Temporal Dynamics of Tet1 and Oct4 Gene Activation Resolve Distinct Stages of Global DNA Demethylation and Transcriptomic Changes in the Final Phases of Induced Pluripotency

2019 ◽  
Author(s):  
Michela Bartoccetti ◽  
Xinlong Luo ◽  
Ben van der Veer ◽  
Rita Khoueiry ◽  
Adrian Janiszewski ◽  
...  
Keyword(s):  
Temporal Dynamics ◽  
Gene Activation ◽  
Dna Demethylation ◽  
Induced Pluripotency ◽  
Transcriptomic Changes

scholarly journals Differential activation of the hprt gene on the inactive X chromosome in primary and transformed Chinese hamster cells.

1989 ◽  
Vol 9 (4) ◽  
pp. 1635-1641 ◽  
Author(s):  
S G Grant ◽  
R G Worton
Keyword(s):  
Cell Lines ◽  
X Chromosome ◽  
Gene Activation ◽  
Chinese Hamster ◽  
Fibroblast Cell ◽  
Dna Demethylation ◽  
Hprt Gene ◽  
Primary Fibroblast ◽  
Chinese Hamster Cells ◽  
Inactive X Chromosome

We have investigated the genetic activation of the hprt (hypoxanthine-guanine phosphoribosyltransferase) gene located on the inactive X chromosome in primary and transformed female diploid Chinese hamster cells after treatment with the DNA methylation inhibitor 5-azacytidine (5azaCR). Mutants deficient in HPRT were first selected by growth in 6-thioguanine from two primary fibroblast cell lines and from transformed lines derived from them. These HPRT- mutants were then treated with 5azaCR and plated in HAT (hypoxanthine-methotrexate-thymidine) medium to select for cells that had reexpressed the hprt gene on the inactive X chromosome. Contrary to previous results with primary human cells, 5azaCR was effective in activating the hprt gene in primary Chinese hamster fibroblasts at a low but reproducible frequency of 2 x 10(-6) to 7 x 10(-6). In comparison, the frequency in independently derived transformed lines varied from 1 x 10(-5) to 5 x 10(-3), consistently higher than in the nontransformed cells. This increase remained significant when the difference in growth rates between the primary and transformed lines was taken into account. Treatment with 5azaCR was also found to induce transformation in the primary cell lines but at a low frequency of 4 x 10(-7) to 8 x 10(-7), inconsistent with a two-step model of transformation followed by gene activation to explain the derepression of hprt in primary cells. Thus, these results indicate that upon transformation, the hprt gene on the inactive Chinese hamster X chromosome is rendered more susceptible to action by 5azaCR, consistent with a generalized DNA demethylation associated with the transformation event or with an increase in the instability of an underlying primary mechanism of X inactivation.

scholarly journals Gene activation precedes DNA demethylation in response to infection in human dendritic cells

2019 ◽  
Vol 116 (14) ◽  
pp. 6938-6943 ◽  
Author(s):  
Alain Pacis ◽  
Florence Mailhot-Léonard ◽  
Ludovic Tailleux ◽  
Haley E. Randolph ◽  
Vania Yotova ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Dendritic Cells ◽  
Transcriptional Activation ◽  
Time Course ◽  
Gene Activation ◽  
Dna Demethylation ◽  
Epigenetic Mark ◽  
Distal Enhancer ◽  
Human Dendritic Cells

DNA methylation is considered to be a relatively stable epigenetic mark. However, a growing body of evidence indicates that DNA methylation levels can change rapidly; for example, in innate immune cells facing an infectious agent. Nevertheless, the causal relationship between changes in DNA methylation and gene expression during infection remains to be elucidated. Here, we generated time-course data on DNA methylation, gene expression, and chromatin accessibility patterns during infection of human dendritic cells withMycobacterium tuberculosis. We found that the immune response to infection is accompanied by active demethylation of thousands of CpG sites overlapping distal enhancer elements. However, virtually all changes in gene expression in response to infection occur before detectable changes in DNA methylation, indicating that the observed losses in methylation are a downstream consequence of transcriptional activation. Footprinting analysis revealed that immune-related transcription factors (TFs), such as NF-κB/Rel, are recruited to enhancer elements before the observed losses in methylation, suggesting that DNA demethylation is mediated by TF binding to cis-acting elements. Collectively, our results show that DNA demethylation plays a limited role to the establishment of the core regulatory program engaged upon infection.

scholarly journals Evidence for a Bigenic Chromatin Subdomain in Regulation of the Fetal-to-Adult Hemoglobin Switch

2008 ◽  
Vol 29 (6) ◽  
pp. 1635-1648 ◽  
Author(s):  
Hugues Beauchemin ◽  
Marie Trudel
Keyword(s):  
Transcriptional Activation ◽  
Gene Activation ◽  
Dna Demethylation ◽  
Open Chromatin ◽  
Chromosome Conformation ◽  
Hemoglobin Switching ◽  
Switching Patterns ◽  
Adult Hemoglobin ◽  
Globin Promoter

