scholarly journals DNA methylation in eukaryotes: kinetics of demethylation and de novo methylation during the life cycle.

Genetics ◽  
1990 ◽  
Vol 124 (2) ◽  
pp. 429-437 ◽  
Author(s):  
S P Otto ◽  
V Walbot
Keyword(s):  
Life Cycle ◽  
De Novo ◽  
Model Species ◽  
Equilibrium Level ◽  
Eukaryotic Dna ◽  
A Cell ◽  
Kinetics Of ◽  
Maintenance Methylation ◽  
Over Time ◽  
De Novo Methylation

Abstract We present a model for the kinetics of methylation and demethylation of eukaryotic DNA; the model incorporates values for de novo methylation and the error rate of maintenance methylation. From the equations, an equilibrium is reached such that the proportion of sites which are newly methylated equals the proportion of sites which become demethylated in a cell generation. This equilibrium is empirically determined as the level of maintenance methylation. We then chose reasonable values for the parameters using maize and mice as model species. In general, if the genome is either hypermethylated or hypomethylated it will approach the equilibrium level of maintenance methylation asymptotically over time; events occurring just once per life cycle to suppress methylation can maintain a relatively hypomethylated state. Although the equations developed are used here as framework for evaluating events in the whole genome, they can also be used to evaluate the rates of methylation and demethylation in specific sites over time.

scholarly journals Primary DNA sequence determines sites of maintenance and de novo methylation by mammalian DNA methyltransferases.

1986 ◽  
Vol 6 (4) ◽  
pp. 1135-1140 ◽  
Author(s):  
A H Bolden ◽  
C M Nalin ◽  
C A Ward ◽  
M S Poonian ◽  
A Weissbach
Keyword(s):  
Dna Sequence ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Dna Methyltransferases ◽  
Methylation Pattern ◽  
Complementary Strand ◽  
Target Strand ◽  
Enzymatic Methylation ◽  
Maintenance Methylation ◽  
De Novo Methylation

Analysis of the enzymatic methylation of oligodeoxynucleotides containing multiple C-G groups showed that hemimethylated sites in duplex oligomers are not significantly methylated by human or murine DNA methyltransferase unless those sites are capable of being methylated de novo in the single- or double-stranded oligomers. Thus, the primary sequence of the target strand, rather than the methylation pattern of the complementary strand, determines maintenance methylation. This suggests that de novo and maintenance methylation are the same process catalyzed by the same enzyme. In addition, the study revealed that complementary strands of oligodeoxynucleotides are methylated at different rates and in different patterns. Both primary DNA sequence and the spacing between C-G groups seem important since in one case studied, maximal methylation required a specific spacing of 13 to 17 nucleotides between C-G pairs.

scholarly journals Inheritance of DNA methylation in Coprinus cinereus

1986 ◽  
Vol 6 (1) ◽  
pp. 195-200
Author(s):  
M E Zolan ◽  
P J Pukkila
Keyword(s):  
Dna Methylation ◽  
Life Cycle ◽  
Homologous Chromosome ◽  
De Novo ◽  
Coprinus Cinereus ◽  
De Novo Methylation

We examined the inheritance of 5-methylcytosine residues at a centromere-linked locus in the basidiomycete Coprinus cinereus. Although methylated and unmethylated tracts were inherited both mitotically and meiotically the lengths of these tracts were variable. This variation was not confined to any one phase of the life cycle of the organism, and it usually involved the simultaneous de novo methylation of at least four HpaII-MspI sites. We also found that the higher levels of methylation at this locus were transmitted through meiosis, regardless of the level of methylation of the homologous chromosome.

De Novo DNA Methylation Is Associated with Granulopoiesis and Megakaryopoiesis but Not Erythropoiesis

Blood ◽  
2016 ◽  
Vol 128 (22) ◽  
pp. 3868-3868 ◽  
Author(s):  
Jens Lichtenberg ◽  
Elisabeth F. Heuston ◽  
Stacie M. Anderson ◽  
NIH Intramural Sequencing Center ◽  
Cheryl A. Keller ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Promoter Methylation ◽  
De Novo ◽  
Cell Type ◽  
Epigenetic Memory ◽  
Venn Diagrams ◽  
A Cell ◽  
Total Dna ◽  
Methylation Peak ◽  
De Novo Methylation

