Molecular Vision 2025; 31:85-97 <http://www.molvis.org/molvis/v31/85>
Received 14 October 2024 | Accepted 26 March 2025 | Published 28 March 2025

DNA methyltransferase 1 regulates epithelial cell functions in corneal and eyelid development

Antonius Christianto,1 Maureen Mongan,1 Bo Xiao,1 Qin Wang,1 Alvaro Puga,1 Michael L. Robinson,2 Ying Xia1

1Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH; 2Department of Biology, Miami University, Miami, OH; Dr. Christianto currently at School of Life Sciences and Technology, Institute Teknologi Bandung, Bandung 40132, Indonesia; Dr. Wang is currently at Nonclinical Safety Assessment, BeiGene (Beijing) Co. Ltd, Beijing 100020, China

Correspondence to: Ying Xia, Department of Environmental and Public Health Sciences, University of Cincinnati, College of Medicine, Cincinnati, OH; email: ying.xia@uc.edu

Abstract

Purpose: DNA methyltransferase 1 (DNMT1) is a crucial enzyme for the development of the retina and lens in the eye, but its roles in the cornea and eyelids are yet to be investigated.

Methods: Ocular surface epithelium (OSE)-specific Dnmt1 knockout mice, denoted as Dnmt1ΔOSE, were generated. Prenatal eye tissues were characterized by hematoxylin and eosin staining; DNMT1 expression, DNA methylation, epithelial differentiation and cell–cell junctions were determined by immunohistochemistry; proliferation was assessed by 5-ethynyl 2´-deoxyuridin labeling and apoptosis evaluated by terminal deoxynucleotidyl transferase dUTP nick-end labeling assay. Keratinocytes derived from Dnmt1F/F mice were infected with adenoviruses carrying either green fluorescent protein or Cre recombinase to obtain wild-type and Dnmt1-deficient cells. In these cells, Dnmt1 expression and epithelial terminal differentiation were evaluated by real-time PCR and/or western blotting; adherence junction and apoptosis were assessed by immunohistochemistry; proliferation was determined by 5-ethynyl 2´-deoxyuridin labeling; transcription factor activities were determined by luciferase reporter assays.

Results: The abundant DNMT1 expression and cytosine methylation (5meC) detected in the ocular surface epithelia of wild-type embryos were largely diminished in that of Dnmt1ΔOSE embryos. Besides lens degeneration, the Dnmt1ΔOSE fetuses had severe abnormalities of the cornea and eyelids. The surface epithelial cells and stromal keratocytes in the knockout corneas were distorted and the eyelids failed to fuse in the knockout embryos, resulting in an eye-open-at-birth phenotype. At the cellular level, DNMT1-deficient OSE had normal proliferation but increased apoptosis and aberrant cell junctions. In addition, the knockout corneal epithelia failed to express corneal-specific keratin 12, and the knockout eyelid epithelia had increased expression of keratin 10, indicating accelerated terminal differentiation. In vitro studies validated that DNMT1 was required for epithelial cell survival, terminal differentiation and cell junctions, and further identified signaling pathways aberrantly activated by its ablation.

Conclusion: DNMT1 maintains survival and differentiation of corneal and eyelid epithelium for the development of the eye.

Introduction

DNA methylation involves covalent addition of a methyl group to the cytosine of DNA, a prevalent epigenetic modification throughout the genome and crucial for regulation of gene expression [13]. This event is catalyzed by DNA methyltransferases (DNMTs). In mammals, there are three DNMTs—DNMT1, DNMT3A and DNMT3B [4]. While DNMT3A and DNMT3B have unique and overlapping roles in de novo methylation, DNMT1 is a key enzyme responsible for preserving the methylation signatures in successive cell generations. Specifically, DNMT1 acts on hemimethylated DNA and copies the parental methylation status to the daughter strand following DNA replication [5,6]. Through these activities, DNMT1 regulates fundamental biological processes, such as inactivation of nonallelic X chromosome, sustaining imprinting signatures and preserving genome stability [7], and is required for normal embryonic and fetal development [8].

There is compelling evidence supporting the roles of DNMT1 in development. In mice, DNMT1 knockout causes severe developmental abnormalities, leading to early embryonic death, accompanied by global DNA hypomethylation, aberrant expression of imprinted genes and chromosomal instability [5,9]. Studies of conditional Dnmt1 knockout mice have revealed additional cell type-specific roles of the gene products in the formation of different tissues. For example, muscle-specific Dnmt1 deletion results in defective myogenic differentiation and myoblast fusion. The promoter of Id-1 is hypomethylated in DNMT1-deficient progenitors, leading to increased expression of Id-1, a transcription factor that negatively regulates myogenesis [10]. Loss of DNMT1 in the intestine causes DNA damage, premature differentiation, apoptosis and subsequent loss of nascent villi [11]. Moreover, depletion of DNMT1 in keratinocytes promotes the early exit of progenitor status, causing premature differentiation and eventually loss of skin tissues [12].

In the eye, DNMT1 is required for neural retina differentiation. Retinal-specific Dnmt1 deletion results in compromised neuronal differentiation and rapid cell death [13,14]. In the lens, DNMT1 is required for lens epithelial cell survival but is dispensable for primary lens fiber differentiation [15]. Little is known about the developmental roles of DNMT1 in other ocular tissues besides the retina and lens. Here, we investigated cornea and eyelid development through mouse analysis, in which the Dnmt1 gene was specifically ablated in the ocular surface epithelium (OSE). Our data showed that DNMT1 was required for survival and differentiation programs of corneal and eyelid epithelia. Thus, DNMT1 inactivation, commonly caused by exposure to environmental chemicals and anticancer agents, could lead to congenital diseases affecting the cornea and eyelid [1619].

