: 4 December 2018; Published: 11 December 2018 Abstract: DNA methylation, one of the major epigenetic mechanisms, plays critical roles in regulating gene expression, genomic stability and cell lineage commitment. The establishment and maintenance of DNA methylation in mammals is achieved by two groups of DNA methyltransferases (DNMTs): DNMT3A and DNMT3B, which are responsible for installing DNA methylation patterns during gametogenesis and early embryogenesis, and DNMT1, which is essential for propagating DNA methylation patterns during replication. Both groups of DNMTs are multi-domain proteins, containing a large N-terminal regulatory region in addition to the C-terminal methyltransferase domain. Recent structure-function investigations of the individual domains or large fragments of DNMT1 and DNMT3A have revealed the molecular basis for their substrate recognition and specificity, intramolecular domain-domain interactions, as well as their crosstalk with other epigenetic mechanisms. These studies highlight a multifaceted regulation for both DNMT1 and DNMT3A/3B, which is essential for the precise establishment and maintenance of lineage-specific DNA methylation patterns in cells. This review summarizes current understanding of the structure and mechanism of DNMT1 and DNMT3A-mediated DNA methylation, with emphasis on the functional cooperation between the methyltransferase and regulatory domains. Keywords: DNMT1; DNMT3A; DNA methyltransferase; maintenance DNA methylation; de novo DNA methylation; allosteric regulation; autoinhibition 1. Introduction DNA methylation represents one of the major epigenetic mechanisms that critically influence gene expression and cell fate commitment [1–6]. In mammals, DNA methylation is essential for the silencing of retrotransposons [7–9], genomic imprinting [10,11] and X-chromosome inactivation [12,13]. Mammalian DNA methylation predominantly occurs at the C-5 position of cytosine within the CpG dinucleotide context, accounting for ~70–80% of CpG sites throughout the genome [14]. The establishment of DNA methylation is achieved by the closely related DNA methyltransferases 3A (DNMT3A) and 3B (DNMT3B), designated as de novo DNA methyltransferases, during germ cell development and early embryogenesis [15,16]. Subsequently, clonal transmission of specific DNA methylation patterns is mainly mediated by DNA methyltransferase 1 (DNMT1), designated as maintenance DNA methyltransferase, in a replication-dependent manner [17,18]. However, the classification of DNMT3A/3B as de novo methyltransferases and DNMT1 as maintenance DNA methyltransferase appears to be an oversimplification, as increasing evidence has revealed an important role of DNMT3A and DNMT3B in DNA methylation maintenance [19,20], while other studies have pointed to the de novo methylation activity of DNMT1 in specific loci [21,22]. A detailed understanding Genes 2018, 9, 620; doi:10.3390/genes9120620 www.mdpi.com/journal/genes Genes 2018, 9, 620 2 of 20 Genes 2018, 9, x FOR PEER REVIEW 2 of 20 ofdetailed the structure understanding and regulation of the structure of DNMT1 and and regu DNMT3A/3Blation of DNMT1 is essential and DNMT3A/3B for elucidating is theiressential roles for in DNAelucidating methylation their roles maintenance in DNA methylation and establishment maintenance in cells. and establishment in cells. Both DNMT1 and and DNMT3A/3B DNMT3A/3B belong belong to to the the class class I methyltransferase I methyltransferase family family [23], [23 featured], featured by bya conserved a conserved catalytic catalytic core coretermed termed Rossmann Rossmann fold, which fold, which consists consists of a mixed of a seven-stranded mixed seven-stranded β-sheet βflanked-sheet by flanked three byα-helices three αon-helices either side on either [24]. These side [enzyme24]. Theses catalyze enzymes the methylation catalyze the reaction methylation in an reactionS-adenosyl-L-methionine in an S-adenosyl-L-methionine (AdoMet)-dependent (AdoMet)-dependent manner, with manner, the cata withlytic the core catalytic harboring core harboring essential essentialmotifs for motifs enzymatic for enzymatic catalysis catalysis and cofactor and cofactor bind binding.ing. In addition, In addition, a asubdomain, subdomain, termed termed target recognition domaindomain (TRD), (TRD), is insertedis inserted between between the centralthe centralβ-sheet β-sheet and the and last theα-helix last ofα-helix the catalytic of the corecatalytic [24]. core The TRD[24]. bearsThe TRD no sequence bears no similaritysequence betweensimilarity