DPPA3 facilitates genome-wide DNA demethylation in mouse primordial germ cells.

BACKGROUND: Genome-wide DNA demethylation occurs in mammalian primordial germ cells (PGCs) as part of the epigenetic reprogramming important for gametogenesis and resetting the epigenetic information for totipotency. Dppa3 (also known as Stella or Pgc7) is highly expressed in mouse PGCs and oocytes and encodes a factor essential for female fertility. It prevents excessive DNA methylation in oocytes and ensures proper gene expression in preimplantation embryos: however, its role in PGCs is largely unexplored. In the present study, we investigated whether or not DPPA3 has an impact on CG methylation/demethylation in mouse PGCs. RESULTS: We show that DPPA3 plays a role in genome-wide demethylation in PGCs even before sex differentiation. Dppa3 knockout female PGCs show aberrant hypermethylation, most predominantly at H3K9me3-marked retrotransposons, which persists up to the fully-grown oocyte stage. DPPA3 works downstream of PRDM14, a master regulator of epigenetic reprogramming in embryonic stem cells and PGCs, and independently of TET1, an enzyme that hydroxylates 5-methylcytosine. CONCLUSIONS: The results suggest that DPPA3 facilitates DNA demethylation through a replication-coupled passive mechanism in PGCs. Our study identifies DPPA3 as a novel epigenetic reprogramming factor in mouse PGCs.

The DNMT3A ADD domain is required for efficient de novo DNA methylation and maternal imprinting in mouse oocytes.

Establishment of a proper DNA methylation landscape in mammalian oocytes is important for maternal imprinting and embryonic development. De novo DNA methylation in oocytes is mediated by the DNA methyltransferase DNMT3A, which has an ATRX-DNMT3-DNMT3L (ADD) domain that interacts with histone H3 tail unmethylated at lysine-4 (H3K4me0). The domain normally blocks the methyltransferase domain via intramolecular interaction and binding to histone H3K4me0 releases the autoinhibition. However, H3K4me0 is widespread in chromatin and the role of the ADD-histone interaction has not been studied in vivo. We herein show that amino-acid substitutions in the ADD domain of mouse DNMT3A cause dwarfism. Oocytes derived from homozygous females show mosaic loss of CG methylation and almost complete loss of non-CG methylation. Embryos derived from such oocytes die in mid-to-late gestation, with stochastic and often all-or-none-type CG-methylation loss at imprinting control regions and misexpression of the linked genes. The stochastic loss is a two-step process, with loss occurring in cleavage-stage embryos and regaining occurring after implantation. These results highlight an important role for the ADD domain in efficient, and likely processive, de novo CG methylation and pose a model for stochastic inheritance of epigenetic perturbations in germ cells to the next generation.

Role of waveform signal parameters in the classification of children as relatively slow and fast myopia progressors.

CLINICAL RELEVANCE: Identification of the baseline chracteristics for children undergoing orthokeratology with relatively fast myopia progression can allow a more accurate determination of the risk/benefit ratio. BACKGROUND: This study aimed to investigate if baseline corneal biomechanics can classify relatively slow and fast myopia progression in children. METHODS: Children aged six to 12 years with low myopia (0.50 to 4.00 D) and astigmatism (less than or equal to 1.25 D), were recruited. Participants were randomised to be fitted with orthokeratology contact lenses with a conventional compression factor (0.75 D, n = 29) or an increased compression factor (1.75 D, n = 33). Relatively fast progressors were defined as participants who had axial elongation of 0.34 mm or above per 2 years. A binomial logistic regression analysis and a classification and regression tree model were used in the data analysis. The corneal biomechanics were measured with a bidirectional applanation device. The axial length was measured by a masked examiner. RESULTS: As there were no significant between-group differences in the baseline data (all p > 0.05), data were combined for analysis. The mean ± SD axial elongation for relatively slow (n = 27) and fast (n = 35) progressors were 0.18 ± 0.14 mm and 0.64 ± 0.23 mm per 2 years, respectively. The area under the curve (p2area1) was significantly higher in relatively fast progressors (p = 0.018). The binomial logistic regression and classification and regression tree model analysis showed that baseline age and p2area1 could differentiate between slow and fast progressors over 2 years. CONCLUSIONS: Corneal biomechanics could be a potential predictor of axial elongation in orthokeratology contact lens-wearing children.