Methods

Animals

Dnmt1F/F/Le-CreTG/- females were crossed with Dnmt1F/F males and the Dnmt1F/F embryos/fetuses with or without a Le-CreTG allele, denoted as Dnmt1ΔOSE or wild-type pups, respectively, were collected for analyses as described before [15]. Genotype was determined by PCR using tail-cut genomic DNA and the primers listed in Appendix 1. Animals were housed in a pathogen-free vivarium in accordance with institutional policies. All animal experiments were approved in advance by the Institutional Animal Care and Use Committee at the University of Cincinnati College of Medicine.

Keratinocyte and stable cell lines

Mouse keratinocytes derived from Dnmt1F/F mice were cultured and maintained in Keratinocyte Serum Free Medium without Calcium Chloride (10,725-018, Gibco, Thermo Fisher Scientific, Waltham, MA) media, as described before [20]. To develop stable reporter cell lines, the Dnmt1F/F cells were infected with lentivirus carrying the pathway luciferase reporters purchased from LipExoGen Biotech (Appendix 2); stable cells were obtained following Blasticidin (R21001, Thermo Fisher Scientific) selection. The cells were subsequently infected with adenoviruses expressing either green fluorescent protein (Ad-GFP) or GFP plus Cre recombinase (Ad-GFP-Cre, or Ad-Cre) at 5 IU for 48 h to generate wild-type and Dnmt1-knockout (deficient) keratinocytes, respectively.

Histology and immunofluorescent staining

The heads of appropriately euthanized dams were collected and fixed in 4% paraformaldehyde (PFA) at 4 °C overnight. Tissues were embedded in paraffin and sectioned at 5 µm with a microtome (MT-980, Research & Manufacturing Co., Inc., Tucson, AZ). Selected serial tissue sections were subjected to hematoxylin (ES701, Azer Scientific, Morgantown, PA) and eosin (ES709, Azer Scientific) staining, and images were captured using Zen 3.1 (Blue edition) under bright-field light microscopy (Zeiss AXIO Scope A1, Göttingen, Germany) at different magnifications.

For immunohistochemistry, tissue sections representing the center of the eye were deparaffinized and immersed in boiled 10 mM citrate buffer (pH 6.0) for 30 min for antigen retrieval. The sections were blocked with phosphate-buffered saline/tween (PBST) containing 5% normal goat serum (PCN5000, Gibco, Thermo Fisher Scientific) for 1 h at room temperature and incubated with a diluted primary antibody overnight at 4 °C followed by secondary antibodies and Hoechst 33,342 (H1399, Thermo Fisher Scientific) staining. The list of antibodies and dilutions for each antibody is listed in Appendix 3. Images were captured using a confocal laser scanning microscope (Zeiss AXIO Observer Z1 LSM 700).

For cultured cell immunofluorescent staining, the DnmtF/F keratinocytes grown on cover glass were infected with Ad-GFP or Ad-Cre in Defined Keratinocyte Serum Free Medium (10,785-012, Gibco, Thermo Fisher Scientific) as described before [20]. After washing with PBS, the cells were fixed with 4% PFA at 4 °C for 20 min followed by incubation with a blocking solution of PBST containing 0.25% bovine serum albumin (BSA; A2153, Sigma-Aldrich, St. Louis, MO) for one hour at room temperature. Immunostaining was performed as that described for tissue sections.

Apoptosis and proliferation

To determine apoptosis, the tissue sections were subjected to terminal deoxynucleotidyl transferase dUTP nick-end labeling assays using the ApopTag® Plus in situ Apoptosis Fluorescein Detection Kit (S7111, Millipore Sigma, Temecula, CA) following the manufacturer’s protocol. Keratinocytes grown on cover glass with Ad-GFP and Ad-Cre infection as described above were examined by immunofluorescent staining with anti-Caspase-3 (CST 9663S, Cell Signaling Technology, Danvers, MA) as the primary antibody, Alexa Fluor™ 594 Goat anti-Rabbit IgG (H+L; A11012, Invitrogen) as the secondary antibody and Hoechst 33,342.

To determine proliferation, 2 h after intraperitoneal injection/incubation with 5-ethynyl 2´-deoxyuridine (EdU; Component A, 5 mg/kg b.w. or 10 µM in growth media), embryos/fetuses were collected from pregnant mice and cultured cells harvested. Tissue sections and keratinocytes were infected with Ad-GFP/Ad-Cre and subjected to an iClick™ EdU Andy Fluor™ 594 Imaging Kit (A005, ABP Biosciences, Beltsville, MD) following the manufacturer's protocol.

Cell apoptosis and proliferation were observed, and images were captured with a Zeiss AXIO Observer Z1 LSM 700 microscope. The staining positive cells were quantified and the percentage of positive staining was calculated versus total cells. The results represent data from at least three sections per embryo and three embryos/genotypes of different litters; data from cultured keratinocytes were quantified in three samples, and only green cells positive for Ad-GFP or Ad-Cre infection were included in quantification.

RNA isolation, reverse transcription and quantitative real-time PCR

Total RNA was extracted from cultured keratinocytes with a PureLink® RNA Mini kit (121,830, Invitrogen, Waltham, MA) following the manufacturer’s protocol. A total of 1 μg RNA was subjected to reverse transcription using a SuperScript™ IV First-Strand Synthesis System (18091050, Invitrogen). The cDNA was mixed with gene-specific primers and SYBR Green QPCR Master Mix, and subjected to quantitative real-time PCR an MX3000p thermal cycler system (Agilent Technologies, St. Clara, CA). Relative gene expression was calculated by the comparative ΔΔCt-method normalized to the constitutively expressed housekeeping gene, Gapdh. Data represented duplicates of at least three independent samples. Primer sequences are listed in Appendix 4.

