Epigenetic Information Research Articles

Epigenetic variations are more substantial than genetic variations in rapid adaptation of oyster to Pacific oyster mortality syndrome.

Disease emergence is accelerating with global changes. Understanding by which mechanisms host populations can rapidly adapt will be crucial for management practices. Pacific oyster mortality syndrome (POMS) imposes a substantial and recurrent selective pressure on oyster populations, and rapid adaptation may arise through genetics and epigenetics. In this study, we used (epi)genome-wide association mapping to show that oysters differentially exposed to POMS displayed genetic and epigenetic signatures of selection. Consistent with higher resistance to POMS, the genes targeted included many genes in several pathways related to immunity. By combining correlation, DNA methylation quantitative trait loci, and variance partitioning, we revealed that a third of phenotypic variation was explained by interactions between the genetic and epigenetic information, ~14% by the genome, and up to 25% by the epigenome alone. Similar to genetically based adaptation, epigenetic mechanisms notably governing immune responses can contribute substantially to the rapid adaptation of hosts to emerging infectious diseases.

Global histone H2B degradation regulates insulin/IGF signaling-mediated nutrient stress.

Eukaryotic organisms adapt to environmental fluctuations by altering their epigenomic landscapes and transcriptional programs. Nucleosomal histones carry vital epigenetic information and regulate gene expression, yet the mechanisms underlying chromatin-bound histone exchange remain elusive. Here, we found that histone H2Bs are globally degraded in Caenorhabditis elegans during starvation. Our genetic screens identified mutations in ubiquitin and ubiquitin-related enzymes that block H2B degradation in starved animals, identifying lysine 31 as the crucial residue for chromatin-bound H2B ubiquitination and elimination. Retention of aberrant nucleosomal H2B increased the association of the FOXO transcription factor DAF-16 with chromatin, generating an ectopic gene expression profile detrimental to animal viability when insulin/IGF signaling was reduced in well-fed animals. Furthermore, we show that the ubiquitin-proteasome system regulates chromosomal histone turnover in human cells. During larval development, C. elegans epidermal cells undergo H2B turnover after fusing with the epithelial syncytium. Thus, histone degradation may be a widespread mechanism governing dynamic changes of the epigenome.

Curated single cell multimodal landmark datasets for R/Bioconductor.

The majority of high-throughput single-cell molecular profiling methods quantify RNA expression; however, recent multimodal profiling methods add simultaneous measurement of genomic, proteomic, epigenetic, and/or spatial information on the same cells. The development of new statistical and computational methods in Bioconductor for such data will be facilitated by easy availability of landmark datasets using standard data classes. We collected, processed, and packaged publicly available landmark datasets from important single-cell multimodal protocols, including CITE-Seq, ECCITE-Seq, SCoPE2, scNMT, 10X Multiome, seqFISH, and G&T. We integrate data modalities via the MultiAssayExperiment Bioconductor class, document and re-distribute datasets as the SingleCellMultiModal package in Bioconductor's Cloud-based ExperimentHub. The result is single-command actualization of landmark datasets from seven single-cell multimodal data generation technologies, without need for further data processing or wrangling in order to analyze and develop methods within Bioconductor's ecosystem of hundreds of packages for single-cell and multimodal data. We provide two examples of integrative analyses that are greatly simplified by SingleCellMultiModal. The package will facilitate development of bioinformatic and statistical methods in Bioconductor to meet the challenges of integrating molecular layers and analyzing phenotypic outputs including cell differentiation, activity, and disease.