ABSTRACT During development, human β-globin locus regulation undergoes two critical switches, the embryonic-to-fetal and fetal-to-adult hemoglobin switches. To define the role of the fetal Aγ-globin promoter in switching, human β-globin-YAC transgenic mice were produced with the Aγ-globin promoter replaced by the erythroid porphobilinogen deaminase (PBGD) promoter (PBGDAγ-YAC). Activation of the stage-independent PBGDAγ-globin strikingly stimulated native Gγ-globin expression at the fetal and adult stages, identifying a fetal gene pair or bigenic cooperative mechanism. This impaired fetal silencing severely suppressed both δ- and β-globin expression in PBGDAγ-YAC mice from fetal to neonatal stages and altered kinetics and delayed switching of adult β-globin. This regulation evokes the two human globin switching patterns in the mouse. Both patterns of DNA demethylation and chromatin immunoprecipitation analysis correlated with gene activation and open chromatin. Locus control region (LCR) interactions detected by chromosome conformation capture revealed distinct spatial fetal and adult LCR bigenic subdomains. Since both intact fetal promoters are critical regulators of fetal silencing at the adult stage, we concluded that fetal genes are controlled as a bigenic subdomain rather than a gene-autonomous mechanism. Our study also provides evidence for LCR complex interaction with spatial fetal or adult bigenic functional subdomains as a niche for transcriptional activation and hemoglobin switching.

Regulatory Roles of GADD45α in Skeletal Muscle and Adipocyte

2019 ◽  
Vol 20 (9) ◽  
pp. 918-925
Author(s):  
Wenjing You ◽  
Ziye Xu ◽  
Tizhong Shan
Keyword(s):  
Skeletal Muscle ◽  
Signal Transduction ◽  
Muscle Development ◽  
Gene Activation ◽  
Growth Arrest ◽  
Dna Demethylation ◽  
Genomic Integrity ◽  
Skeletal Muscle Development ◽  
Preadipocyte Differentiation ◽  
Cellular Processes

GADD45α, a member of the GADD45 family proteins, is involved in various cellular processes including the maintenance of genomic integrity, growth arrest, apoptosis, senescence, and signal transduction. In skeletal muscle, GADD45α plays an important role in regulating mitochondrial biogenesis and muscle atrophy. In adipocytes, GADD45α regulates preadipocyte differentiation, lipid accumulation, and thermogenesis metabolism. Moreover, it has been recently demonstrated that GADD45α promotes gene activation by inducing DNA demethylation. The epigenetic function of GADD45α is important for preadipocyte differentiation and transcriptional regulation during development. This article mainly reviews and discusses the regulatory roles of GADD45α in skeletal muscle development, adipocyte progenitor differentiation, and DNA demethylation.

DNA methylation in differentiating mouse teratocarcinoma and erythroleukemia cells

1984 ◽  
Vol 62 (7) ◽  
pp. 584-591 ◽  
Author(s):  
Luc Aujame ◽  
Jane Craig ◽  
Michael W. McBurney
Keyword(s):  
Gene Activation ◽  
Methylation Pattern ◽  
Dna Demethylation ◽  
Globin Genes ◽  
Dna Hypomethylation ◽  
Erythroleukemia Cells ◽  
Ec Cells ◽  
Murine Erythroleukemia ◽  
Mouse Teratocarcinoma ◽  
Derivatives Of

We have measured the content of 5-methylcytosine (5MC) in the genomic DNA of differentiated and undifferentiated cultures of murine embryonal carcinoma (EC) and murine erythroleukemia (MEL) cells. A large proportion of deoxycytosine residues were methylated in EC cells (4.6%) and this proportion dropped significantly (4.1%) following differentiation. The alpha-1 globin genes were heavily methylated at HpaII sites in EC cells and in differentiated derivatives of these EC cells. The MEL cells had only 3.3% of their genomic deoxycytidine methylated and no significant change occurred following differentiation. The alpha-1 globin genes of MEL cells were much less methylated than the same genes in EC cells and no change in this methylation pattern accompanied the induction of hemoglobin synthesis. In EC × MEL cell hybrids which express the alpha-1 globin genes from both parents, the EC-derived genes had become demethylated. These results are consistent with the general model that DNA hypomethylation is correlated with expression of that DNA and that gene activation is accompanied by DNA demethylation. We have also measured the 5MC content of DNA isolated from nuclease-treated EC nuclei. Unexpectedly, the DNase I sensitive chromatin contained a large proportion of 5MC. This result, along with the work of others, suggests that nuclease sensitivity may often reflect the transcriptional activity of chromatin in somatic cells, but is not indicative of the active state in pluripotent EC cells.

scholarly journals Histone Code Modifications on Pluripotential Nuclei of Reprogrammed Somatic Cells

2004 ◽  
Vol 24 (13) ◽  
pp. 5710-5720 ◽  
Author(s):  
Hironobu Kimura ◽  
Masako Tada ◽  
Norio Nakatsuji ◽  
Takashi Tada
Keyword(s):  
Transcriptional Activation ◽  
Es Cells ◽  
Gene Activation ◽  
Embryonic Stem ◽  
Dna Demethylation ◽  
Gene Activity ◽  
Current Evidence ◽  
Hybrid Cells ◽  
Promoter Regions ◽  
Somatic Genome