Western blotting

Cells grown on a culture dish were lysed with RIPA buffers (0.5M EDTA pH 8, 0.1% SDS, 1% NP-40, 5M NaCl, 1M Tris-HCl pH 7.6, 2.5 g NaDOC, protease inhibitor). A total of 50 µg cell lysates were subjected to SDS PAGE, followed by western blotting using anti-DNMT1 and anti-β-actin. Sources and dilutions of the primary and secondary antibodies are listed in Appendix 3. Immunoblotting was detected by chemiluminescence and images were captured with a Gel Imaging System (UVP Transilluminator, Analytik Jena Company, Upland, CA). Signals were quantified by ImageJ software and the signal intensity of DNMT1 was compared with that of β-actin as the loading control.

Luciferase activities

Ad-GFP– or Ad-Cre–infected Dnmt1F/F reporter cells in 24-well plates were lysed and the activity of luciferase was measured using a luciferase assay system (Rapid detection of Firefly Luciferase activity, E1500, Promega, Madison WI). Relative luciferase activities were quantified after normalization with the cell's total protein. The results represent duplicate data from four biologic samples of each adenovirus transfection, Ad-GFP and Ad-Cre.

Statistical analysis

At least three independent samples were used in all experiments for data analysis. Statistical analysis was performed using a Student’s two-tailed paired t test for comparison between groups. The exact number of biologic replicates and statistical analysis used for each experiment are included in the figure legends. Values of p < 0.05 (*), p < 0.01 (**) and p < 0.001 (***) were considered statistically significant.

Results

Abnormal corneal and eyelid development in Dnmt1 ocular surface epithelium knockout mice

We crossed Dnmt1F/F mice with mice carrying one Le-Cre allele that expressed Cre recombinase in the OSE [21]. The resultant Dnmt1F/F/Le-Cre mice, denoted as Dnmt1ΔOSE, should have Dnmt1 specifically knocked out in the OSE, whereas the Dnmt1F/F littermates were considered as wild-type controls. We collected E15.5 embryos to determine DNMT1 expression. In the wild-type embryos, DNMT1 was expressed ubiquitously in the epithelial and stromal cells of the ocular surface tissues, including the lens, cornea and eyelids. In Dnmt1ΔOSE embryos, while DNMT1 expression was still abundant in stromal cells, it was largely absent in the OSE (arrowheads, Figure 1A). Concurrently, DNMT1-mediated 5-methylcytosine (5meC) was abundant in the OSE of the wild-type embryos but undetectable in that of the knockout embryos (arrowheads, Figure 1B).

To determine whether defective DNMT1 expression and DNA methylation affected eye development, we examined the histology of wild-type and Dnmt1ΔOSE eyes at E14.5–E16.5, encompassing the late embryogenic to early fetal developmental phases. Consistent with a previous report [15], OSE DNMT1 ablation caused lens degeneration. The knockout lens lost capsule epithelial cells and was smaller in size compared with those of wild-type embryos (Figure 2). The knockout lens was also frequently associated with anterior cell clusters (Figure 2, hash #) fused to the corneal endothelium as well as posterior debris located between the lens and the retina.

Unlike the Dnmt1ΔOSE lens, in which degeneration was evident in the E14.5 embryos, the knockout cornea and eyelids at this stage appeared to be normal; however, they exhibited clear abnormalities from E15.5 onward. The knockout corneas protruded anteriorly and became thicker and the knockout eyelids failed to fuse, leaving the corneal surface exposed at E16.5. In contrast, the wild-type had thinner corneas and their upper and lower eyelids were fused over the cornea. Corneal and eyelid abnormalities were observed only in Dnmt1F/F/Le-Cre but not Dnmt1+/F/Le-Cre fetuses, indicating that Dnmt1 deletion was autosomal recessive for corneal and eyelid defects (Appendix 4). These observations also suggest that Le-Cre expression is not responsible for the defective phenotypes observed in Dnmt1F/F/Le-Cre pups. Thus, DNMT1 expression in the OSE is required for corneal and eyelid development at late embryogenesis in addition to its role in lens development.

DNA methyltransferase 1 is required for corneal epithelial organization and differentiation

During embryonic development, the corneal epithelium is comprised of uniformed epithelial cells aligned in two layers above the basement membrane. We detected well-organized epithelial layers in the corneas of wild-type fetuses; however, we found irregular-shaped epithelial cells arranged in a distorted pattern with large intercellular spaces in the corneas of knockout fetuses (arrows, Figure 3A). Some of the basal Dnmt1ΔOSE corneal epithelial cells were detached from the basement membrane (asterisks, Figure 3A). The wild-type and Dnmt1ΔOSE corneal stroma was also strikingly different. The corneal stroma of wild-type fetuses was packed with residential keratocytes aligned parallel to the basement membrane, whereas the corneal stroma of Dnmt1ΔOSE fetuses, filled with irregular-shaped keratocytes, was nearly twice the thickness of that in wild-type (Figure 3A,B). Similar observations were made in both E15.5 and E16.5 embryos/fetuses (Figure 3 and Appendix 4).

The stromal thickness in Dnmt1ΔOSE embryos was not due to an increased number of keratocytes, but corresponded to larger intercellular spaces (Figures 3A,B). These observations led to the hypothesis that DNMT1 loss impairs the barrier function of the corneal epithelium, which in turn causes fluid accumulation and edema of the corneas. To test the hypothesis, we determined cell–cell junctions that constituted the epithelial barrier by establishing tight cell connections. One of the cell junctions is mediated by E-cadherin (E-Cad), a transmembrane protein and a key component of the adherens junctions to establish cell–cell contacts [22]. While E-Cad was detected on the plasma membrane of corneal epithelial cells, apparent differences were found between wild-type and Dnmt1ΔOSE (Figure 3C). E-Cad was evenly distributed on the plasma membrane at the cell–cell and cell–basement membrane junctions in wild-type corneas. It was also located at the cell–cell junction in Dnmt1ΔOSE corneas but was missing on ectopic spots between the epithelial and basement membranes (arrows, Figure 3C). Another key cell junction is mediated by Zonula Occludens-1 (ZO-1), also a transmembrane protein and a component of the tight junction complexes that regulate paracellular movement of ions and solutes between cells [23]. ZO-1 proteins were located predominantly on the plasma membrane of the corneal epithelium in wild-type embryos; however, they displayed diffused distribution throughout the cytosol in the knockout corneal epithelium (Figure 3D).