Abstract A027: DNA methylation-based fetal niche and repetitive element profiling predict overall survival in clear cell renal cell carcinoma

Abstract Background: Fetal cell origin DNA methylation signature (FCO) estimates the proportion of cells in a mixture of cell types that are of fetal origin. Machine learning-based methods can predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. In this study, we applied the FCO signature and RE methylation prediction to clear cell renal cell carcinoma (ccRCC) samples to study FCO and RE alterations in ccRCC carcinogenesis and survival. Methods: The FCO algorithm was applied to 47 ccRCC tumor samples and four adjacent normal samples from the Dartmouth Renal Tumor Biobank. 319 ccRCC tumor samples and 160 adjacent normal samples from The Cancer Genome Atlas (TCGA) were used for external validation. Linear regression models were used to compare the FCO signal between ccRCC tumor and normal samples adjusting for sex and age. Cox proportional hazard models were employed to study FCO with overall survival outcome in ccRCC samples, adjusting for sex, age, and tumor stage. The survival groups were dichotomized to FCO = 0% vs. FCO > 0%. The REMP package from Bioconductor was used to project LINE1 element methylation in 47 ccRCC samples. LINE1 median level methylation was compared by tumor grade. Cox proportional hazard models were employed to study LINE1 methylation level as a continuous variable with overall survival in ccRCC samples, adjusting for sex, age, and tumor stage. Results: The FCO signal is significantly lower in Dartmouth Renal Tumor Biobank archived ccRCC tumor samples compared to adjacent normal samples (Δ = 42.9%, p = 5.7e-11). By comparing the overall survival between FCO = 0% and FCO > 0% groups, we observed significantly worse survival outcomes in ccRCC patients with zero levels of FCO (HR: 2.46, 95% CI: 1.16, 5.18). Similar results were observed in TCGA samples. A significant decrease of FCO was found in ccRCC tumor samples compared to adjacent normal samples (Δ = 32.9%, p = 2.2e-308). A 1% increase in FCO is significantly associated with a better survival outcome (HR: 0.97, 95%CI 0.95, 0.99). For RE methylation prediction, we observed that the median LINE1 methylation level decreases with ccRCC tumor grade. A higher level of LINE1 median methylation is significantly associated with a better survival outcome (p = 0.01). Conclusion: Normal kidney samples possess a fetal niche reflected by DNA methylation, while ccRCC tumorigenesis depletes the fetal cells in normal kidneys. The depletion of FCO is associated with worse survival outcomes in ccRCC. The repetitive element LINE1 methylation level decreases with tumor grade and is related to ccRCC survival outcomes. These findings promise future investigations on the epigenetically targetable fetal niche and repetitive elements in ccRCC carcinogenesis and therapeutics. Citation Format: Ze Zhang, Lucas Salas. DNA methylation-based fetal niche and repetitive element profiling predict overall survival in clear cell renal cell carcinoma [abstract]. In: Proceedings of the AACR Special Conference: Advances in Kidney Cancer Research; 2023 Jun 24-27; Austin, Texas. Philadelphia (PA): AACR; Cancer Res 2023;83(16 Suppl):Abstract nr A027.

Advances in biological functions and mechanisms of histone variants in plants.

Nucleosome is the basic subunit of chromatin, consisting of approximately 147bp DNA wrapped around a histone octamer, containing two copies of H2A, H2B, H3 and H4. A linker histone H1 can bind nucleosomes through its conserved GH1 domain, which may promote chromatin folding into higher-order structures. Therefore, the complexity of histones act importantly for specifying chromatin and gene activities. Histone variants, encoded by separate genes and characterized by only a few amino acids differences, can affect nucleosome packaging and stability, and then modify the chromatin properties. Serving as carriers of pivotal genetic and epigenetic information, histone variants have profound significance in regulating plant growth and development, response to both biotic and abiotic stresses. At present, the biological functions of histone variants in plant have become a research hotspot. Here, we summarize recent researches on the biological functions, molecular chaperons and regulatory mechanisms of histone variants in plant, and propose some novel research directions for further study of plant histone variants research field. Our study will provide some enlightens for studying and understanding the epigenetic regulation and chromatin specialization mediated by histone variant in plant.

