scholarly journals Base-resolution maps of 5-formylcytosine and 5-carboxylcytosine reveal genome-wide DNA demethylation dynamics

Cell Research ◽  
2015 ◽  
Vol 25 (3) ◽  
pp. 386-389 ◽  
Author(s):  
Xingyu Lu ◽  
Dali Han ◽  
Boxuan Simen Zhao ◽  
Chun-Xiao Song ◽  
Li-Sheng Zhang ◽  
...  
Keyword(s):  
Dna Demethylation ◽  
Genome Wide

Genome-wide reprogramming by DNA demethylation during mouse oocyte growth and early development

2014 ◽  
Author(s):  
Akihiko Sakashita ◽  
Yosuke Iseki ◽  
Mei Nakajima ◽  
Takuya Wakai ◽  
Hisato Kobayashi ◽  
...  
Keyword(s):  
Early Development ◽  
Dna Demethylation ◽  
Mouse Oocyte ◽  
Oocyte Growth ◽  
Genome Wide

scholarly journals PHYTOCHROMES B1/B2 ARE KEY REGULATORS OF EPIGENOME REPROGRAMMING DURING TOMATO FRUIT DEVELOPMENT

2020 ◽  
Author(s):  
Ricardo Bianchetti ◽  
Nicolas Bellora ◽  
Luis A de Haro ◽  
Rafael Zuccarelli ◽  
Daniele Rosado ◽  
...  
Keyword(s):  
Fruit Development ◽  
Epigenetic Modification ◽  
Tomato Fruit ◽  
Dna Demethylation ◽  
Temperature Perception ◽  
Genome Wide ◽  
Fruit Development And Ripening ◽  
Histone Modifying Enzymes ◽  
Level Of Understanding ◽  
Agronomical Traits

AbstractPhytochrome-mediated light and temperature perception has been shown to be a major regulator of fruit development. Furthermore, chromatin remodelling via DNA demethylation has been described as a crucial mechanism behind the fruit ripening process; however, the molecular basis underlying the triggering of this epigenetic modification remains largely unknown. Here, an integrative analyses of the methylome, siRNAome and transcriptome of tomato fruits from phyA and phyB1B2 null mutants was performed, revealing that PHYB1 and PHYB2 influences genome-wide DNA methylation during fruit development and ripening. The experimental evidence indicates that PHYB1B2 signal transduction relies on a gene expression network that includes chromatin organization factors (DNA methylases/demethylases, histone-modifying enzymes and remodelling factors) and transcriptional regulators, ultimately leading to altered mRNA profile of photosynthetic and ripening-associated genes. This new level of understanding provides insights into the orchestration of epigenetic mechanisms in response to environmental cues affecting agronomical traits in fleshy fruits.

TRIM28 maintains genome imprints and regulates development of porcine SCNT embryos

Reproduction ◽  
2021 ◽  
Vol 161 (4) ◽  
pp. 411-424
Author(s):  
Yanhui Zhai ◽  
Meng Zhang ◽  
Xinglan An ◽  
Sheng Zhang ◽  
Xiangjie Kong ◽  
...  
Keyword(s):  
Somatic Cell Nuclear Transfer ◽  
Nuclear Transfer ◽  
Transcript Abundance ◽  
Dna Demethylation ◽  
Epigenetic Variability ◽  
Promoter Regions ◽  
Cell Stage ◽  
Genome Wide ◽  
Developmental Progression ◽  
Imprinting Gene

Pre-implantation embryos undergo genome-wide DNA demethylation, however certain regions, like imprinted loci remain methylated. Further, the mechanisms ensuring demethylation resistance by TRIM28 in epigenetic reprogramming remain poorly understood. Here, TRIM28 was knocked down in oocytes, and its effects on porcine somatic cell nuclear transfer (SCNT) embryo development was examined. Our results showed that SCNT embryos constructed from TRIM28 knockdown oocytes had significantly lower cleavage (53.9 ± 3.4% vs 64.8 ± 2.7%) and blastocyst rates (12.1 ± 4.3% vs 19.8 ± 1.9%) than control-SCNT embryos. The DNA methylation levels at the promoter regions of the imprinting gene IGF2 and H19 were significantly decreased in the 4-cell stage, and the transcript abundance of other imprinting gene was substantially increased. We also identified an aberrant two-fold decrease in the expression of CXXC1and H3K4me3 methyltransferase (ASH2L and MLL2), and the signal intensity of H3K4me3 had a transient drop in SCNT 2-cell embryos. Our results indicated that maternal TRIM28 knockdown disrupted the genome imprints and caused epigenetic variability in H3K4me3 levels, which blocked the transcription activity of zygote genes and affected the normal developmental progression of porcine SCNT embryos.