The corneal epithelium comprises stratified squamous epithelium that express distinct keratin intermediate filaments during embryonic development [24]. Keratin 14 (K14) is the basal epithelial cell marker expressed in all epithelial cells as early as E9.5 [25], whereas K12, a corneal-specific keratin essential for epithelial integrity and function, starts to express at E15.5 [26]. Examination of these keratins in wild-type and Dnmt1ΔOSE E15.5 embryos showed that K14 was evenly distributed on the plasma membrane of wild-type corneal epithelial cells but exhibited an uneven and sporadic distribution and was largely absent in basal cells above the basement membrane of Dnmt1ΔOSE corneas (Figure 3E). Moreover, K12, located on the plasma membrane of the suprabasal corneal epithelial cells in wild-type embryos, was completely undetectable within the corneas of Dnmt1ΔOSE embryos (Figure 3F). Together, our data indicate that DNMT1 is required to maintain the integrity and differentiation of the corneal epithelium, and that its deficiency causes a disorganized epithelium as well as stroma and corneal edema.

The role of DNA methyltransferase 1 in eyelid morphogenesis

A massive morphogenetic event in the late embryonic development of the mammalian eye is closure of the upper and lower eyelids, resulting in an enclosed eyelid covering the corneal surface [27,28]. Mouse eyelid closure occurs between E15.5 and E16.5, and the eyelids remain fused at birth. Thus, mice are normally born with their eyes closed, whereas newborn pups display an “eye-open” at birth (EOB) phenotype when the eyelids fail to fuse prenatally [29]. The observations that eyelids fail to fuse in Dnmt1ΔOSE E16.5 fetuses has led us to ask whether this defect resulted ultimately in the EOB phenotype. To address the question, we examined E17.5, E18.5 and postnatal day 1 (P1) pups and found that, unlike wild-type mice, which had fully closed eyelids, Dnmt1ΔOSE pups had partially open eyelids (Figure 4).

Prior to eyelid closure, the peridermal cells at the eyelid tip undergo morphological changes, leading to the formation of a protrusion that presumably initiates the centripetal epithelial movement for lid closure [30]. To understand how Dnmt1 knockout impairs closure, we examined the tips of wild-type and Dnmt1ΔOSE eyelids at E15.5, a developmental stage at the onset of lid closure. Eyelid tip epithelial protrusion was evident in the wild-type but not the knockout embryos (arrowhead, Figure 5A). The knockout eyelid tip instead appeared to fold posteriorly and became thicker (asterisk, Figure 5A); its epithelial cells were less compact with larger intercellular spaces, and some of the suprabasal cells had condensed chromatin (arrows, Figure 5A). Similar abnormalities were observed in the eyelid tip of E14.5 and E16.5 Dnmt1ΔOSE embryos (Appendix 4), indicating that DNMT1 ablation prevented the normal formation of eyelid tip protrusion.

To determine if DNMT1 ablation impaired the structural integrity of the eyelid tip like that seen in the cornea, we assessed E-Cad and ZO-1 via immunohistochemistry. Both ZO-1 and E-Cad were detected in the knockout eyelids, but their distributions were somewhat different from that of wild-type eyelids (Figure 5B). In the wild-type eyelid tips, ZO-1 was evenly distributed on the plasma membrane of basal and suprabasal epithelial cells, but in Dnmt1ΔOSE it was scattered throughout the cytosol in the suprabasal cells (asterisk, Figure 5B). E-Cad, on the other hand, was located on the plasma membrane of the eyelid tip epithelial cells in both genotypes, although it appeared to be less abundant in the basal epithelial cells of the knockout eyelids.

The embryonic eyelid is composed of stroma covered by epidermal layers at the anterior surface and conjunctival epithelium on the posterior side [31]. To assess the roles of DNMT1 in anterior and posterior eyelid epithelial differentiation, we determined the expression of K14, a marker of basal proliferative keratinocytes, and K10, which is expressed only in terminally differentiated suprabasal keratinocytes [25]. K14 expression was detected in the basal epithelial cells on both anterior and posterior surfaces of the eyelids, with no major differences observed between wild-type and Dnmt1ΔOSE E14.5–E16.5 embryos (Appendix 5). K10 was detected in the suprabasal layers of the anterior epithelium, and the level of expression gradually increased as the embryos grew older (arrowheads, Figure 5C). Compared with wild-type eyelids, Dnmt1ΔOSE eyelids showed increased K10 expression, both in intensity and in cell layers. In particular, eyelid tip cells were K10-negative in wild-type embryos but became K10-positive in Dnmt1ΔOSE embryos. Thus, DNMT1 loss impairs lid closure through potentiating differentiation and blocking the protrusion of lid tip epithelial cells.

DNA methyltransferase 1 regulates cell proliferation and apoptosis

Because DNMT1 has been shown to regulate proliferation and apoptosis in many organ-formation processes [11,32], we determined these roles in the OSE of E14.5 to E16.5 embryos. An EdU labeling assay was used to assess proliferation and a terminal deoxynucleotidyl transferase dUTP nick-end labeling assay was used to determine apoptosis. Quantification of the labeling data showed that DNMT1 ablation did not change proliferation but increased apoptosis in the OSE (Figure 6A–D). The number of apoptotic cells in all ocular surface epithelia, including the eyelid (EL), cornea (CO) and lens (LN), was significantly higher in Dnmt1ΔOSE than in wild-type embryos. The eyelid tip of the knockout, but not wild-type, embryos showed abundant apoptotic cells, corroborated with histological data showing cells with condensed nuclei in this region (Figure 5A and Figure 6B). The knockout corneas, on the other hand, displayed increased apoptosis of basal epithelial cells located between the epithelial layer and the stroma (Appendix 6). Neither proliferation nor apoptosis was altered in the stroma of the Dnmt1ΔOSE ocular surface (Appendix 7). These observations suggest that DNMT1 is required for the survival of corneal and eyelid epithelia, like that established previously in the lens epithelium [15].