DNMT1 between and DNMT1 DNMT3s; and instead, DNMT3s; it participates instead, it inparticipates DNA binding in DNA to ensure binding substrate to ensure specificity substrate of specificity each enzyme. of each enzyme. To ensure proper proper programming programming of of DNA DNA methylat methylationion patterns patterns in cell in cell linage linage commitment, commitment, the thefunctions functions of DNMTs of DNMTs are subject are subject to a tostringent a stringent regu regulationlation during during development development [25,26]. [25 ,Unlike26]. Unlike their theirbacterial bacterial counterparts counterparts that contain that contain only onlythe me thethyltransferase methyltransferase (MTase) (MTase) domain, domain, both bothDNMT1 DNMT1 and andDNMT3s DNMT3s are aremulti-domain multi-domain proteins, proteins, containing containing a large a large regulatory regulatory region region in in addition addition to to the C-terminal MTaseMTase domain domain (Figure (Figure1)[ 181), 27[18,27].]. Recent Recent studies studies have generatedhave generated a large bodya large of structuralbody of andstructural functional and informationfunctional information on both groups on ofboth enzymes, groups including of enzymes, the molecular including basis the underlyingmolecular basis their enzyme-substrateunderlying their recognition,enzyme-substrate and the recognition, regulatory rolesand ofthe their regulatory N-terminal roles segments of their in the N-terminal substrate specificity,segments in enzymatic the substrate activity specificity, as well enzymatic as genomic acti targeting.vity as well This as review genomic provides targeting. an overview This review on theprovides recent an progress overview in structural on the andrecent mechanistic progress understandingin structural and ofDNMT1 mechanistic and DNMT3A,understanding with anof emphasisDNMT1 and on howDNMT3A, the regulatory with an and emphasis MTase domainson how ofthe each regulatory enzyme cooperateand MTase in maintenancedomains of each and deenzyme novo cooperate DNA methylation, in maintenance respectively. and de novo DNA methylation, respectively. Figure 1.1.Domain Domain architectures architectures ofhuman of human DNA methyltransferases:DNA methyltransferases: DNMT1, DNMT1, DNMT3A DNMT3A and DNMT3B, and andDNMT3B, regulator and DNMT3L, regulator withDNMT3L, individual with domainsindividual marked domains by marked residue numbers.by residue numbers. 2. Structure and Mechanism of DNMT1 DNMT1 is comprised of ~1600 amino acids, with an N-terminal regulatory region covering two thirds of thethe sequence,sequence, a highly conserved (GK)n repeat and a a C-terminal MTase MTase domain (Figure (Figure 11).). The regulatoryregulatory regionregion startsstarts withwith aa ~300~300 aminoamino acid-longacid-long N-terminalN-terminal domain (NTD) harboring a variety ofof proteinprotein and/orand/or DNA interaction sites, followed by a replicationreplication foci-targetingfoci-targeting sequencesequence (RFTS)(RFTS) domain,domain, a CXXCa CXXC zinc zinc finger finger domain domain and aand pair a of pair bromo-adjacent-homology of bromo-adjacent-homology (BAH) domains (BAH) (Figuredomains1). (Figure The function 1). The of DNMT1function inof replication-dependent DNMT1 in replication-dependent DNA methylation DNA maintenance methylation is supportedmaintenance by is its supported localization by in its replication localization foci in during replication the S foci phase, during and inthe vitro S phase,a 3–40 and fold in enzymatic vitro a 3– preference40 fold enzymatic for hemimethylated preference for CpG hemimethylated sites [18,28], an epigeneticCpG sites mark[18,28], enriched an epigenetic at the replication mark enriched foci [29 at]. Howthe replication the regulatory foci domains[29]. How of DNMT1the regulatory are coordinated domains inof attainingDNMT1 itsare enzymatic coordinated and in spatiotemporal attaining its regulationsenzymatic and remains spatiotemporal a long-lasting regulations topic of interest. remains Nevertheless, a long-lasting recent topic structure-function of interest. Nevertheless, studies of variousrecent structure-function DNMT1 fragments studies under differentof various DNA DNMT1 binding fragments states [30 under–33] havedifferent started DNA to illuminate binding states how different[30–33] have domains started of thisto illuminate enzyme orchestrate how different its activity domains in maintenanceof this enzyme DNA orchestrate methylation. its activity
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