Novel compound heterozygous mutations in UHRF1 are associated with atypical immunodeficiency, centromeric instability and facial anomalies syndrome with distinctive genome-wide DNA hypomethylation.

Immunodeficiency, centromeric instability and facial anomalies (ICF) syndrome is in most cases caused by mutations in either DNA methyltransferase (DNMT)3B, zinc finger and BTB domain containing 24, cell division cycle associated 7 or helicase lymphoid-specific. However, the causative genes of a few ICF patients remain unknown. We, herein, identified ubiquitin-like with plant homeodomain and really interesting new gene finger domains 1 (UHRF1) as a novel causative gene of one such patient with atypical symptoms. This patient is a compound heterozygote for two previously unreported mutations in UHRF1: c.886C > T (p.R296W) and c.1852C > T (p.R618X). The R618X mutation plausibly caused nonsense-mediated decay, while the R296W mutation changed the higher order structure of UHRF1, which is indispensable for the maintenance of CG methylation along with DNMT1. Genome-wide methylation analysis revealed that the patient had a centromeric/pericentromeric hypomethylation, which is the main ICF signature, but also had a distinctive hypomethylation pattern compared to patients with the other ICF syndrome subtypes. Structural and biochemical analyses revealed that the R296W mutation disrupted the protein conformation and strengthened the binding affinity of UHRF1 with its partner LIG1 and reduced ubiquitylation activity of UHRF1 towards its ubiquitylation substrates, histone H3 and proliferating cell nuclear antigen -associated factor 15 (PAF15). We confirmed that the R296W mutation causes hypomethylation at pericentromeric repeats by generating the HEK293 cell lines that mimic the patient's UHRF1 molecular context. Since proper interactions of the UHRF1 with LIG1, PAF15 and histone H3 are essential for the maintenance of CG methylation, the mutation could disturb the maintenance process. Evidence for the importance of the UHRF1 conformation for CG methylation in humans is, herein, provided for the first time and deepens our understanding of its role in regulation of CG methylation.

Orthokeratology lenses with increased compression factor (OKIC): A 2-year longitudinal clinical trial for myopia control.

PURPOSE: To investigate the effectiveness of orthokeratology (ortho-k) lenses and corneal changes with increased compression factor for myopia control over a 2-year period. METHODS: Young participants (age: 6-<12 years), with low myopia (0.50-4.00 D) and low astigmatism (≤1.25 D), were recruited and allowed to choose to wear either single-vision spectacles or ortho-k lenses (randomly assigned to compression factor of either 0.75 or 1.75 D). Axial length and cycloplegic refraction were measured at six monthly intervals for two years by a masked examiner. The myopia control effectiveness was determined by axial elongation. RESULTS: A significant number of control (63 %) dropped out, mainly due to concern about myopia progression (58 %). A total of 75 participants (mean age: 9.3 ± 1.0 years; control: n = 11, ortho-k [0.75 D]: n = 29, ortho-k [1.75 D]: n = 35) completed the study. Considering ortho-k groups only, the mean axial elongation of participants wearing ortho-k lenses of conventional compression factor (0.75 D) and increased compression factor (1.75 D) were 0.53 ± 0.29 and 0.35 ± 0.29 mm, respectively, over the 2-year study period. The between-group differences in corneal health were not significant at all visits. CONCLUSION: Participants wearing ortho-k lenses of increased compression factor further slowed axial elongation by 34%, when compared with the conventional compression factor without compromising corneal health. Further investigations are warranted to confirm the potential mechanism of an increased compression factor for improved myopia control effectiveness.

CMIC: predicting DNA methylation inheritance of CpG islands with embedding vectors of variable-length k-mers.