DNA methyltransferase 1 regulates molecular and cellular activities in cultured keratinocytes

To investigate the roles of DNMT1 in epithelial development in vitro, we isolated epithelial cells from the skin of Dnmt1F/F mice and developed keratinocyte lines using a protocol we have recently developed to obtain epidermal stem cell-like characteristics and extensive subculture capacity [20]. Infection of the cells with Ad-Cre resulted in a marked reduction in DNMT1 mRNA and protein, whereas infection with Ad-GFP did not have such an effect (Figure 7A,B). When placed in differentiation media, Ad-GFP– and Ad-Cre–infected Dnmt1F/F cells showed the same level of K14 expression; however, Ad-Cre–infected cells, but not Ad-GFP–infected cells, exhibited higher expression of K1 and K10, indicating terminal epidermal differentiation (Figure 7C). Additionally, compared with Ad-GFP–infected cells, Ad-Cre infection significantly increased active Caspase-3 positive cells, suggesting increased apoptosis, without an apparent change in EdU positivity for proliferation (Figure 7D).

To address whether DNMT1 ablation disrupted cell–cell junctions in vitro, as seen in the OSE, we infected Dnmt1F/F cells with Ad-GFP and Ad-Cre, and examined E-Cad expression and localization. Clear E-Cad localization was detected on the plasma membrane in Ad-GFP–infected cells, but it disappeared in Ad-Cre–infected cells (Figure 7E). Additionally, in contrast to neighboring Ad-Cre–negative cells displaying regular epithelial morphology with polygonal shapes, Ad-Cre–positive cells lost their epithelial shape and became either round or stretched.

Taking advantage of the easily manipulatable feature of cultured keratinocytes, we further explored the signaling pathways affected by DNMT1 loss. To achieve this, we made stable Dnmt1F/F cells carrying luciferase reporters for specific signaling pathways. Infection of the stable cells with Ad-Cre significantly increased SRE-luc activities for MAPK signaling, TCF-luc for WNT signaling, RORγ for retinoic acid signaling and Gli-luc for Hedgehog signaling compared with those infected with Ad-GFP (Figure 7F). On the other hand, neither Ad-Cre nor Ad-GFP infection changed the activities of XRE-luc for AhR signaling, suggesting that DNMT1 loss led to the activation of specific signaling and transcription programs.

Discussion

Due to its crucial role in global DNA methylation, DNMT1 has been extensively studied in the development of different embryonic tissues that involve dynamic reprograming of the epigenome [11,13,14,3335]. Here we determined the developmental roles of DNMT1 in previously unexplored tissues, i.e., the OSE cells of the cornea and eyelid. We showed that DNMT1 is required for survival and proper differentiation of the OSE to maintain structural integrity and morphogenesis, and its ablation in OSE leads to corneal edema and eyelid closure defects in the late phase of embryogenesis. These observations suggest that DNMT1 deficiency could be one of the mechanisms underlying congenital corneal dystrophy and eyelid anomaly [36,37].

In the cornea, DNMT1 ablation severely impairs the epithelial architecture, resulting in a loss of cell–cell junctions and distorted cell structure and organization. The basal epithelium of Dnmt1ΔOSE corneas has increased apoptosis along with loss of adherent junctions in the cell–cell and cell–basement membrane interface. These events, as well as the lack of K12 expression, are likely responsible for a disintegrated and leaking epithelium, resulting in a thicker stroma and edema of the cornea. Increased apoptosis may also cause the loss of adherence junctions, although DNMT1 depletion could directly disrupt adherence junctions through activation of SNAIL for transcriptional repression of E-Cad expression [38,39]. Like in corneal epithelia, DNMT1 depletion has been shown to potentiate apoptosis in other cell types, and it may be doing so through activation of p53 to initiate the apoptotic pathway [5,15]. DNMT1 deficiency also leads to massive apoptosis of the lens epithelium [15], and this lens damage may further potentiate persistent hyaloid vascular cell accumulation at posterior to the Dnmt1ΔOSE lens [40].

The structural abnormalities of Dnmt1ΔOSE corneas and eyelids corresponded to increased apoptosis of epithelial cells. DNMT1 is well known as a negative regulator of apoptosis [41], and its repression leads to rapid loss of DNA methylation and subsequent cell death through hypomethylation of pro-apoptotic genes, widespread DNA damage and genomic instability [33] [42]. We observed a 10–20% increase in apoptosis in Dnmt1ΔOSE eyelid and corneal epithelia. This level of cell death could be sufficient to create open space to generate mechanical tension and induce shape changes in neighboring cells. The tension may also cause reorganization of the extracellular environment and tissue remodeling [43,44]. Additionally, signaling molecules released from the dead cells may act in trans to influence remodeling and activities of the surrounding cells [45,46]. DNMT1 is a positive regulator of cell proliferation through promoter hypermethylation and downregulation of genes involved in blocking cell cycle progression [47]; however, its knockout in OSE does not appear to affect proliferation in the cornea and eyelids, as well as the lens [15]. It is possible that the proliferation program of OSE is less susceptible to DNMT1 loss in contrast to the survival program, which is sensitive to disruption by DNMT1 deficiency.