scholarly journals Dnmt1 binds and represses genomic retroelements via DNA methylation in mouse early embryos

2020 ◽  
Vol 48 (15) ◽  
pp. 8431-8444 ◽  
Author(s):  
Byungkuk Min ◽  
Jung Sun Park ◽  
Young Sun Jeong ◽  
Kyuheum Jeon ◽  
Yong-Kook Kang
Keyword(s):  
Dna Methylation ◽  
Cpg Islands ◽  
Endogenous Retrovirus ◽  
Dna Demethylation ◽  
Mouse Development ◽  
Genome Wide ◽  
Early Embryos ◽  
Dna Adenine Methylase ◽  
Early Mouse ◽  
Early Developmental

Abstract Genome-wide passive DNA demethylation in cleavage-stage mouse embryos is related to the cytoplasmic localization of the maintenance methyltransferase DNMT1. However, recent studies provided evidences of the nuclear localization of DNMT1 and its contribution to the maintenance of methylation levels of imprinted regions and other genomic loci in early embryos. Using the DNA adenine methylase identification method, we identified Dnmt1-binding regions in four- and eight-cell embryos. The unbiased distribution of Dnmt1 peaks in the genic regions (promoters and CpG islands) as well as the absence of a correlation between the Dnmt1 peaks and the expression levels of the peak-associated genes refutes the active participation of Dnmt1 in the transcriptional regulation of genes in the early developmental period. Instead, Dnmt1 was found to associate with genomic retroelements in a greatly biased fashion, particularly with the LINE1 (long interspersed nuclear elements) and ERVK (endogenous retrovirus type K) sequences. Transcriptomic analysis revealed that the transcripts of the Dnmt1-enriched retroelements were overrepresented in Dnmt1 knockdown embryos. Finally, methyl-CpG-binding domain sequencing proved that the Dnmt1-enriched retroelements, which were densely methylated in wild-type embryos, became demethylated in the Dnmt1-depleted embryos. Our results indicate that Dnmt1 is involved in the repression of retroelements through DNA methylation in early mouse development.

scholarly journals FACT complex is required for DNA demethylation at heterochromatin during reproduction in Arabidopsis

2018 ◽  
Vol 115 (20) ◽  
pp. E4720-E4729 ◽  
Author(s):  
Jennifer M. Frost ◽  
M. Yvonne Kim ◽  
Guen Tae Park ◽  
Ping-Hung Hsieh ◽  
Miyuki Nakamura ◽  
...  
Keyword(s):  
Genomic Imprinting ◽  
Nucleosome Occupancy ◽  
Dna Demethylation ◽  
Embryo Viability ◽  
Chromatin States ◽  
Specific Recognition ◽  
Genome Wide ◽  
Target Sites ◽  
Recognition Protein

The DEMETER (DME) DNA glycosylase catalyzes genome-wide DNA demethylation and is required for endosperm genomic imprinting and embryo viability. Targets of DME-mediated DNA demethylation reside in small, euchromatic, AT-rich transposons and at the boundaries of large transposons, but how DME interacts with these diverse chromatin states is unknown. The STRUCTURE SPECIFIC RECOGNITION PROTEIN 1 (SSRP1) subunit of the chromatin remodeler FACT (facilitates chromatin transactions), was previously shown to be involved in the DME-dependent regulation of genomic imprinting in Arabidopsis endosperm. Therefore, to investigate the interaction between DME and chromatin, we focused on the activity of the two FACT subunits, SSRP1 and SUPPRESSOR of TY16 (SPT16), during reproduction in Arabidopsis. We found that FACT colocalizes with nuclear DME in vivo, and that DME has two classes of target sites, the first being euchromatic and accessible to DME, but the second, representing over half of DME targets, requiring the action of FACT for DME-mediated DNA demethylation genome-wide. Our results show that the FACT-dependent DME targets are GC-rich heterochromatin domains with high nucleosome occupancy enriched with H3K9me2 and H3K27me1. Further, we demonstrate that heterochromatin-associated linker histone H1 specifically mediates the requirement for FACT at a subset of DME-target loci. Overall, our results demonstrate that FACT is required for DME targeting by facilitating its access to heterochromatin.