BACKGROUND: Epigenetic modifications established in mammalian gametes are largely reprogrammed during early development, however, are partly inherited by the embryo to support its development. In this study, we examine CpG island (CGI) sequences to predict whether a mouse blastocyst CGI inherits oocyte-derived DNA methylation from the maternal genome. Recurrent neural networks (RNNs), including that based on gated recurrent units (GRUs), have recently been employed for variable-length inputs in classification and regression analyses. One advantage of this strategy is the ability of RNNs to automatically learn latent features embedded in inputs by learning their model parameters. However, the available CGI dataset applied for the prediction of oocyte-derived DNA methylation inheritance are not large enough to train the neural networks. RESULTS: We propose a GRU-based model called CMIC (CGI Methylation Inheritance Classifier) to augment CGI sequence by converting it into variable-length k-mers, where the length k is randomly selected from the range [Formula: see text] to [Formula: see text], N times, which were then used as neural network input. N was set to 1000 in the default setting. In addition, we proposed a new embedding vector generator for k-mers called splitDNA2vec. The randomness of this procedure was higher than the previous work, dna2vec. CONCLUSIONS: We found that CMIC can predict the inheritance of oocyte-derived DNA methylation at CGIs in the maternal genome of blastocysts with a high F-measure (0.93). We also show that the F-measure can be improved by increasing the parameter N, that is, the number of sequences of variable-length k-mers derived from a single CGI sequence. This implies the effectiveness of augmenting input data by converting a DNA sequence to N sequences of variable-length k-mers. This approach can be applied to different DNA sequence classification and regression analyses, particularly those involving a small amount of data.

Low Input Genome-Wide DNA Methylation Analysis with Minimal Library Amplification.

Whole genome bisulfite sequencing (WGBS) is a high-throughput DNA sequencing-based technique that is used to determine genome-wide DNA methylation patterns at base resolution. Library construction by post-bisulfite adaptor tagging (PBAT ) extends the application of WGBS to several hundred cells and minimizes the required number of library amplification cycles. We herein describe a PBAT protocol to prepare WGBS libraries from 200 cells and introduce the outline of a downstream bioinformatic analysis. The prepared library can typically generate 800 million sequencing reads, which is sufficient to cover the human and mouse genomes approximately 15 times, using the Illumina NovaSeq 6000 sequencing system.

International multi-centre study of potential benefits of ultraviolet radiation protection using contact lenses.

PURPOSE: To examine the effects of long-term ultraviolet radiation (UVR) blocking wearing contact lenses on ocular surface health, eye focus and macular pigment. METHOD: 210 pre-presbyopic patients were recruited from Birmingham UK, Brisbane Australia, Hong Kong China, Houston USA and Waterloo Canada (n = 42 at each site). All patients had worn contact lenses for ≥ 5 years, half (test group) of a material incorporating a UVR-blocking filter. Ocular health was assessed using slit-lamp biomicroscopy and UV autofluorescence. Accommodation was measured subjectively with a push-up test and overcoming lens-induced defocus. Objective stimulus response and dynamic measures of the accommodative response were quantified with an open-field aberrometer. Macular pigment optical density (MPOD) was assessed using heterochromatic flicker photometry (MPS II). RESULTS: The two groups of participants were matched for age, sex, race, body-mass-index, diet, lifestyle, UVR exposure, refractive error and visual acuity. Limbal (p = 0.035), but not bulbar conjunctival redness (p = 0.903) was lower in eyes that had worn UVR-blocking contact lenses compared to controls. The subjective (8.0 ± 3.7D vs 7.3 ± 3.3D; p = 0.125) and objective (F = 1.255, p = 0.285) accommodative response was higher in the test group, but the differences did not reach significance. However, the accommodative latency was shorter in eyes that had worn UVR-blocking contact lenses (p = 0.003). There was no significant different in MPOD with UVR filtration (p = 0.869). CONCLUSIONS: Blocking the transmission of UVR is beneficial in maintaining the eye's ability to focus, suggesting that presbyopia maybe delayed in long-term UVR-blocking contact lenses wearers. These lenses also provide protection to the critical limbal region.

Production of functional oocytes requires maternally expressed PIWI genes and piRNAs in golden hamsters.