DNA methylation is a key regulator of differentiation through distinct methylation patterns to establish the unique identity of differentiated cell types [48,49]. Here we showed that DNMT1 is dispensable for the differentiation of K14-positive basal epithelia but has distinct effects on terminal differentiation of cornea and eyelid epithelia. In the cornea, DNMT1 is essential for the development of K12-positive cells, which are corneal epithelial cells that specify maturation [24,26]. As DNMT1 has been shown to regulate progenitor differentiation in many tissues [14,50,51], its inhibition may occur in corneal progenitors to compromise the differentiation of corneal-specific epithelial cells, leading to diseases such as corneal dystrophy [52,53]. In the eyelid, epidermal terminal differentiation is developmentally accelerated in Dnmt1ΔOSE embryos. These observations are consistent with the established functions of DNMT1 in the epidermis, where it suppresses terminal differentiation through the methylation of epidermal differentiation gene promoters [12]. This accelerated terminal differentiation and increased apoptosis in the eyelid tip of E15.5 embryos may contribute to lid closure defects in the Dnmt1ΔOSE mice.

Cultured murine keratinocytes possess epithelial stem-like features and can be induced into terminal differentiation [20]. This in vitro model is therefore suitable to characterize the roles of DNMT1 in epithelial development because, like in OSE, DNMT1 ablation in these cells potentiates differentiation and apoptosis, and disrupts adherence junctions. Moreover, DNMT1 ablation in these cells led to the activation of some, but not all, signaling reporters, suggesting that reporter activation was not due to nonspecific global promoter hypomethylation. Some activated signaling pathways may contribute to the eye phenotypes seen in Dnmt1ΔOSE embryos. Hyperactivation of WNT signaling, for example, disrupts eyelid and corneal morphogenesis during mouse embryonic development and perturbs cell proliferation and differentiation of the epithelium [54]. Similarly, excessive activation of the growth factor receptor/SRE pathway leads to aberrant differentiation and morphogenesis of multiple ocular cell types/tissues [55,56], whereas overactivation of Hedgehog signaling impairs cell motility, morphology and developmental eye tissue closure [57]. Thus, DNMT1 loss may activate multiple signaling pathways to derail differentiation, apoptosis and morphogenetic programs. As DNMT1 activities can be manipulated through diet [58] and environmental factors [59], understanding its roles in eye development could lead to development of strategies in disease prevention and treatment.

Appendix 1. Supplementary Table 1.

Appendix 2. Supplementary Table 2.

Appendix 3. Supplementary Table 3.

Appendix 4. Supplementary Figure 1.

Appendix 5. Supplementary Figure 2.

Appendix 6. Supplementary Figure 3.

Appendix 7. Supplementary Figure 4.

Acknowledgments

The work was supported in part by National Institute of Health grants RO1HD098106 (YX) and R21ES033342 (YX).