ABSTRACT Following hybridization with embryonic stem (ES) cells, somatic genomes are epigenetically reprogrammed and acquire pluripotency. This results in the transcription of somatic genome-derived tissue-specific genes upon differentiation. During nuclear reprogramming, it is expected that DNA and chromatin modifications, believed to function in cell-type-specific epigenotype memory, should be significantly modified. Indeed, current evidence indicates that acetylation and methylation of histone H3 and H4 amino termini play a major role in the regulation of gene activity through the modulation of chromatin conformation. Here, we show that the reprogrammed somatic genome of ES hybrid cells becomes hyperacetylated at H3 and H4, while lysine 4 (K4) of H3 becomes globally hyper-di- and -tri-methylated. In the Oct4 promoter region, histones H3 and H4 are acetylated and H3-K4 is highly tri-methylated on both the ES and reprogrammed somatic genomes, which correlates with gene activation and DNA demethylation. However, H3-K4 is also di- and tri-methylated in the promoter regions of Neurofilament-M (Nfm), Nfl, and Thy-1, which are all silent in both ES and hybrid cells. Thus, H3-K4 di- and tri-methylation of reprogrammed somatic genomes is independent of gene activity and represents one of the major events that occurs during somatic genome reprogramming towards a transcriptional activation-permissive state.

scholarly journals Epigenetic Drifts during Long-Term Intestinal Organoid Culture

Cells ◽  
2021 ◽  
Vol 10 (7) ◽  
pp. 1718
Author(s):  
Torsten Thalheim ◽  
Susann Siebert ◽  
Marianne Quaas ◽  
Maria Herberg ◽  
Michal R. Schweiger ◽  
...  
Keyword(s):  
Gene Activation ◽  
Growth Conditions ◽  
Dna Demethylation ◽  
Metabolic Adaptation ◽  
Long Term Culture ◽  
Organoid Culture ◽  
Transcriptional Changes ◽  
Tissue Of Origin ◽  
And Control

Organoids retain the morphological and molecular patterns of their tissue of origin, are self-organizing, relatively simple to handle and accessible to genetic engineering. Thus, they represent an optimal tool for studying the mechanisms of tissue maintenance and aging. Long-term expansion under standard growth conditions, however, is accompanied by changes in the growth pattern and kinetics. As a potential explanation of these alterations, epigenetic drifts in organoid culture have been suggested. Here, we studied histone tri-methylation at lysine 4 (H3K4me3) and 27 (H3K27me3) and transcriptome profiles of intestinal organoids derived from mismatch repair (MMR)-deficient and control mice and cultured for 3 and 20 weeks and compared them with data on their tissue of origin. We found that, besides the expected changes in short-term culture, the organoids showed profound changes in their epigenomes also during the long-term culture. The most prominent were epigenetic gene activation by H3K4me3 recruitment to previously unmodified genes and by H3K27me3 loss from originally bivalent genes. We showed that a long-term culture is linked to broad transcriptional changes that indicate an ongoing maturation and metabolic adaptation process. This process was disturbed in MMR-deficient mice, resulting in endoplasmic reticulum (ER) stress and Wnt activation. Our results can be explained in terms of a mathematical model assuming that epigenetic changes during a long-term culture involve DNA demethylation that ceases if the metabolic adaptation is disturbed.

scholarly journals cAMP Signaling Regulates DNA Demethylation by Augmenting the Intracellular Labile Ferrous Iron Pool

2017 ◽  
Author(s):  
Vladimir Camarena ◽  
David W. Sant ◽  
Tyler C. Huff ◽  
Sushmita Mustafi ◽  
Ryan K. Muir ◽  
...  
Keyword(s):  
Gene Transcription ◽  
Phosphodiesterase Inhibitors ◽  
Cell Types ◽  
Dna Demethylation ◽  
G Protein Coupled Receptors ◽  
Camp Signaling ◽  
Multiple Cell ◽  
Iron Pool ◽  
Transcriptomic Changes ◽  
G Protein Coupled

AbstractIt is widely accepted that cAMP regulates gene transcription principally by activating the protein kinase A (PKA)-targeted transcription factors. Here, we show that cAMP enhances the generation of 5-hydroxymethylcytosine (5hmC) in multiple cell types. 5hmC is converted from 5-methylcytosine (5mC) by Tet methylcytosine dioxygenases, for which Fe(II) is an essential cofactor. The promotion of 5hmC was mediated by a prompt increase of the intracellular labile Fe(II) pool (LIP). cAMP enhanced the acidification of endosomes for Fe(II) release to the LIP likely through RapGEF2. The effect of cAMP on Fe(II) and 5hmC was confirmed by adenylate cyclase activators, phosphodiesterase inhibitors, and most notably by stimulation of G protein-coupled receptors (GPCR). The transcriptomic changes caused by cAMP occurred in concert with 5hmC elevation in differentially transcribed genes. Collectively, these data show a previously unrecognized regulation of gene transcription by GPCR-cAMP signaling through augmentation of the intracellular labile Fe(II) pool and DNA demethylation.

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