Reprogramming of the paternal genome upon fertilization involves genome-wide oxidation of 5-methylcytosine Khursheed Iqbala,1, Seung-Gi Jinb,1, Gerd P. Pfeiferb,2, and Piroska E. Szabóa,2 Departments of aMolecular and Cellular Biology and bCancer Biology, Beckman Research Institute of the City of Hope, Duarte, CA 91010 Edited by Peter A. Jones, University of Southern California, Los Angeles, CA, and accepted by the Editorial Board January 28, 2011 (received for review September 17, 2010) Genome-wide erasure of DNA cytosine-5 methylation has been direct removal of 5mC by DNA glycosylase activity has been reported to occur along the paternal pronucleus in fertilized oocytes identified (27, 28), but these proteins do not have mammalian in an apparently replication-independent manner, but the mecha- homologs. Furthermore, it was reported that the protein nism of this reprogramming process has remained enigmatic. Re- GADD45A promotes demethylation of CpG-methylated DNA cently, considerable amounts of 5-hydroxymethylcytosine (5hmC), (29), perhaps in conjunction with excision repair activities (23, most likely derived from enzymatic oxidation of 5-methylcytosine 30). However, a role of GADD45A in DNA demethylation has (5mC) by TET proteins, have been detected in certain mammalian fi fi tissues. 5hmC has been proposed as a potential intermediate in not been con rmed (31, 32). Speci cally addressing active de- active DNA demethylation. Here, we show that in advanced pro- methylation of the paternal genome in zygotes, Okada et al. have nuclear-stage zygotes the paternal pronucleus contains substantial used a siRNA knockdown strategy in oocytes followed by in- amounts of 5hmC but lacks 5mC. The converse is true for the tracytoplasmic sperm injection to screen for candidate DNA maternal pronucleus, which retains 5mC but shows little or no 5hmC demethylase genes. Okada et al. identified the elongator com- signal. Importantly, 5hmC persists into mitotic one-cell, two-cell, and plex, and in particular its subunit Elp3, as a component required later cleavage-stage embryos, suggesting that 5mC oxidation is not for zygotic DNA demethylation in the paternal pronucleus (33). CELL BIOLOGY followed immediately by genome-wide removal of 5hmC through Taking all available information into account, perhaps the most excision repair pathways or other mechanisms. This conclusion is considerable evidence suggests that cytidine deaminases work in fi supported by bisul te sequencing data, which shows only limited conjunction with DNA glycosylases to remove 5mC in a DNA conversion of modified cytosines to cytosines at several gene loci. repair pathway (19–26). However, if not strand-specifically co- It is likely that 5mC oxidation is carried out by the Tet3 oxidase. Tet3, but not Tet1 or Tet2, was expressed at high levels in oocytes ordinated, excision repair would put the genome at risk for DNA and zygotes, with rapidly declining levels at the two-cell stage. double-strand breakage, and this is expected to be detrimental at Our results show that 5mC oxidation is part of the early life cycle those critical stages of development when the reprogramming of mammals. events take place. One plausible mechanism for demethylation of 5mC, without ethylation at the 5-position of cytosines is an important the need for a DNA repair process, is oxidation of the methyl Mcomponent of the epigenetic code (1, 2). Cell differentia- group followed by secondary reactions that eventually lead to tion, X chromosome inactivation, reprogramming, and malig- restoration of cytosine. Recently, Kriaucionis and Heintz and nant transformation are major events characterized by remark- Tahiliani et al. made the important discovery that substantial able changes in the epigenome and involve remodeling of DNA amounts of 5-hydroxymethylcytosine (5hmC), initially thought to methylation patterns (3–10). Despite the relatively stable and be only a rare DNA damage product (34), are present in mouse heritable features of DNA methylation in somatic cells, genome- Purkinje and granule neurons and in embryonic stem cells (35, wide DNA demethylation occurs both in developing primordial 36). An enzymatic activity involved in producing 5hmC from germ cells and in fertilized oocytes (zygotes) (11, 12). In zygotes, 5mC by oxidation was identified as TET1 (36). The two other a striking asymmetric DNA demethylation of the two parental mammalian homologs of TET1, TET2, and TET3, all containing genomes seems to occur within the same oocyte cytoplasm, be- α ginning as early as 6 h after fertilization, when the paternal ge- a dioxygenase motif involved in Fe(II) and -ketoglutarate nome undergoes active DNA demethylation but the maternal binding and catalytic activity, were shown to posses similar ac- genome resists demethylation (13–15). This process appears to tivities as well (37). be largely independent of DNA replication. The maternal ge- The goal of our study was to investigate if 5mC oxidation nome later on undergoes passive demethylation in the absence of occurs in fertilized oocytes and is part of the apparent DNA maintenance methyltransferase DNMT1 during DNA replica- demethylation process that takes place during this early de- tion in cleavage-stage embryos (11, 13, 16). velopmental stage. The replication-independent DNA demethylation of the pa- ternal genome points to the existence of a mammalian DNA demethylase activity. However, the identity of such an activity Author contributions: G.P.P. and P.E.S. designed research; K.I. and S.