References

  1. Jin B, Li Y, Robertson KD. DNA methylation: superior or subordinate in the epigenetic hierarchy? Genes Cancer. 2011; 2:607-17. [PMID: 21941617]
  2. Bird A. DNA methylation patterns and epigenetic memory. Genes Dev. 2002; 16:6-21. [PMID: 11782440]
  3. Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, Bailey DK, Huebert DJ, McMahon S, Karlsson EK, Kulbokas EJ, , 3rd Gingeras TR, Schreiber SL, Lander ES. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell. 2005; 120:169-81. [PMID: 15680324]
  4. Kikuchi A, Onoda H, Yamaguchi K, Kori S, Matsuzawa S, Chiba Y, Tanimoto S, Yoshimi S, Sato H, Yamagata A, Shirouzu M, Adachi N, Sharif J, Koseki H, Nishiyama A, Nakanishi M, Defossez PA, Arita K. Structural basis for activation of DNMT1. Nat Commun. 2022; 13:7130 [PMID: 36414620]
  5. Egger G, Jeong S, Escobar SG, Cortez CC, Li TW, Saito Y, Yoo CB, Jones PA, Liang G. Identification of DNMT1 (DNA methyltransferase 1) hypomorphs in somatic knockouts suggests an essential role for DNMT1 in cell survival. Proc Natl Acad Sci U S A. 2006; 103:14080-5. [PMID: 16963560]
  6. Uysal F, Sukur G, Cinar O. DNMT enzymes differentially alter global DNA methylation in a stage-dependent manner during spermatogenesis. Andrologia. 2022; 54e14357 [PMID: 34997784]
  7. Heard E. Delving into the diversity of facultative heterochromatin: the epigenetics of the inactive X chromosome. Curr Opin Genet Dev. 2005; 15:482-9. [PMID: 16107314]
  8. Martienssen R, Lippman Z, May B, Ronemus M, Vaughn M. Transposons, tandem repeats, and the silencing of imprinted genes. Cold Spring Harb Symp Quant Biol. 2004; 69:371-9. [PMID: 16117670]
  9. Li E, Bestor TH, Jaenisch R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell. 1992; 69:915-26. [PMID: 1606615]
  10. Liu R, Kim KY, Jung YW, Park IH. Dnmt1 regulates the myogenic lineage specification of muscle stem cells. Sci Rep. 2016; 6:35355 [PMID: 27752090]
  11. Elliott EN, Sheaffer KL, Schug J, Stappenbeck TS, Kaestner KH. Dnmt1 is essential to maintain progenitors in the perinatal intestinal epithelium. Development. 2015; 142:2163-72. [PMID: 26023099]
  12. Sen GL, Reuter JA, Webster DE, Zhu L, Khavari PA. DNMT1 maintains progenitor function in self-renewing somatic tissue. Nature. 2010; 463:563-7. [PMID: 20081831]
  13. Nasonkin IO, Merbs SL, Lazo K, Oliver VF, Brooks M, Patel K, Enke RA, Nellissery J, Jamrich M, Le YZ, Bharti K, Fariss RN, Rachel RA, Zack DJ, Rodriguez-Boulan EJ, Swaroop A. Conditional knockdown of DNA methyltransferase 1 reveals a key role of retinal pigment epithelium integrity in photoreceptor outer segment morphogenesis. Development. 2013; 140:1330-41. [PMID: 23406904]
  14. Rhee KD, Yu J, Zhao CY, Fan G, Yang XJ. Dnmt1-dependent DNA methylation is essential for photoreceptor terminal differentiation and retinal neuron survival. Cell Death Dis. 2012; 3e427 [PMID: 23171847]
  15. Hoang TV, Horowitz ER, Chaffee BR, Qi P, Flake RE, Bruney DG, Rasor BJ, Rosalez SE, Wagner BD, Robinson ML. Lens development requires DNMT1 but takes place normally in the absence of both DNMT3A and DNMT3B activity. Epigenetics. 2017; 12:27-40. [PMID: 27824296]
  16. Chow RL, Lang RA. Early eye development in vertebrates. Annu Rev Cell Dev Biol. 2001; 17:255-96. [PMID: 11687490]
  17. Azuma N, Yamaguchi Y, Handa H, Tadokoro K, Asaka A, Kawase E, Yamada M. Mutations of the PAX6 gene detected in patients with a variety of optic-nerve malformations. Am J Hum Genet. 2003; 72:1565-70. [PMID: 12721955]
  18. Mihelec M, St Heaps L, Flaherty M, Billson F, Rudduck C, Tam PP, Grigg JR, Peters GB, Jamieson RV. Chromosomal rearrangements and novel genes in disorders of eye development, cataract and glaucoma. Twin Res Hum Genet. 2008; 11:412-21. [PMID: 18637741]
  19. Reis LM, Semina EV. Conserved genetic pathways associated with microphthalmia, anophthalmia, and coloboma. Birth Defects Res C Embryo Today. 2015; 105:96-113. [PMID: 26046913]
  20. Wang J, Mongan M, Zhang X, Xia Y. Isolation and long-term expansion of murine epidermal stem-like cells. PLoS One. 2021; 16e0254731 [PMID: 34270586]
  21. Ashery-Padan R, Marquardt T, Zhou X, Gruss P. Pax6 activity in the lens primordium is required for lens formation and for correct placement of a single retina in the eye. Genes Dev. 2000; 14:2701-11. [PMID: 11069887]
  22. Hartsock A, Nelson WJ. Adherens and tight junctions: structure, function and connections to the actin cytoskeleton. Biochim Biophys Acta. 2008; 1778:660-9. [PMID: 17854762]
  23. Schneeberger EE, Lynch RD. The tight junction: a multifunctional complex. Am J Physiol Cell Physiol. 2004; 286:C1213-28. [PMID: 15151915]
  24. Tanifuji-Terai N, Terai K, Hayashi Y, Chikama T, Kao WW. Expression of keratin 12 and maturation of corneal epithelium during development and postnatal growth. Invest Ophthalmol Vis Sci. 2006; 47:545-51. [PMID: 16431949]
  25. Byrne C, Tainsky M, Fuchs E. Programming gene expression in developing epidermis. Development. 1994; 120:2369-83. [PMID: 7525178]
  26. Kurpakus MA, Maniaci MT, Esco M. Expression of keratins K12, K4 and K14 during development of ocular surface epithelium. Curr Eye Res. 1994; 13:805-14. [PMID: 7531631]
  27. Harris MJ, Juriloff DM. Eyelid development and fusion induced by cortisone treatment in mutant, lidgap-Miller, foetal mice. A scanning electron microscope study. J Embryol Exp Morphol. 1986; 91:1-18. [PMID: 3711778]
  28. Findlater GS, McDougall RD, Kaufman MH. Eyelid development, fusion and subsequent reopening in the mouse. J Anat. 1993; 183:121-9. [PMID: 8270467]
  29. Teramoto S, Fujii S, Yoshida A, Shirasu Y. Morphological and genetic characteristics of the open-eyelid mutant spontaneously occurring in NC-strain mice. Jikken Dobutsu. 1988; 37:455-62. [PMID: 3149245]
  30. Tawfik HA, Abdulhafez MH, Fouad YA, Dutton JJ. Embryologic and Fetal Development of the Human Eyelid. Ophthalmic Plast Reconstr Surg. 2016; 32:407-14. [PMID: 27124372]
  31. Sevel D. A reappraisal of the development of the eyelids. Eye (Lond). 1988; 2:123-9. [PMID: 3197869]