Many animals have a conserved adaptive genome defence system known as the Piwi-interacting RNA (piRNA) pathway, which is essential for germ cell development and function. Disruption of individual mouse Piwi genes results in male but not female sterility, leading to the assumption that PIWI genes play little or no role in mammalian oocytes. Here, we report the generation of PIWI-defective golden hamsters, which have defects in the production of functional oocytes. The mechanisms involved vary among the hamster PIWI genes, whereby the lack of PIWIL1 has a major impact on gene expression, including hamster-specific young transposon de-silencing, whereas PIWIL3 deficiency has little impact on gene expression in oocytes, although DNA methylation was reduced to some extent in PIWIL3-deficient oocytes. Our findings serve as the foundation for developing useful models to study the piRNA pathway in mammalian oocytes, including humans.

A convolutional neural network-based regression model to infer the epigenetic crosstalk responsible for CG methylation patterns.

BACKGROUND: Epigenetic modifications, including CG methylation (a major form of DNA methylation) and histone modifications, interact with each other to shape their genomic distribution patterns. However, the entire picture of the epigenetic crosstalk regulating the CG methylation pattern is unknown especially in cells that are available only in a limited number, such as mammalian oocytes. Most machine learning approaches developed so far aim at finding DNA sequences responsible for the CG methylation patterns and were not tailored for studying the epigenetic crosstalk. RESULTS: We built a machine learning model named epiNet to predict CG methylation patterns based on other epigenetic features, such as histone modifications, but not DNA sequence. Using epiNet, we identified biologically relevant epigenetic crosstalk between histone H3K36me3, H3K4me3, and CG methylation in mouse oocytes. This model also predicted the altered CG methylation pattern of mutant oocytes having perturbed histone modification, was applicable to cross-species prediction of the CG methylation pattern of human oocytes, and identified the epigenetic crosstalk potentially important in other cell types. CONCLUSIONS: Our findings provide insight into the epigenetic crosstalk regulating the CG methylation pattern in mammalian oocytes and other cells. The use of epiNet should help to design or complement biological experiments in epigenetics studies.

Corneal thickness changes in myopic children during and after short-term orthokeratology lens wear.

PURPOSE: To evaluate thickness changes in the central and mid-peripheral cornea (CCT and mPCT), corneal epithelium (CET and mPET) and stroma (CST and mPST) of myopic children during and after short-term orthokeratology (ortho-k) lens wear, with conventional (CCF, 0.75 D) and increased compression factors (ICF, 1.75 D). METHODS: This was a self-controlled case series study. Subjects wore a CCF lens in one eye and an ICF lens in the other. Anterior segment optical coherence tomography images were captured weekly for 1 month during lens wear and for 2 weeks after discontinuing lens wear. CCT and CET (central 3-mm cornea) and mPCT and mPET (within a 4-6 mm diameter annulus) were measured. Stromal thickness (ST) was determined by subtracting epithelium thickness (ET) from corneal thickness (CT). The repeatability of the analytical software was also investigated on age-matched spectacle-wearing subjects (n = 98). RESULTS: Excluding three outliers (>3 S.D.s), the coefficient of repeatability and intraclass correlation coefficients of 98 spectacle-wearing subjects ranged from 2.63 to 4.64 µm and from 0.90 to 0.99, respectively. For the weekly-change study, CCT and CET in both eyes were significantly thinner after lens wear (p < 0.001) and CET thinning in the ICF eyes were significantly higher (p < 0.02). CCT changes were mainly contributed by CET. CST, mPCT, mPET and mPST changes were not significant (p > 0.20) in either eye. CT (all sublayers) rebounded to baseline values 2 weeks after discontinuing lens wear (0.99 > p > 0.12). CONCLUSIONS: Significant reductions in CT and ET, but not ST, were observed within 1 month of ortho-k lens wear. Wearing ICF lenses resulted in a higher reduction in CET. Corneal thickness changes were reversible after discontinuing lens wear.

Repeatability of corneal biomechanics waveform signal parameters derived from Ocular Response Analyzer in children.