Epidemiological and clinical profile of amyotrophic lateral sclerosis in Ethiopia: a 5-year multicenter retrospective study

Background Amyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease that results in progressive weakness of skeletal muscles including respiratory muscles. Epidemiological and clinical aspects of ALS are derived from a few world regions with very little representation of low- and middle-income countries. We therefore set out to determine the epidemiological and clinical phenotype of individuals with ALS in Ethiopia. Methods Multicenter retrospective analysis was conducted using clinical records from ALS patients seen in Ethiopia at Tikur Anbessa Specialized Hospital and Yehuleshet specialty clinic between January 2016 and August 2021. The data collected included clinical characteristics, disease-related symptoms, a revised ALS functional rating scale, and medications. Results Patients in Ethiopia had a younger age of onset with a mean age of disease onset of 51.9 years. 2.9% of patients had juvenile ALS, and the male-to-female ratio was almost 2:1. 4.9% had a positive family history of the disease. 68% of patients had spinal region involvement at onset, while 32% had bulbar region involvement at onset. Riluzole was used by 31% of ALS patients. 20.6% of patients had some respiratory symptoms, but none received a standard respiratory function assessment. 33.3% of patients were wheelchair-bound. Conclusion In this retrospective study spanning 5 years, we examined the clinical phenotype of ALS in Ethiopian patients. Our findings suggest that most patients had clinically definite ALS with spinal region involvement. Further research, including genetic and epigenetic information, is necessary to understand the early onset of the disease in Ethiopia.

Phosphoproteomics Reveal New Candidates in Abnormal Spermatogenesis of Pseudomales in Cynoglossus semilaevis.

Phosphorylation is a post-translational modification that contributes to versatile protein functions in spermatogenesis, and the variations they generate usually results in abnormal spermatogenesis or sperm dysfunction. The sex-reversal phenomenon exists in Chinese tongue sole under certain conditions such that individuals with a ZW genotype can acquire a male phenotype and are thus called pseudomales. Pseudomale tongue sole can reach sexual maturity but produce only Z-type sperm, and the Z sperm carries paternal epigenetic information. Whether phosphorylation plays a role in the sperm abnormality of pseudomales is unknown. In this study, a phosphoproteomic analysis was performed to compare protein phosphorylation profiles between pseudomale and male testes. Altogether, we identified 14,253 phosphopeptides matching with 4843 proteins, with 1329 differentially phosphorylated peptides corresponding to 1045 differentially phosphorylated proteins (DPPs). Phosphorylation at 781 sites was upregulated and at 548 sites was downregulated. Four motifs were identified among differentially phosphorylated peptides, which were "SP", "SD", "RxxS", and "TP". Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses suggested that the cell cycle and DNA/RNA processing were significantly enriched with the genes encoding DPPs. To analyze DPP function in depth, a protein-protein interaction network was constructed, and Ran-binding protein 2 was found to play a central role in spermatogenesis by regulating several processes such as the cell cycle, eukaryotic translation, ubiquitination, and minichromosome maintenance. In kinase-associated network analyses, two "mitogen-activated protein kinase (Mapk)-centered" clusters were identified that may account for abnormal spermatogenesis in pseudomales. One cluster was centered on Mapk6, which predominantly regulated the cell cycle by interacting with several cyclin-dependent kinases, and the other was centered on the "testis-expressed kinase 1-like (Tesk1l)/Pim1l-Mapk4l- testis-expressed 14 (Tex14)" kinase cascade, which might contribute to spermatogenesis by regulating β-catenin. Taken together, these data suggested the new candidates involved in pseudomale sperm abnormalities and provided clues to discover the phosphorylated regulatory mechanism underlying tongue sole spermatogenesis.

Chemically induced reprogramming to reverse cellular aging.