scholarly journals PROSER1 mediates TET2 O-GlcNAcylation to regulate DNA demethylation on UTX-dependent enhancers and CpG islands

2021 ◽  
Vol 5 (1) ◽  
pp. e202101228
Author(s):  
Xiaokang Wang ◽  
Wojciech Rosikiewicz ◽  
Yurii Sedkov ◽  
Tanner Martinez ◽  
Baranda S Hansen ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Target Genes ◽  
Cpg Islands ◽  
Dna Demethylation ◽  
Dna Hypermethylation ◽  
Genome Wide ◽  
Associated Proteins ◽  
Tet Enzymes ◽  
Tet Protein ◽  
First Time

DNA methylation at enhancers and CpG islands usually leads to gene repression, which is counteracted by DNA demethylation through the TET protein family. However, how TET enzymes are recruited and regulated at these genomic loci is not fully understood. Here, we identify TET2, the glycosyltransferase OGT and a previously undescribed proline and serine rich protein, PROSER1 as interactors of UTX, a component of the enhancer-associated MLL3/4 complexes. We find that PROSER1 mediates the interaction between OGT and TET2, thus promoting TET2 O-GlcNAcylation and protein stability. In addition, PROSER1, UTX, TET1/2, and OGT colocalize on many genomic elements genome-wide. Loss of PROSER1 results in lower enrichment of UTX, TET1/2, and OGT at enhancers and CpG islands, with a concomitant increase in DNA methylation and transcriptional down-regulation of associated target genes and increased DNA hypermethylation encroachment at H3K4me1-predisposed CpG islands. Furthermore, we provide evidence that PROSER1 acts as a more general regulator of OGT activity by controlling O-GlcNAcylation of multiple other chromatin signaling pathways. Taken together, this study describes for the first time a regulator of TET2 O-GlcNAcylation and its implications in mediating DNA demethylation at UTX-dependent enhancers and CpG islands and supports an important role for PROSER1 in regulating the function of various chromatin-associated proteins via OGT-mediated O-GlcNAcylation.

scholarly journals Epigenomic co-localization and co-evolution reveal a key role for 5hmC as a communication hub in the chromatin network of ESCs

2014 ◽  
Author(s):  
David Juan ◽  
Juliane Perner ◽  
Enrique Carrillo de Santa Pau ◽  
Simone Marsili ◽  
David Ochoa ◽  
...  
Keyword(s):  
Communication Network ◽  
Dna Demethylation ◽  
Communication Model ◽  
Evolutionary Analysis ◽  
Manual Annotation ◽  
Nucleosome Remodeling ◽  
Location Data ◽  
Genome Wide ◽  
Related Proteins

Epigenetic communication through histone and cytosine modifications is essential for gene regulation and cell identity. Here, we propose a framework that is based on a chromatin communication model to get insight on the function of epigenetic modifications in ESCs. The epigenetic communication network was inferred from genome-wide location data plus extensive manual annotation. Notably, we found that 5-hydroxymethylcytosine (5hmC) is the most influential hub of this network, connecting DNA demethylation to nucleosome remodeling complexes and to key transcription factors of pluripotency. Moreover, an evolutionary analysis revealed a central role of 5hmC in the co-evolution of chromatin-related proteins. Further analysis of regions where 5hmC colocalizes with specific interactors shows that each interaction points to chromatin remodelling, stemness, differentiation or metabolism. Our results highlight the importance of cytosine modifications in the epigenetic communication of ESCs.

scholarly journals Recent evolution of a TET-controlled and DPPA3/STELLA-driven pathway of passive DNA demethylation in mammals

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Christopher B. Mulholland ◽  
Atsuya Nishiyama ◽  
Joel Ryan ◽  
Ryohei Nakamura ◽  
Merve Yiğit ◽  
...  
Keyword(s):  
Pluripotent Stem Cells ◽  
Large Scale ◽  
Unique Feature ◽  
Mammalian Species ◽  
Dna Demethylation ◽  
Evolutionary Divergence ◽  
Mammalian Development ◽  
Active Demethylation ◽  
Global Hypomethylation ◽  
Genome Wide

