Lashings of DNA Methylation, Forkfuls of Chromatin Remodeling
Total Page:16
File Type:pdf, Size:1020Kb
Downloaded from genesdev.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press PERSPECTIVE Lashings of DNA methylation, forkfuls of chromatin remodeling Richard R. Meehan,1 Sari Pennings, and Irina Stancheva Genes and Development Group, Department of Biomedical Sciences, University of Edinburgh, Edinburgh EH8 9XD, Scotland, UK Epigenetic control of gene expression in animals and distributed with equal probability either in the DNA plants is often correlated with changes in cytosine meth- wrapped around the nucleosome or in the linker region ylation at specific chromosomal loci. This leads to the (Reik et al. 2001). irreversible promoter silencing of many genes, trans- posons, and endogenous retroviruses (Bestor 2000; Mar- Is chromatin remodeling necessary for DNA tienssen and Colot 2001). How DNA methylation pat- methylation in vivo? terns are set up during development, especially in the context of chromatin, is not well understood. Cytosine Somatic methylation patterns undergo dramatic remod- methyltransferases catalyze the transfer of a methyl eling during gametogenesis with further changes after group onto the C-5 position of cytosine from the univer- fertilization and during the cleavage stages of the preim- sal cofactor SAM (Bestor 2000). Two main types of meth- plantation mouse blastocyst (Reik et al. 2001). This re- yltransferase activity exist in mammals: a de novo activ- sults in a genome-wide loss of methylation during the ity and a maintenance activity. Dnmt3a and Dnmt3b preimplantation period, after which new patterns of have been identified as de novo methyltransferases, DNA methylation are imposed through the combined which methylate cytosine at CpG dinucleotides on both action of the de novo and, subsequently, maintenance strands with little sequence specificity (Okano et al. methyltransferases. Dnmt3a and Dnmt3b show 1998; Lyko et al. 1999). Dnmt1 is predominantly a post- nonoverlapping functions in mouse development, with replicative maintenance methyltransferase, which rec- Dnmt3b specifically required for de novo methylation of ognizes hemimethylated substrates, and acts to restore centromeric minor satellite repeats (Okano et al. 1999). methylated cytosines at CpGs on the newly duplicated In view of the lack of any evidence for sequence speci- strand (Lyko et al. 1999; Bestor 2000). Mutation studies ficity by de novo methyltransferase enzymes in vitro, it in mice have shown that the methyltransferase genes are is tempting to speculate that in vivo, the targeting of necessary for embryonic (Dnmt1 and Dnmt3b) and post- Dnmt3a and Dnmt3b to specific loci may be regulated at natal (Dnmt3a) development (Lei et al. 1996; Okano et the level of chromatin. al. 1999). All three enzymes have been shown to meth- So what might determine the accessibility of these en- ylate naked DNA substrates in vitro. However, compli- zymes to their chromatin templates? A potential clue cating the issue is the in vivo evidence suggesting that came from a genetic screen aiming to identify genes that patterns of DNA methylation are established and main- are required for maintenance of normal cytosine meth- tained within a nucleosomal infrastructure (Bird and ylation patterns in the flowering plant Arabidopsis Wolffe 1999). As yet we know little about the mechanis- thaliana. Mutation in a gene named DDM1 (decrease in tic basis of Dnmt3a and Dnmt3b activity in vivo, but in DNA methylation) causes a 70% reduction of genomic the case of Dnmt1 it has been shown that this mainte- cytosine methylation, mainly at repeated sequences nance methyltransferase enzyme can be targeted to (Vongs et al. 1993). The DNA within the centromeres of PCNA, an auxiliary component of the DNA replication Arabidopsis has a structural role, but also encodes sev- complex (Chuang et al. 1997). It is probable that chro- eral genes (Tabata et al. 2000). It is possible that the matin assembly precedes DNA methylation behind the phenotypic defect of ddm1 mutants is caused by activa- replication fork. Assembly of DNA into nucleosomes tion of cryptic heterochromatic genes and transposons can prevent access by methyltransferases to their in vivo induced by loss of DNA methylation (Jeddeloh et al. substrates (Kladde and Simpson 1994). Yet in the ge- 1999). There is a progressive effect of ddm1 on low copy nome, methylated CpGs are sequences leading to loss of cytosine methylation over multiple generations, which suggests that ddm1 muta- tions impair the efficiency of DNA methylation after 1Corresponding author. replication (Kakutani et al. 1996). DDM1 is not a meth- E-MAIL Richard.Meehan@ed.ac.uk; FAX 0131-650-3714. Article and publication are at http://www.genesdev.org/cgi/doi/10.1101/ yltransferase. Instead, it encodes a member of the SNF2- gad.954901. like helicase subfamily, many members of which are GENES & DEVELOPMENT 15:3231–3236 © 2001 by Cold Spring Harbor Laboratory Press ISSN 0890-9369/01 $5.00; www.genesdev.org 3231 Downloaded from genesdev.cshlp.org on September 