A hallmark of eukaryotic aging is a loss of epigenetic information, a process that can be reversed. We have previously shown that the ectopic induction of the Yamanaka factors OCT4, SOX2, and KLF4 (OSK) in mammals can restore youthful DNA methylation patterns, transcript profiles, and tissue function, without erasing cellular identity, a process that requires active DNA demethylation. To screen for molecules that reverse cellular aging and rejuvenate human cells without altering the genome, we developed high-throughput cell-based assays that distinguish young from old and senescent cells, including transcription-based aging clocks and a real-time nucleocytoplasmic compartmentalization (NCC) assay. We identify six chemical cocktails, which, in less than a week and without compromising cellular identity, restore a youthful genome-wide transcript profile and reverse transcriptomic age. Thus, rejuvenation by age reversal can be achieved, not only by genetic, but also chemical means.

Histone H1 facilitates restoration of H3K27me3 during DNA replication by chromatin compaction

During cell renewal, epigenetic information needs to be precisely restored to maintain cell identity and genome integrity following DNA replication. The histone mark H3K27me3 is essential for the formation of facultative heterochromatin and the repression of developmental genes in embryonic stem cells. However, how the restoration of H3K27me3 is precisely achieved following DNA replication is still poorly understood. Here we employ ChOR-seq (Chromatin Occupancy after Replication) to monitor the dynamic re-establishment of H3K27me3 on nascent DNA during DNA replication. We find that the restoration rate of H3K27me3 is highly correlated with dense chromatin states. In addition, we reveal that the linker histone H1 facilitates the rapid post-replication restoration of H3K27me3 on repressed genes and the restoration rate of H3K27me3 on nascent DNA is greatly compromised after partial depletion of H1. Finally, our in vitro biochemical experiments demonstrate that H1 facilitates the propagation of H3K27me3 by PRC2 through compacting chromatin. Collectively, our results indicate that H1-mediated chromatin compaction facilitates the propagation and restoration of H3K27me3 after DNA replication.

Frontiers in aging special issue: DNA repair and interventions in aging perspective on "loss of epigenetic information as a cause of mammalian aging".

The recently published article in Cell by the Sinclair lab and collaborators entitled "Loss of Epigenetic Information as a Cause of Mammalian Aging" [1] implicates heritable changes in gene expression as the basis for aging, a postulate consistent with the emerging information theory of aging. Sinclair's group and colleagues induced epigenetic changes, i.e., DNA and histone modifications, via double-strand breaks (DSBs) catalyzed by the I-Pol endonuclease at specific genomic loci. The genomic DNA breaks, introduced without inducing insertion or deletion mutations (indels) in a mouse model, were targeted to 19 non-coding regions and one region in ribosomal DNA (rDNA), the latter shown to not have a significant effect on the function or transcription of rDNA [1]. With that experimental model in place, the authors present experimental evidence supporting a model that epigenetic changes drive aging via this inducible DNA break mechanism. After demonstrating the phenotypic alterations of this accelerated aging, they attempt to reverse selective phenotypes by resetting the altered epigenetic landscape. Establishing a causal relationship between epigenetic changes and aging, and how this connection might be manipulated to overturn cellular features of aging, is provocative and merits further study.

Exploring the phenomenon of quantum teleportation of epigenetic information in plants: Implications for the transfer of genome-stored experiences to close relatives

Quantum teleportation is a fascinating phenomenon that has garnered significant attention in the field of physics. Recent research suggest that quantum teleportation may extend beyond the realm of fundamental particles and apply to complex biological systems. In this review article, the phenomenon of quantum teleportation of epigenetic information in plants and its potential implications for the transfer of genome-stored experience to close relatives is explored. The article begins by providing an introduction to the concept of quantum teleportation and its underlying principles. Then, the emerging field of epigenetics is delved into, discussing the role of epigenetic modifications in plant adaptation and response to environmental stimuli. Subsequently, the existing evidence for the transfer of epigenetic information between plants through horizontal gene transfer is presented, along with the exploration of the possibility of quantum teleportation as an alternative mechanism for such transfers. The implications of quantum teleportation for the transfer of genome-stored experience are discussed, including the potential impact on plant evolution and adaptation. Furthermore, the challenges and limitations in studying quantum phenomena in biological systems are addressed, and future directions for research in this exciting field are proposed. In conclusion, while the phenomenon of quantum teleportation of epigenetic information in plants holds promise, further investigation is required to fully understand its mechanisms and implications. This knowledge will provide insights into the feasibility and mechanisms of quantum teleportation in plants.