Abstract Previous research has shown that progressive DNA demethylation is a feature of erythroid differentiation (Hogart et al. 2012, Genome Res., 22:1407-18; Shearstone et al. 2011, Science, 334:799-802), but the epigenetic changes that occur during granulopoiesis and megakaryopoiesis have not been well characterized. To establish a comprehensive map of changes in DNA methylation, we have extended our analysis of DNA methylation to include megakaryocytes (MEG) and their progenitors (CFU-MEG), as well as granulocyte macrophage progenitors (GMP), common myeloid progenitors (CMP) and hematopoietic stem cells (HSC; Lin- Sca-1+, c-kit+). Erythroblasts (ERY), their progenitors (CFU-E), MEG, CFU-MEG, GMP, CMP and HSC were isolated by FACS from adult C57BL/6J mouse bone marrow. We performed whole genome DNA methylation profiling using Methyl Binding Domain 2 (MBD2) pulldown with subsequent high-throughput sequencing to detect regions containing 5 or more methylated CpGs within a 200bp window. Using the reduced representation bilsulfite sequencing data of Shearstone et al. as a benchmark, we identified CCAT (Xu et al. 2010, Bioinformatics, 26:1199-1204) as the best performing peak calling software to detect de novo methylation, and used CCAT to generate DNA methylation profiles for our isolated hematopoietic populations. We confirmed that erythropoiesis undergoes global demethylation (Figure 1). Epigenetic memory is a feature of erythropopiesis, with the majority of methylation peaks detected in erythroblasts also found in their progenitors. For example, 34,427 of the 36,135 CFU-E peaks are also found in HSC. Using Ingenuity Pathway Analysis (IPA), we found that the CFU-E genes with de novo promoter methylation (380 genes) were associated with the "DNA methylation and transcriptional repression signaling pathway" (p=9.6E-5), supporting the model of suppression of DNA methylation and epigenetic memory as a feature of erythropoiesis. In contrast, we found that compared to CFU-E, CFU-MEG undergo de novo methylation. Specifically, we detected 25,531 methylation peaks in CFU-MEG that are not present in HSC or CMP (Figure 1). Genes with de novo promoter methylation in CFU-MEG (1227 genes) were associated with silencing of extracellular signaling pathways, including disruption of MAPK and FAK signaling (p=1.4E-5). We have developed a systems biology data ranch named SBR-Blood (Lichtenberg et al. 2016, Nucleic Acid Res., 44:D925-31) that includes 228 publicly available epigenetic and RNA expression profiling datasets. Using SBR-Blood, we correlated the increased methylation in CFU-MEG with increased expression of the de novo methylation genes Dnmt3A/B genes (6 and 34-fold respectively), and decreased expression of the maintenance methylation gene Dnmt1 (1.5-fold). Compared to HSC, GMP acquired 15,115 de novo methylation peaks and CMP gained 4020 de novo peaks (Figure 1). Promoter-specific de novo methylation in 784 GMP genes was associated with silencing of Endothelin-1 signaling (p=8.1E-5), an observation confirmed using RNASeq expression profiles in SBR-Blood (e.g. AC-complex 20-fold decrease). In summary, we have shown that in contrast to erythropoiesis, megakaryopoiesis and granulopoiesis are associated with specific de novo methylation that defines their respective lineages. Figure 1 Venn diagrams, annotated with total DNA methylation peak counts for a cell type, depicting the intersections between the peaks of DNA methylation profiles in megakaryopoiesis and granulopoiesis, compared to erythropoiesis. Figure 1. Venn diagrams, annotated with total DNA methylation peak counts for a cell type, depicting the intersections between the peaks of DNA methylation profiles in megakaryopoiesis and granulopoiesis, compared to erythropoiesis. Disclosures No relevant conflicts of interest to declare.

scholarly journals A Gene Essential for De Novo Methylation and Development in Ascobolus Reveals a Novel Type of Eukaryotic DNA Methyltransferase Structure

Cell ◽  
1997 ◽  
Vol 91 (2) ◽  
pp. 281-290 ◽  
Author(s):  
Fabienne Malagnac ◽  
Birgit Wendel ◽  
Christophe Goyon ◽  
Godeleine Faugeron ◽  
Denise Zickler ◽  
...  
Keyword(s):  
Dna Methyltransferase ◽  
De Novo ◽  
Eukaryotic Dna ◽  
De Novo Methylation

scholarly journals Roles of Cell Division and Gene Transcription in the Methylation of CpG Islands

1999 ◽  
Vol 19 (10) ◽  
pp. 6690-6698 ◽  
Author(s):  
Christina M. Bender ◽  
Mark L. Gonzalgo ◽  
Felicidad A. Gonzales ◽  
Carvell T. Nguyen ◽  
Keith D. Robertson ◽  
...  
Keyword(s):  
Cell Division ◽  
Gene Transcription ◽  
De Novo ◽  
Cpg Island ◽  
Cpg Islands ◽  
Exon 2 ◽  
T24 Cells ◽  
The Relationship ◽  
Kinetics Of ◽  
De Novo Methylation