PURPOSE: To investigate the repeatability of waveform signal parameters, measured with the Ocular Response Analyzer (ORA), in children. METHODS: Two sets of ORA measurements, with a 10-min break between them, were performed on children, aged six to <11 years old, either wearing single-vision spectacles (SVS) or orthokeratology (ortho-k) lenses. Intraclass correlation coefficients (ICCs) were used to assess agreements between two sets of measurements (37 waveform signal parameters). Bland-Altman (BA) plots were used to further analyse waveform signal parameters which had ICC 95 % confidence interval (95 % CI) between 0.50 to >0.90 (regarded as moderate to excellent agreement). RESULTS: A total of 30 participants [15 SVS, 15 ortho-k (3.6 ± 2.4 months)] completed the study. Since no significant between-group differences were detected in demographic data (p > 0.28) and all waveform signal parameters (p > 0.05), data from the two groups of participants were pooled for the analysis of repeatability. Six parameters, h2, h21, p1area, p1area1, p2area, and p2area1, achieved ICCs (95 % CI) of 0.82-0.85 (0.61-0.93). The mean (SD) of these six parameters were 372 (91), 248 (61), 4077 (854), 1762 (399), 2359 (670), and 1020 (300), respectively. Bland-Altman plots and 95 % limits of agreement (95 % LoA) showed considerable agreement for all six parameters, the mean difference (95 % LoA) were -3 (-101 to 94), -2 (-67.56-62.70), 111 (-723 to 946), 102 (-334 to 539), 25 (-718 to 768), and -3 (-350 to 343), respectively. CONCLUSIONS: Six waveform signal parameters (h2, h21, p1area, p1area1, p2area, and p2area1), which represent or are related to the areas under the waveform at the peaks in the signal, had moderate to excellent agreement in children. Results of the current study provides fundamental information for further studies on the potential clinical application of these waveform signal parameters in children.

Infection control challenges in setting up community isolation and treatment facilities for patients with coronavirus disease 2019 (COVID-19): Implementation of directly observed environmental disinfection.

BACKGROUND: Extensive environmental contamination by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been reported in hospitals during the coronavirus disease 2019 (COVID-19) pandemic. We report our experience with the practice of directly observed environmental disinfection (DOED) in a community isolation facility (CIF) and a community treatment facility (CTF) in Hong Kong. METHODS: The CIF, with 250 single-room bungalows in a holiday camp, opened on July 24, 2020, to receive step-down patients from hospitals. The CTF, with 500 beds in open cubicles inside a convention hall, was activated on August 1, 2020, to admit newly diagnosed COVID-19 patients from the community. Healthcare workers (HCWs) and cleaning staff received infection control training to reinforce donning and doffing of personal protective equipment and to understand the practice of DOED, in which the cleaning staff observed patient and staff activities and then performed environmental disinfection immediately thereafter. Supervisors also observed cleaning staff to ensure the quality of work. In the CTF, air and environmental samples were collected on days 7, 14, 21, and 28 for SARS-CoV-2 detection by RT-PCR. Patient compliance with mask wearing was also recorded. RESULTS: Of 291 HCWs and 54 cleaning staff who managed 243 patients in the CIF and 674 patients in the CTF from July 24 to August 29, 2020, no one acquired COVID-19. All 24 air samples and 520 environmental samples collected in the patient area of the CTF were negative for SARS-CoV-2. Patient compliance with mask wearing was 100%. CONCLUSION: With appropriate infection control measures, zero environmental contamination and nosocomial transmission of SARS-CoV-2 to HCWs and cleaning staff was achieved.

Reprogramming of the histone H3.3 landscape in the early mouse embryo.

Epigenetic reprogramming of the zygote involves dynamic incorporation of histone variant H3.3. However, the genome-wide distribution and dynamics of H3.3 during early development remain unknown. Here, we delineate the H3.3 landscapes in mouse oocytes and early embryos. We unexpectedly identify a non-canonical H3.3 pattern in mature oocytes and zygotes, in which local enrichment of H3.3 at active chromatin is suppressed and H3.3 is relatively evenly distributed across the genome. Interestingly, although the non-canonical H3.3 pattern forms gradually during oogenesis, it quickly switches to a canonical pattern at the two-cell stage in a transcription-independent and replication-dependent manner. We find that incorporation of H3.1/H3.2 mediated by chromatin assembly factor CAF-1 is a key process for the de novo establishment of the canonical pattern. Our data suggest that the presence of the non-canonical pattern and its timely transition toward a canonical pattern support the developmental program of early embryos.