-G.J. performed re- has remained enigmatic and controversial for over a decade (17, search; K.I., S.-G.J., G.P.P., and P.E.S. analyzed data; and G.P.P. and P.E.S. wrote the paper. 18). Activation-induced cytidine deaminases or related activities The authors declare no conflict of interest. may work in conjunction with DNA glycosylases to remove 5- This article is a PNAS Direct Submission. P.A.J. is a guest editor invited by the Editorial methylcytosine (5mC) from DNA. After deamination of 5mC to Board. thymine has been catalyzed by the deaminase, the mismatched 1K.I. and S.-G.J. contributed equally to this work. – thymine will be excised from the resulting G:T base pairs (19 2To whom correspondence may be addressed. E-mail: [email protected] or pszabo@coh. 26). The base excision repair pathway can then be further en- org. gaged to incorporate cytosine bases, resulting in replacement of This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. 5mC with C (20). In plants, a demethylase pathway involving 1073/pnas.1014033108/-/DCSupplemental. www.pnas.org/cgi/doi/10.1073/pnas.1014033108 PNAS Early Edition | 1of6 Downloaded by guest on October 2, 2021 Results Using specific antibodies, we determined the levels of 5mC and 5hmC in male and female pronuclei in zygotes and in early cleavage-stage embryos. We used a recently available commer- cial polyclonal antibody directed against 5hmC. Initially, we verified the specificity of this antibody toward 5hmCs versus 5mCs or unmodified cytosines placed at identical positions within CpG sequences in synthetic single-stranded 76-mer oli- gonucleotide substrates (38). In immuno-dot blot assays, we observed that this antibody is specific for 5hmC and does not react with substrates containing only unmodified cytosines, nor does it react with substrates containing 5mC (Fig. S1A). We then tested the suitability of the anti-5hmC antibody for immunos- taining experiments using human 293T cells. As initially deter- mined by immuno-dot blot assays, this cell line contains de- tectable levels of 5hmC (Fig. S1B). A nuclear staining pattern was observed with the anti-5hmC antibody (Fig. S1C). To test for specificity of the staining reaction, we preincubated the antibody with synthetic oligonucleotides containing C, 5mC, or 5hmC. As shown in Fig. S1C, the nuclear staining was completely elimi- nated by preincubation of the antibody with 5hmC-containing oligonucleotides but not by competition with the other oligo- nucleotides attesting to the suitability of the antibody for im- munocytochemistry. We hypothesized that 5hmC might be detectable as a potential intermediate during DNA demethylation in zygotes. Using the anti-5hmC antibody, we observed intense staining of the paternal pronucleus in mouse zygotes (Fig. 1A), whereas 5hmC staining Fig. 1. 5hmC is present in the male pronucleus of mouse zygotes. (A)A was almost completely absent from the maternal pronucleus. To mouse zygote was double-stained with anti-5hmC antibody (green) and further test the specificity of the staining pattern, we carried out anti-5mC antibody (red). The smaller maternal pronucleus is closer to the competition experiments with synthetic oligonucleotides and polar body (pb). A bright-field image is shown on the far left. (B) Additional observed that the staining of zygotes for 5hmC is specific(Fig. zygotes were double-stained with anti-5hmC antibody (green) and anti-5mC S2). Simultaneous double-staining with an established anti-5mC antibody (red). Merged images are shown. (C) Zygotes obtained by in vitro antibody (16), which does not react with 5hmC (38), detected fertilization were double-stained similarly. Two polyspermic zygotes (to the right) exhibit 5hmC staining in two paternal pronuclei. (D) 5mC and 5hmC 5mC in the maternal but not in the paternal pronucleus (Fig. 1 A staining reveal two separate chromosome sets at metaphase of zygote di- and B). Thus, the two staining patterns are mutually exclusive, vision. A confocal image is shown. (E) Individual chromosomes are largely suggesting that 5mC has been converted to 5hmC specifically in stained for either 5mC (likely originated from the maternal pronucleus) or the paternal pronucleus. Fig. 1 A and B show late pronuclear 5hmC (likely from the paternal pronucleus) at anaphase of zygote division. stages (PN4–PN5). In vitro fertilized zygotes have similar stain- Two Z sections of the same zygote are shown. ing patterns. Bispermic zygotes exhibit 5hmC staining in both paternal pronuclei (Fig. 1C).