ABSTRACT De novo methylation of CpG islands within the promoters of eukaryotic genes is often associated with their transcriptional repression, yet the methylation of CpG islands located downstream of promoters does not block transcription. We investigated the kinetics of mRNA induction, demethylation, and remethylation of the p16promoter and second-exon CpG islands in T24 cells after 5-aza-2′-deoxycytidine (5-Aza-CdR) treatment to explore the relationship between CpG island methylation and gene transcription. The rates of remethylation of both CpG islands were associated with time but not with the rate of cell division, and remethylation of thep16 exon 2 CpG island occurred at a higher rate than that of the p16 promoter. We also examined the relationship between the remethylation of coding sequence CpG islands and gene transcription. The kinetics of remethylation of the p16exon 2, PAX-6 exon 5, c-ABL exon 11, andMYF-3 exon 3 loci were examined following 5-Aza-CdR treatment because these genes contain exonic CpG islands which are hypermethylated in T24 cells. Remethylation occurred most rapidly in the p16, PAX-6, and c-ABL genes, shown to be transcribed prior to drug treatment. These regions also exhibited higher levels of remethylation in single-cell clones and subclones derived from 5-Aza-CdR-treated T24 cells. Our data suggest that de novo methylation is not restricted to the S phase of the cell cycle and that transcription through CpG islands does not inhibit their remethylation.

scholarly journals DNA methylation associated with repeat-induced point mutation in Neurospora crassa.

1995 ◽  
Vol 15 (10) ◽  
pp. 5586-5597 ◽  
Author(s):  
M J Singer ◽  
B A Marcotte ◽  
E U Selker
Keyword(s):  
Dna Methylation ◽  
Neurospora Crassa ◽  
Point Mutation ◽  
Cytosine Methylation ◽  
De Novo ◽  
Sexual Cycle ◽  
Cpg Dinucleotides ◽  
Maintenance Methylation ◽  
De Novo Methylation ◽  
Repeat Induced Point Mutation

Repeat-induced point mutation (RIP) is a process that efficiently detects DNA duplications prior to meiosis in Neurospora crassa and peppers them with G:C to A:T mutations. Cytosine methylation is typically associated with sequences affected by RIP, and methylated cytosines are not limited to CpG dinucleotides. We generated and characterized a collection of methylated and unmethylated amRIP alleles to investigate the connection(s) between DNA methylation and mutations by RIP. Alleles of am harboring 84 to 158 mutations in the 2.6-kb region that was duplicated were heavily methylated and triggered de novo methylation when reintroduced into vegetative N. crassa cells. Alleles containing 45 and 56 mutations were methylated in the strains originally isolated but did not become methylated when reintroduced into vegetative cells. This provides the first evidence for de novo methylation in the sexual cycle and for a maintenance methylation system in Neurospora cells. No methylation was detected in am alleles containing 8 and 21 mutations. All mutations in the eight primary alleles studied were either G to A or C to T, with respect to the coding strand of the am gene, suggesting that RIP results in only one type of mutation. We consider possibilities for how DNA methylation is triggered by some sequences altered by RIP.

scholarly journals Dynamics of Viral RNA Synthesis during Measles Virus Infection

2005 ◽  
Vol 79 (11) ◽  
pp. 6900-6908 ◽  
Author(s):  
Sébastien Plumet ◽  
W. Paul Duprex ◽  
Denis Gerlier
Keyword(s):  
Measles Virus ◽  
Rna Synthesis ◽  
De Novo ◽  
Reference Model ◽  
Viral Rna ◽  
De Novo Synthesis ◽  
A Cell ◽  
Nucleoprotein N ◽  
Kinetics Of

ABSTRACT We propose a reference model of the kinetics of a viral RNA-dependent RNA polymerase (vRdRp) activities and its regulation during infection of eucaryotic cells. After measles virus infects a cell, mRNAs from all genes immediately start to accumulate linearly over the first 5 to 6 h and then exponentially until ∼24 h. The change from a linear to an exponential accumulation correlates with de novo synthesis of vRdRp from the incoming template. Expression of the virus nucleoprotein (N) prior to infection shifts the balance in favor of replication. Conversely, inhibition of protein synthesis by cycloheximide favors the latter. The in vivo elongation speed of the viral polymerase is ∼3 nucleotides/s. A similar profile with fivefold-slower kinetics can be obtained using a recombinant virus expressing a structurally altered polymerase. Finally, virions contain only encapsidated genomic, antigenomic, and 5′-end abortive replication fragment RNAs.