A Rice Immunophilin Homolog, OsFKBP12, Is a Negative Regulator of Both Biotic and Abiotic Stress Responses.

A class of proteins that were discovered to bind the immunosuppressant drug FK506, called FK506-binding proteins (FKBPs), are members of a sub-family of immunophilins. Although they were first identified in human, FKBPs exist in all three domains of life. In this report, a rice FKBP12 homolog was first identified as a biotic stress-related gene through suppression subtractive hybridization screening. By ectopically expressing OsFKBP12 in the heterologous model plant system, Arabidopsis thaliana, for functional characterization, OsFKBP12 was found to increase susceptibility of the plant to the pathogen, Pseudomonas syringae pv. tomato DC3000 (Pst DC3000). This negative regulatory role of FKBP12 in biotic stress responses was also demonstrated in the AtFKBP12-knockout mutant, which exhibited higher resistance towards Pst DC3000. Furthermore, this higher-plant FKBP12 homolog was also shown to be a negative regulator of salt tolerance. Using yeast two-hybrid tests, an ancient unconventional G-protein, OsYchF1, was identified as an interacting partner of OsFKBP12. OsYchF1 was previously reported as a negative regulator of both biotic and abiotic stresses. Therefore, OsFKBP12 probably also plays negative regulatory roles at the convergence of biotic and abiotic stress response pathways in higher plants.

Maternal DNMT3A-dependent de novo methylation of the paternal genome inhibits gene expression in the early embryo.

De novo DNA methylation (DNAme) during mammalian spermatogenesis yields a densely methylated genome, with the exception of CpG islands (CGIs), which are hypomethylated in sperm. While the paternal genome undergoes widespread DNAme loss before the first S-phase following fertilization, recent mass spectrometry analysis revealed that the zygotic paternal genome is paradoxically also subject to a low level of de novo DNAme. However, the loci involved, and impact on transcription were not addressed. Here, we employ allele-specific analysis of whole-genome bisulphite sequencing data and show that a number of genomic regions, including several dozen CGI promoters, are de novo methylated on the paternal genome by the 2-cell stage. A subset of these promoters maintains DNAme through development to the blastocyst stage. Consistent with paternal DNAme acquisition, many of these loci are hypermethylated in androgenetic blastocysts but hypomethylated in parthenogenetic blastocysts. Paternal DNAme acquisition is lost following maternal deletion of Dnmt3a, with a subset of promoters, which are normally transcribed from the paternal allele in blastocysts, being prematurely transcribed at the 4-cell stage in maternal Dnmt3a knockout embryos. These observations uncover a role for maternal DNMT3A activity in post-fertilization epigenetic reprogramming and transcriptional silencing of the paternal genome.

Fighting COVID-19 in Hong Kong: The effects of community and social mobilization.

The globalized world economy has been affected by the COVID-19 pandemic since early February 2020. In the midst of this global public health crisis, a prompt review of the counterinsurgencies that have occurred in different jurisdictions is helpful. This article examines the experience of Hong Kong (HKSAR), which successfully limited its number of confirmed cases to approximately 1100 until early June 2020. Considering the limited actions that the government has taken against the pandemic, we emphasize the prominent role of Hong Kong's civil society through highlighting the strong and spontaneous mobilization of its local communities originating from their experiences during the SARS outbreak in 2003 and the social unrest in 2019, as well as their doubts regarding the pandemic assessments and recommendations of the HKSAR and WHO authorities. This article suggests that the influence of civil society should not be overlooked in the context of pandemic management.

Orthokeratology with increased compression factor (OKIC): study design and preliminary results.