AbstractGenome-wide DNA demethylation is a unique feature of mammalian development and naïve pluripotent stem cells. Here, we describe a recently evolved pathway in which global hypomethylation is achieved by the coupling of active and passive demethylation. TET activity is required, albeit indirectly, for global demethylation, which mostly occurs at sites devoid of TET binding. Instead, TET-mediated active demethylation is locus-specific and necessary for activating a subset of genes, including the naïve pluripotency and germline marker Dppa3 (Stella, Pgc7). DPPA3 in turn drives large-scale passive demethylation by directly binding and displacing UHRF1 from chromatin, thereby inhibiting maintenance DNA methylation. Although unique to mammals, we show that DPPA3 alone is capable of inducing global DNA demethylation in non-mammalian species (Xenopus and medaka) despite their evolutionary divergence from mammals more than 300 million years ago. Our findings suggest that the evolution of Dppa3 facilitated the emergence of global DNA demethylation in mammals.

Epigenetic targeting of clear cell renal cell carcinoma (ccRCC) with ascorbic acid (AA) via upregulation of Ten-Eleven Translocation (TET) methylcytosine dioxygenase activity.

2017 ◽  
Vol 35 (6_suppl) ◽  
pp. 479-479
Author(s):  
Niraj Konchady Shenoy ◽  
Tushar Bhagat ◽  
Lance C. Pagliaro ◽  
Thomas E. Witzig ◽  
Amit Verma
Keyword(s):  
Cell Cycle ◽  
Cell Line ◽  
Dna Demethylation ◽  
High Dose ◽  
Proliferation Inhibition ◽  
Genome Wide ◽  
Smad7 Expression ◽  
Tet Enzymes ◽  
Ccrcc Cell

479 Background: We and others have previously shown that the ccRCC epigenome is characterized by widespread DNA hypermethylation (CCR 2014, Nature 2014). Various important tumor suppressor genes (TSGs), such as SMAD7 (inhibitor of oncogenic TGF-β signaling), are under-expressed due to aberrantly methylated promoters or enhancers. We hypothesized that the hypermethylation in ccRCC could be due to low activity of the TET enzymes, which convert methylcytosine (5-mc) to hydroxymethylcytosine (5-hmc). Loss of function of TET enzymes can occur with an inactivating mutation (TET-2 is mutated in about 6% of ccRCC (Science Signaling 2013) or hypoactivity of normal TET enzymes, through inhibition by metabolic intermediates. AA is an essential co-factor for TET enzymes (JACS 2015). We hypothesized that high dose AA treatment of ccRCC could potentially increase the functional activity of TET enzymes leading to demethylation of the RCC genome, and enhance expression of TSGs. Methods: In vitro TET activity was performed on ccRCC cell line 769P with increasing doses of AA (L-AA). Genome wide quantitative 5-mc and 5-hmc was evaluated using mass spectrometry. SMAD7 expression was determined using qRT-PCR. Proliferation assay (MTT) was performed with AA in combination with pazopanib. Cell cycle and apoptosis assays were performed. Results: AA, at doses achieved only by the intravenous route (1-10mM), increased TET activity in ccRCC cell line 769P. Genome wide 5-mc was significantly reduced and 5-hmc was increased, correlating with increase in TET activity. SMAD7 expression was increased with AA treatment. High dose AA led to proliferation inhibition with a cell cycle arrest in the G1 phase, and had a synergistic effect with pazopanib. Since AA leads to the generation of H2O2 in-vitro, catalase was used as control. This did not reverse the effect of AA on epigenetic changes; and proliferation inhibition was seen despite catalase control. Conclusions: High dose AA causes TET mediated DNA demethylation of the hypermethylated RCC genome, resulting in the re-expression of TSGs, and proliferation inhibition. Sequencing and xenograft studies are underway.