Primary DNA sequence determines sites of maintenance and de novo methylation by mammalian DNA methyltransferases

1986 ◽  
Vol 6 (4) ◽  
pp. 1135-1140
Author(s):  
A H Bolden ◽  
C M Nalin ◽  
C A Ward ◽  
M S Poonian ◽  
A Weissbach
Keyword(s):  
Dna Sequence ◽  
Dna Methyltransferase ◽  
De Novo ◽  
Dna Methyltransferases ◽  
Methylation Pattern ◽  
Complementary Strand ◽  
Target Strand ◽  
Enzymatic Methylation ◽  
Maintenance Methylation ◽  
De Novo Methylation

Analysis of the enzymatic methylation of oligodeoxynucleotides containing multiple C-G groups showed that hemimethylated sites in duplex oligomers are not significantly methylated by human or murine DNA methyltransferase unless those sites are capable of being methylated de novo in the single- or double-stranded oligomers. Thus, the primary sequence of the target strand, rather than the methylation pattern of the complementary strand, determines maintenance methylation. This suggests that de novo and maintenance methylation are the same process catalyzed by the same enzyme. In addition, the study revealed that complementary strands of oligodeoxynucleotides are methylated at different rates and in different patterns. Both primary DNA sequence and the spacing between C-G groups seem important since in one case studied, maximal methylation required a specific spacing of 13 to 17 nucleotides between C-G pairs.

scholarly journals Inheritance of DNA methylation in Coprinus cinereus.

1986 ◽  
Vol 6 (1) ◽  
pp. 195-200 ◽  
Author(s):  
M E Zolan ◽  
P J Pukkila
Keyword(s):  
Dna Methylation ◽  
Life Cycle ◽  
Homologous Chromosome ◽  
De Novo ◽  
Coprinus Cinereus ◽  
De Novo Methylation

We examined the inheritance of 5-methylcytosine residues at a centromere-linked locus in the basidiomycete Coprinus cinereus. Although methylated and unmethylated tracts were inherited both mitotically and meiotically the lengths of these tracts were variable. This variation was not confined to any one phase of the life cycle of the organism, and it usually involved the simultaneous de novo methylation of at least four HpaII-MspI sites. We also found that the higher levels of methylation at this locus were transmitted through meiosis, regardless of the level of methylation of the homologous chromosome.

scholarly journals Methylation Patterns of Papillomavirus DNA, Its Influence on E2 Function, and Implications in Viral Infection

2003 ◽  
Vol 77 (23) ◽  
pp. 12450-12459 ◽  
Author(s):  
Kitai Kim ◽  
Peggy A. Garner-Hamrick ◽  
Chris Fisher ◽  
Denis Lee ◽  
Paul F. Lambert
Keyword(s):  
Life Cycle ◽  
De Novo ◽  
Biological Activities ◽  
Methylation Status ◽  
Host Cells ◽  
Long Control Region ◽  
Global Methylation ◽  
Cpg Dinucleotides ◽  
Differentiation Status ◽  
De Novo Methylation

ABSTRACT The biological activities of the papillomavirus E2 protein in transcription, replication, and maintenance of the papillomavirus genome rely on the E2 protein's ability to bind that genome specifically. The E2 binding sites (E2BSs), located within the long control region (LCR) of human papillomavirus (HPV) genomes, contain potential sites for 5′methylation at cytosine (CpG) residues. The E2 protein's capacity to bind E2BS in vitro is inhibited by methylation of these cytosines (59). Herein, we describe experiments to assess the influence of methylation on E2 function in cells. E2's ability to activate transcription was inhibited by the global methylation of CpG dinucleotides in E2-responsive transcriptional templates or when only the CpG dinucleotides within the E2BSs of a transcriptional template were methylated. Thus at least one biological activity of E2 that is dependent on its ability to bind DNA in a site-specific manner is influenced by the methylation status of its cognate binding site. The activity of DNA methylases is influenced by the differentiation status of mammalian cells. The life cycle of HPVs is tied to the differentiation of its host cells within stratified squamous epithelia. To investigate whether methylation of the papillomavirus genomes is influenced by the differentiation status of host epithelial cells, we analyzed HPV16 DNA harvested from a cervical epithelial cell line that was isolated from an HPV16-infected patient. We found, using bisulfite treatment to discriminate between methylated and unmethylated cytosines, that the HPV16 LCR was selectively hypomethylated in highly differentiated cell populations. In contrast, the HPV16 LCR from poorly differentiated, basal cell-like cells contained multiple methylated cytosines and were often methylated at E2BSs, particularly E2BS2. These experiments indicate that the methylation state of the viral genome, and particular that of E2BSs, may vary during the viral life cycle, providing a novel means for modulating E2 function. These studies also uncovered an extensive pattern of methylation at non-CpG dinucleotides indicative of de novo methylation. The potential implications of this de novo methylation pattern are discussed.

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