OBJECTIVE: To present the study design and the baseline data of a prospective cohort study investigating the safety, refractive correction and effectiveness of myopia control in subjects fitted with orthokeratology (ortho-k) lenses of different compression factors. METHODS AND ANALYSIS: This study is a 2-year longitudinal, double-masked, partially randomised study. Myopic children aged between 6 and 10 years are recruited and they may choose to participate in either the ortho-k or spectacle-wearing group. Subjects in the ortho-k group are randomly assigned to wear ortho-k lenses of either conventional compression factor (CCF, 0.75 D) or increased compression factor (ICF, 1.75 D). For the ortho-k subjects, the time and between-group effects within the first month of lens wear were analysed. RESULTS: Sixty-nine ortho-k subjects (CCF: 34; ICF: 35) and 30 control subjects were recruited. There were no significant differences in baseline demographic data among the three groups of subjects (p>0.19). At the 1-month visit, the first fit success rates were 97% and 100% in the CCF and ICF ortho-k group, respectively. A higher percentage of ICF subjects could achieve full correction (CCF: 88.2%; ICF: 94.3%). The change in axial length was significantly higher in the ICF group (CCF, 0.003 mm; ICF, -0.031 mm) (p<0.05). No significant between-group differences in daytime vision or in the coverage and depth of corneal staining between the two ortho-k groups (p>0.05) were observed at any visit. CONCLUSION: ICF did not compromise the corneal integrity and the lens centration within the first month of lens wear. The preliminary performance of ortho-k lenses with ICF of 1.00D shows that it was safe to be used in the longer term for the investigation of myopia control. TRIAL REGISTRATION NUMBER: NCT02643342.

Polycomb Group Proteins Regulate Chromatin Architecture in Mouse Oocytes and Early Embryos.

In mammals, chromatin organization undergoes drastic reorganization during oocyte development. However, the dynamics of three-dimensional chromatin structure in this process is poorly characterized. Using low-input Hi-C (genome-wide chromatin conformation capture), we found that a unique chromatin organization gradually appears during mouse oocyte growth. Oocytes at late stages show self-interacting, cohesin-independent compartmental domains marked by H3K27me3, therefore termed Polycomb-associating domains (PADs). PADs and inter-PAD (iPAD) regions form compartment-like structures with strong inter-domain interactions among nearby PADs. PADs disassemble upon meiotic resumption from diplotene arrest but briefly reappear on the maternal genome after fertilization. Upon maternal depletion of Eed, PADs are largely intact in oocytes, but their reestablishment after fertilization is compromised. By contrast, depletion of Polycomb repressive complex 1 (PRC1) proteins attenuates PADs in oocytes, which is associated with substantial gene de-repression in PADs. These data reveal a critical role of Polycomb in regulating chromatin architecture during mammalian oocyte growth and early development.

Characterization of genetic-origin-dependent monoallelic expression in mouse embryonic stem cells.

Monoallelic gene expression occurs in various mammalian cells and can be regulated genetically, epigenetically and/or stochastically. We identified 145 monoallelically expressed genes (MoEGs), including seven known imprinted genes, in mouse embryonic stem cells (ESCs) derived from reciprocal F1 hybrid blastocysts and cultured in 2i/LIF. As all MoEGs except for the imprinted genes were expressed in a genetic-origin-dependent manner, we focused on this class of MoEGs for mechanistic studies. We showed that a majority of the genetic-origin-dependent MoEGs identified in 2i/LIF ESCs remain monoallelically expressed in serum/LIF ESCs, but become more relaxed or even biallelically expressed upon differentiation. These MoEGs and their regulatory regions were highly enriched for single nucleotide polymorphisms. In addition, some MoEGs were associated with retrotransposon insertions/deletions, consistent with the fact that certain retrotransposons act as regulatory elements in pluripotent stem cells. Interestingly, most MoEGs showed allelic differences in enrichment of histone H3K27me and H3K4me marks, linking allelic epigenetic differences and monoallelic expression. In contrast, there was little or no allelic difference in CpG methylation or H3K9me. Taken together, our study highlights the impact of genetic variation including single nucleotide polymorphisms and retrotransposon insertions/deletions on monoallelic epigenetic marks and expression in ESCs.