28, 2021 - Published by Cold Spring Harbor Laboratory Press Meehan et al. able to disrupt histone–DNA interactions (Jeddeloh et al. mally repressed by DNA methylation in the Lsh−/− mu- 1999). Another putative family member, ATRX, is local- tants. As the authors point out, neither loss of methyl- ized to pericentromeric heterochromatin in human and ation at repetitive sequences nor at the imprinted genes mouse (McDowell et al. 1999). Mutations in ATRX give observed in Lsh−/− mice seems to be essential for prena- rise to developmental abnormalities and ␣-thalassaemia, tal development. which are accompanied by changes in the pattern of This raises the question, what causes the early embry- methylation of several highly repeated sequences includ- onic lethality of both Dnmt1- and Dnmt3b-deficient ing the rDNA arrays, a Y-specific satellite, and subtelo- mice? One possibility is that Lsh-deficient mice show meric repeats. This circumstantial evidence suggests hypomethylation at a later stage of development than that ATRX, like DDM1, may act as a transcriptional mice lacking maintenance and de novo methyltransfer- regulator through an effect on chromatin conformation ases. It is also worth noting that loss of Dnmt1 function and DNA methylation. in mice and toad blastocysts affects the ability of embry- Further support for this type of mechanism comes onic cells to differentiate properly, which can result in from a recent paper by Dennis and colleagues (Dennis et programmed cell death (Jackson-Grusby et al. 2001; al. 2001), which describes a new regulator of global DNA Stancheva et al. 2001). The apoptotic phenotype is criti- methylation levels in mice, lymphoid specific helicase cally dependent on the level of hypomethylation, as toad (Lsh). Previous work showed that Lsh, also known as blastulae that have a 50% depletion in DNA methyl- Proliferation-Associated SNF2-like Gene (PASG), is ex- ation levels appear to develop normally (Stancheva and pressed ubiquitously in fetal mouse tissues and is linked Meehan 2000). A reduction in DNA methylation below with cell proliferation (Raabe et al. 2001), as well as be- this threshold results in premature gene activation and ing essential in postnatal murine development (Geiman phenotypic abnormalities. It is possible that the degree and Muegge 2000; Geiman et al. 2001). Lsh−/− mice die of hypomethylation occurring in Dnmt and Lsh mutants within a few hours after birth with reduced body weight distinguishes their different phenotypes. and a pathology suggesting that renal failure may be the direct cause of mortality. On the basis of the high level of Is Lsh involved in remodeling heterochromatin? identity between Lsh and DDM1 (see Fig. 1), the authors examined global methylation levels in fetal and newborn That the loss of a single protein should have such a dra- mice. Lsh−/− mice turned out to have reduced levels of matic impact on DNA methylation levels is all the more global cytosine methylation (50–60% of wild-type levels) remarkable because in Arabidopsis and mice, DNA in the absence of any changes in the levels or activity of methyltransferase activity in itself is unaffected in ddm/ Dnmt1, Dnmt3a, and Dnmt3b. In particular, the authors Lsh mutant extracts (Kakutani et al. 1995; Dennis et al. found that methylation was much reduced at both sat- 2001). In addition, the primary amino acid sequence of ellite DNA and many dispersed repetitive sequences. Lsh/DDM1 does not offer any indication of an associa- The effect of the Lsh mutation on the methylation status tion (either by homology or conserved domains) with the of low copy sequences was more variable and stage-spe- methyltransferase activity. This points to an indirect ef- cific. The imprinted H19 gene, but not the Igf2r locus, fect of Lsh on DNA methylation. was hypomethylated compared to control embryos. Based on amino acid sequence, Lsh is (like DDM1) -globin, Pgk1, and Pgk2 genes were hypomethylated in most closely related in its seven conserved ATPase/he- day 13.5 Lsh−/− embryos but not in newborn Lsh−/− mice. licase motifs to the SNF2 subfamily (Geiman et al. 2001). It is possible that Lsh, like ATRX, is targeted to specific Most members of the SNF2 family of proteins appear to regions during development. In this respect, it will be of have the capacity to alter chromatin structure. Central interest to determine whether there are associated to this activity is their DNA-dependent ATPase domain changes in transcription from sequences that are nor- (for review, see Kingston and Narlikar 1999; Flaus and Figure 1. Schematic representation of SNF2-like ATPase amino acid sequences homologous to mouse Lsh/PASG. Shown are human PASG (hPASG); Arabi- dopsis thaliana DDM1 (DDM1); Saccharomyces ce- revisiae ORF homolog (YFR038w); murine ISWI (mSNF2h); murine SNF2 (mBRG1); and murine CHD1 (mCHD1). The last three proteins represent members of the ISWI, SNF2, and CHD subfamilies. Conserved pro- tein domains are indicated by gray filled rectangles: ATPase domain (ATPase); helicase domain (H); SANT domain (S); bromodomain (B); and chromodomain (C).