  32. Bai Y, Lang L, Zhao W, Niu R. Long Non-Coding RNA HOXA11-AS Promotes Non-Small Cell Lung Cancer Tumorigenesis Through microRNA-148a-3p/DNMT1 Regulatory Axis. Onco Targets Ther. 2019; 12:11195-206. [PMID: 31908486]
  33. Liao J, Karnik R, Gu H, Ziller MJ, Clement K, Tsankov AM, Akopian V, Gifford CA, Donaghey J, Galonska C, Pop R, Reyon D, Tsai SQ, Mallard W, Joung JK, Rinn JL, Gnirke A, Meissner A. Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells. Nat Genet. 2015; 47:469-78. [PMID: 25822089]
  34. Takebayashi S, Tamura T, Matsuoka C, Okano M. Major and essential role for the DNA methylation mark in mouse embryogenesis and stable association of DNMT1 with newly replicated regions. Mol Cell Biol. 2007; 27:8243-58. [PMID: 17893328]
  35. Bestor TH. The DNA methyltransferases of mammals. Hum Mol Genet. 2000; 9:2395-402. [PMID: 11005794]
  36. Weiss JS, Rapuano CJ, Seitz B, Busin M, Kivelä TT, Bouheraoua N, Bredrup C, Nischal KK, Chawla H, Borderie V, Kenyon KR, Kim EK, Møller HU, Munier FL, Berger T, Lisch W. IC3D Classification of Corneal Dystrophies-Edition 3. Cornea. 2024; 43:466-527. [PMID: 38359414]
  37. Al-Mujaini A, Yahyai MA, Ganesh A. Congenital Eyelid Anomalies: What General Physicians Need To Know. Oman Med J. 2021; 36e279 [PMID: 34267952]
  38. Espada J, Peinado H, Lopez-Serra L, Setién F, Lopez-Serra P, Portela A, Renart J, Carrasco E, Calvo M, Juarranz A, Cano A, Esteller M. Regulation of SNAIL1 and E-cadherin function by DNMT1 in a DNA methylation-independent context. Nucleic Acids Res. 2011; 39:9194-205. [PMID: 21846773]
  39. Bowler EH, Smith-Vidal A, Lester A, Bell J, Wang Z, Bell CG, Wang Y, Divecha N, Skipp PJ, Ewing RM. Deep proteomic analysis of Dnmt1 mutant/hypomorphic colorectal cancer cells reveals dysregulation of epithelial-mesenchymal transition and subcellular re-localization of Beta-Catenin. Epigenetics. 2020; 15:107-21. [PMID: 31448663]
  40. Khokhar S, Dhull C. Commentary: Understanding angiogenic factors in pathogenesis of persistent fetal vasculature. Indian J Ophthalmol. 2019; 67:1622-3. [PMID: 31546494]
  41. Yan L, Geng Q, Cao Z, Liu B, Li L, Lu P, Lin L, Wei L, Tan Y, He X, Li L, Zhao N, Lu C. Insights into DNMT1 and programmed cell death in diseases. Biomed Pharmacother. 2023; 168115753 [PMID: 37871559]
  42. Georgia S, Kanji M, Bhushan A. DNMT1 represses p53 to maintain progenitor cell survival during pancreatic organogenesis. Genes Dev. 2013; 27:372-7. [PMID: 23431054]
  43. Pérez-Garijo A, Steller H. Spreading the word: non-autonomous effects of apoptosis during development, regeneration and disease. Development. 2015; 142:3253-62. [PMID: 26443630]
  44. Wickman G, Julian L, Olson MF. How apoptotic cells aid in the removal of their own cold dead bodies. Cell Death Differ. 2012; 19:735-42. [PMID: 22421963]
  45. Essien SA, Ahuja I, Eisenhoffer GT. Apoptotic extracellular vesicles carrying Mif regulate macrophage recruitment and compensatory proliferation in neighboring epithelial stem cells during tissue maintenance. PLoS Biol. 2024; 22e3002194 [PMID: 39495793]
  46. Pérez-Garijo A, Fuchs Y, Steller H. Apoptotic cells can induce non-autonomous apoptosis through the TNF pathway. Elife. 2013; 2e01004 [PMID: 24066226]
  47. Baylin SB, Herman JG, Graff JR, Vertino PM, Issa JP. Alterations in DNA methylation: a fundamental aspect of neoplasia. Adv Cancer Res. 1998; 72:141-96. [PMID: 9338076]
  48. Ehrlich M, Lacey M. DNA methylation and differentiation: silencing, upregulation and modulation of gene expression. Epigenomics. 2013; 5:553-68. [PMID: 24059801]
  49. O’Neill KM, Irwin RE, Mackin SJ, Thursby SJ, Thakur A, Bertens C, Masala L, Loughery JEP, McArt DG, Walsh CP. Depletion of DNMT1 in differentiated human cells highlights key classes of sensitive genes and an interplay with polycomb repression. Epigenetics Chromatin. 2018; 11:12 [PMID: 29598829]
  50. Liu J, Banerjee A, Herring CA, Attalla J, Hu R, Xu Y, Shao Q, Simmons AJ, Dadi PK, Wang S, Jacobson DA, Liu B, Hodges E, Lau KS, Gu G. Neurog3-Independent Methylation Is the Earliest Detectable Mark Distinguishing Pancreatic Progenitor Identity. Dev Cell. 2019; 48:49-63.e7. [PMID: 30620902]
  51. Chappell C, Beard C, Altman J, Jaenisch R, Jacob J. DNA methylation by DNA methyltransferase 1 is critical for effector CD8 T cell expansion. J Immunol. 2006; 176:4562-72. [PMID: 16585546]
  52. Klintworth GK. Corneal dystrophies. Orphanet J Rare Dis. 2009; 4:7 [PMID: 19236704]
  53. Irvine AD, Corden LD, Swensson O, Swensson B, Moore JE, Frazer DG, Smith FJ, Knowlton RG, Christophers E, Rochels R, Uitto J, McLean WH. Mutations in cornea-specific keratin K3 or K12 genes cause Meesmann’s corneal dystrophy. Nat Genet. 1997; 16:184-7. [PMID: 9171831]
  54. Mizoguchi S, Suzuki K, Zhang J, Yamanaka O, Liu CY, Okada Y, Miyajima M, Kokado M, Kao WW, Yamada G, Saika S. Disruption of eyelid and cornea morphogenesis by epithelial β-catenin gain-of-function. Mol Vis. 2015; 21:793-803. [PMID: 26283861]
  55. Makrides N, Wang Q, Tao C, Schwartz S, Zhang X. Jack of all trades, master of each: the diversity of fibroblast growth factor signalling in eye development. Open Biol. 2022; 12210265 [PMID: 35016551]
  56. Freeman M. Reiterative use of the EGF receptor triggers differentiation of all cell types in the Drosophila eye. Cell. 1996; 87:651-60. [PMID: 8929534]
  57. Gordon HB, Lusk S, Carney KR, Wirick EO, Murray BF, Kwan KM. Hedgehog signaling regulates cell motility and optic fissure and stalk formation during vertebrate eye morphogenesis. Development. 2018; 145dev165068 [PMID: 30333214]
  58. da Mota JCNL, Ribeiro AA, Carvalho LM, Esteves GP, Sieczkowska SM, Goessler KF, Gualano B, Nicoletti CF. Impact of Methyl-Donor Micronutrient Supplementation on DNA Methylation Patterns: A Systematic Review and Meta-Analysis of in vitro, Animal, and Human Studies. Lifestyle Genom. 2023; 16:192-213. [PMID: 37935134]
  59. Keil KP, Lein PJ. DNA methylation: a mechanism linking environmental chemical exposures to risk of autism spectrum disorders? Environ Epigenet. 2016; 2dvv012 [PMID: 27158529]