Global DNA Demethylation During Physiological Erythropoiesis In Vivo

Blood ◽  
2010 ◽  
Vol 116 (21) ◽  
pp. 2083-2083 ◽  
Author(s):  
Jeffrey R Shearstone ◽  
Ramona Pop ◽  
Merav Socolovsky
Keyword(s):  
Dna Methylation ◽  
Dna Replication ◽  
Methylation Level ◽  
Genomic Dna ◽  
Terminal Differentiation ◽  
Significant Loss ◽  
Dna Demethylation ◽  
Erythroid Terminal Differentiation ◽  
Genome Wide ◽  
Erythroid Maturation

Abstract Abstract 2083 In the mammalian genome cytosine residues that are followed by guanine (5’-CpG-3’ dinucleotides) are frequently methylated, a modification that is associated with transcriptional silencing. Two genome-wide waves of demethylation, in primordial germ cells and in the early pre-implantation embryo, erase methylation marks and are each followed by de novo methylation, setting up a pattern subsequently inherited throughout development [1]. While no global methylation changes are thought to occur during further somatic development, methylation does alter at gene-specific loci, contributing to tissue-specific patterns of gene expression. We set out to study dynamic changes in DNA methylation during erythropoiesis. We used flow cytometry and the cell surface markers CD71 and Ter119 to subdivide freshly isolated fetal liver cells into a developmental sequence of six subsets, from the least mature Subset 0 (S0), to the most mature Subset 5 (S5) [2]. We measured DNA methylation in genomic DNA prepared from freshly sorted S0 to S5 cells. Surprisingly, we found that demethylation at the erythroid-specific β-globin locus control region (LCR) was coincident with progressive genome-wide methylation loss. Both global demethylation as well as demethylation at the β-globin LCR began with the upregulation of CD71 at the onset of erythroid terminal differentiation, and continued with erythroid maturation, with global hypomethylation persisting during enucleation. We employed several distinct methodologies to measure global DNA methylation level. Using Enzyme-Linked Immunosorbent Assay (ELISA), we found that genomic DNA isolated from increasingly mature erythroblasts had progressively reduced binding to a 5-methylcytosine-specific antibody. We also used the LUminometric Methylation Assay (LUMA) to compare the genome-wide cleavage of CCGG sites by each of the isoschizomers HpaII and MspI, which are methylation sensitive and insensitive, respectively. Both the ELISA and LUMA assays showed a global, progressive and significant loss of DNA methylation with erythroid differentiation: 70% of CpG dinucleotides genome-wide were methylated in S0, decreasing to 40–50% by S4/5 (p<0.01). Further, using pyrosequencing of bisulfite-converted DNA, we found a similar decrease in CpG methylation in the promoters of genes whose transcription is silenced with erythroid maturation, notably PU.1 and Fas. To characterize the global loss in methylation further, we examined the status of imprinted genes and of repetitive transposable elements, since both represent genetic loci that are usually stably and highly methylated in somatic cells. We found loss of methylation in imprinted loci, including PEG3 and the H19 Differentially Methylated Region (DMR). We also found a significant loss of methylation at the Long Interspersed Nuclear Element (LINE-1), a repetitive retrotransposon, whose methylation level decreased from over 90% in S0 cells, to 70% in S4/5. Mechanistically, global demethylation was associated with a rapid decline in the DNA methyltransferases DNMT3a and DNMT3b. However, exogenous re-expression of these enzymes in vitro was not sufficient to reverse the process. Both global and erythroid-specific demethylation required rapid DNA replication, triggered with the onset of erythroid terminal differentiation. We were able to slow down demethylation quantitatively by slowing down the rate of DNA replication with aphidicolin, an inhibitor of DNA polymerase α. Global loss of DNA methylation was not associated with a global increase in transcription, as determined by GeneChip analysis, nor was it associated with increased transcription of the LINE-1 retrotransposon. We propose that global demethylation is a consequence of global cellular mechanisms required for the rapid demethylation and induction of β-globin and other erythroid genes. Our findings suggest mechanisms of global demethylation in development and disease, and show that contrary to previously held dogma, DNA demethylation occurs globally during physiological somatic cell differentiation. References: 1. Reik W, Dean W, Walter J (2001) Epigenetic reprogramming in mammalian development. Science 293: 1089–1093. 2. Socolovsky M, Murrell M, Liu Y, Pop R, Porpiglia E, et al. (2007) Negative Autoregulation by FAS Mediates Robust Fetal Erythropoiesis. PLoS Biol 5: e252. Disclosures: No relevant conflicts of interest to declare.

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