Transcriptomic profiling of Parkinson's disease brains reveals disease stage specific gene expression changes

Parkinson´s disease (PD) is a progressive neurodegenerative disorder characterized by both motor and non-motor symptoms. Aggravation of symptoms is mirrored by accumulation of protein aggregates mainly composed by alpha-synuclein in different brain regions, called Lewy bodies (LB). Previous studies have identified several molecular mechanisms as autophagy and inflammation playing a role in PD pathogenesis. Increased insights into mechanisms involved in early disease stages and driving the progression of the LB pathology are required for the development of disease-modifying strategies. Here, we aimed to elucidate disease stage-specific transcriptomic changes in brain tissue of well-characterized PD and control donors. We collected frontal cortex samples from 84 donors and sequenced both the coding and non-coding RNAs. We categorized our samples into groups based on their degree of LB pathology aiming to recapitulate a central aspect of disease progression. Using an analytical pipeline that corrected for sex, age at death, RNA quality, cell composition and unknown sources of variation, we found major disease stage-specific transcriptomic changes. Gene expression changes were most pronounced in donors at the disease stage when microscopic LB changes first occur in the sampled brain region. Additionally, we identified disease stage-specific enrichment of brain specific pathways and immune mechanisms. On the contrary, we showed that mitochondrial mechanisms are enriched throughout the disease course. Our data-driven approach also suggests a role for several poorly characterized lncRNAs in disease development and progression of PD. Finally, by combining genetic and epigenetic information, we highlighted two genes (MAP4K4 and PHYHIP) as candidate genes for future functional studies. Together our results indicate that transcriptomic dysregulation and associated functional changes are highly disease stage-specific, which has major implications for the study of neurodegenerative disorders.

O-173 Cellular and developmental damage from oocyte cryopreservation

Abstract Compared to somatic or sperm cells, mammalian oocytes are much more sensitive to cryopreservation mainly because of the large volume, cytoskeleton, and presence of the zona pellucida. Connections with the surrounding cumulus cells also are challenging to preserve in immature oocytes. Besides the genetic and epigenetic information enclosed in the nucleus, oocytes contain organelles and cytoplasmic factors that are necessary for the early embryo development. Therefore, exposure to cryoprotectant and freezing temperatures can easily damage the oocyte’s complex cellular structure and developmental competence, which leads to poor success in fertilization, lower embryo quality, and reduced pregnancy rates. Using the domestic cat as a model, our laboratory has studied damages in cumulus-oocyte complexes (immature oocytes) occurring at each step of the cryopreservation process. Specifically, this included the impact of cryoprotectants on microtubules, the effect of osmotic changes on the overall structures, as well as sensitivity of the nuclear chromatin and epigenetic patterns to freezing temperatures. Based on those findings, it has been possible to design mitigating solutions like customized ultra-rapid freezing or vitrification protocols, Laser-warming methods, or post-warming reanimations. New horizons have also been explored to move away from issues and limitations related to cryopreservation. Approaches like storage of oocytes for the long-term at non-freezing temperatures are currently being developed based on encouraging data generated in preliminary studies. For instance, incorporation of trehalose into the oocyte followed by microwave-assisted dehydration can allow to remove enough water while creating a protective trehalose glass compatible with survival and storage at non-freezing temperatures. Interestingly, transcriptomic and proteomic studies have already shown that stresses and damages induced by dehydration versus cryopreservation are different and may be easier to overcome.

Intrinsic catalytic properties of histone H3 lysine-9 methyltransferases preserve monomethylation levels under low S-adenosylmethionine

S-adenosylmethionine (SAM) is the methyl donor for site-specific methylation reactions on histone proteins, imparting key epigenetic information. During SAM-depleted conditions that can arise from dietary methionine restriction, lysine di- and tri-methylation are reduced while sites such as Histone-3 lysine-9 (H3K9) are actively maintained, allowing cells to restore higher-state methylation upon metabolic recovery. Here, we investigated if the intrinsic catalytic properties of H3K9 histone methyltransferases (HMTs) contribute to this epigenetic persistence. We employed systematic kinetic analyses and substrate binding assays using four recombinant H3K9 HMTs (i.e., EHMT1, EHMT2, SUV39H1, and SUV39H2). At both high and low (i.e., sub-saturating) SAM, all HMTs displayed the highest catalytic efficiency (kcat/KM) for monomethylation compared to di- and trimethylation on H3 peptide substrates. The favored monomethylation reaction was also reflected in kcat values, apart from SUV39H2 which displayed a similar kcat regardless of substrate methylation state. Using differentially methylated nucleosomes as substrates, kinetic analyses of EHMT1 and EHMT2 revealed similar catalytic preferences. Orthogonal binding assays revealed only small differences in substrate affinity across methylation states, suggesting that catalytic steps dictate the monomethylation preferences of EHMT1, EHMT2, and SUV39H1. To link invitro catalytic rates with nuclear methylation dynamics, we built a mathematical model incorporating measured kinetic parameters and a time course of mass spectrometry-based H3K9 methylation measurements following cellular SAM depletion. The model revealed that the intrinsic kinetic constants of the catalytic domains could recapitulate invivo observations. Together, these results suggest catalytic discrimination by H3K9 HMTs maintains nuclear H3K9me1, ensuring epigenetic persistence after metabolic stress.

Distant sequence regions of JBP1 contribute to J-DNA binding.

Base-J (β-D-glucopyranosyloxymethyluracil) is a modified DNA nucleotide that replaces 1% of thymine in kinetoplastid flagellates. The biosynthesis and maintenance of base-J depends on the base-J-binding protein 1 (JBP1) that has a thymidine hydroxylase domain and a J-DNA-binding domain (JDBD). How the thymidine hydroxylase domain synergizes with the JDBD to hydroxylate thymine in specific genomic sites, maintaining base-J during semi-conservative DNA replication, remains unclear. Here, we present a crystal structure of the JDBD including a previously disordered DNA-contacting loop and use it as starting point for molecular dynamics simulations and computational docking studies to propose recognition models for JDBD binding to J-DNA. These models guided mutagenesis experiments, providing additional data for docking, which reveals a binding mode for JDBD onto J-DNA. This model, together with the crystallographic structure of the TET2 JBP1-homologue in complex with DNA and the AlphaFold model of full-length JBP1, allowed us to hypothesize that the flexible JBP1 N-terminus contributes to DNA-binding, which we confirmed experimentally. Α high-resolution JBP1:J-DNA complex, which must involve conformational changes, would however need to be determined experimentally to further understand this unique underlying molecular mechanism that ensures replication of epigenetic information.

First person – Benjamin Walters

ABSTRACT First Person is a series of interviews with the first authors of a selection of papers published in Journal of Cell Science, helping researchers promote themselves alongside their papers. Benjamin Walters is first author on ‘ Divergent functions of histone acetyltransferases KAT2A and KAT2B in keratinocyte self-renewal and differentiation’, published in JCS. Benjamin conducted the research described in this article while a PhD student with the A*STAR Research Attachment Programme (ARAP) in Dr Chin Yan Lim's lab at Institute of Medical Biology, Singapore. He is now a Hope Funds for Cancer Research Postdoctoral Fellow in the lab of Bluma Lesch at Yale School of Medicine, USA, where he is currently interested in exploring how parental experiences can affect the health of offspring through the inheritance of germline epigenetic information.

Impaired histone inheritance promotes tumor progression

Faithful inheritance of parental histones is essential to maintain epigenetic information and cellular identity during cell division. Parental histones are evenly deposited onto the replicating DNA of sister chromatids in a process dependent on the MCM2 subunit of DNA helicase. However, the impact of aberrant parental histone partition on human disease such as cancer is largely unknown. In this study, we construct a model of impaired histone inheritance by introducing MCM2-2A mutation (defective in parental histone binding) in MCF-7 breast cancer cells. The resulting impaired histone inheritance reprograms the histone modification landscapes of progeny cells, especially the repressive histone mark H3K27me3. Lower H3K27me3 levels derepress the expression of genes associated with development, cell proliferation, and epithelial to mesenchymal transition. These epigenetic changes confer fitness advantages to some newly emerged subclones and consequently promote tumor growth and metastasis after orthotopic implantation. In summary, our results indicate that impaired inheritance of parental histones can drive tumor progression.

Introduction to the Compendium on Early Cardiovascular Disease.

Introduction to the Compendium on Early Cardiovascular Disease.

Polycomb protein SCML2 mediates paternal epigenetic inheritance through sperm chromatin.

Sperm chromatin retains small amounts of histones, and chromatin states of sperm mirror gene expression programs of the next generation. However, it remains largely unknown how paternal epigenetic information is transmitted through sperm chromatin. Here, we present a novel mouse model of paternal epigenetic inheritance, in which deposition of Polycomb repressive complex 2 (PRC2) mediated-repressive H3K27me3 is attenuated in the paternal germline. By applying modified methods of assisted reproductive technology using testicular sperm, we rescued infertility of mice missing Polycomb protein SCML2, which regulates germline gene expression by establishing H3K27me3 on bivalent promoters with other active marks H3K4me2/3. We profiled epigenomic states (H3K27me3 and H3K4me3) of testicular sperm and epididymal sperm, demonstrating that the epididymal pattern of the sperm epigenome is already established in testicular sperm and that SCML2 is required for this process. In F1 males of X-linked Scml2-knockout mice, which have a wild-type genotype, gene expression is dysregulated in the male germline during spermiogenesis. These dysregulated genes are targets of SCML2-mediated H3K27me3 in F0 sperm. Further, dysregulation of gene expression was observed in the mutant-derived wild-typeF1 preimplantation embryos. Together, we present functional evidence that the classic epigenetic regulator Polycomb mediates paternal epigenetic inheritance through sperm chromatin.

Transgenerational sperm DMRs escape DNA methylation erasure during embryonic development andepigenetic inheritance.

Germline transmission of epigenetic information is a critical component of epigenetic inheritance. Previous studies have suggested that an erasure of DNA methylation is required to develop stem cells in the morula embryo. An exception involves imprinted genes that escape this DNA methylation erasure. Transgenerational differential DNA methylation regions (DMRs) have been speculated to be imprinted-like and escape this erasure. The current study was designed to assess if morula embryos escape the erasure of dichlorodiphenyltrichloroethane-induced transgenerational sperm DMR methylation. Observations demonstrate that the majority (98%) of transgenerational sperm DMR sites retain DNA methylation and are not erased, so appearing similar to imprinted-like sites. Interestingly, observations also demonstrate that the majority of low-density CpG genomic sites had a significant increase in DNA methylation in the morula embryo compared to sperm. This is in contrast to the previously observed DNA methylation erasure of higher-density CpG sites. The general erasure of DNA methylation during embryogenesis appears applicable to high-density DNA methylation sites (e.g. CpG islands) but neither to transgenerational DMR methylation sites nor to low-density CpG deserts, which constitute the vast majority of the genome's DNA methylation sites. The role of epigenetics during embryogenesis appears more dynamic than the simple erasure of DNA methylation.