Journal: Nucleic Acids Research

Article Title: Transient DNMT1 suppression reveals hidden heritable marks in the genome

doi: 10.1093/nar/gku1386

Figure Lengend Snippet: Modeling the major DNA methylation transition in early embryos using embryonic stem cells. ( A ) Inactivation of DNMT1 in Dnmt1 tet/tet ES cells generates a genome wide phase of passive demethylation (purple line) by preventing the methylation maintenance process. Using this ES cell model, we predict that heritable imprinted marks (gDMDs) will lose their methylation following suppression of DNMT1 and not recover their original levels upon reactivation of DNMT1. We also predict that regions of the genome will maintain variable levels of DNA methylation in the absence of DNMT1. We expect that soon after DNMT1 re-expression, methylation levels in most regions of the genome will recover their original levels (green and gray line), exposing regions that do not recover their methylation (orange line). ( B ) In the course of inhibition of Dnmt1 expression by doxycycline in Dnmt1 tet/tet ES cells (red dotted line), DNMT1 (blue line) protein was undetectable after 3 days . Subsequent to Dnmt1 reactivation (green dotted line), DNMT1 protein levels returned to initial levels after 2 days (blue line). (C–E) DNA methylation of repeat sequences and imprinted genes following the depletion and re-expression of Dnmt1 in Dnmt1 tet/tet ES cells after 21 days. Methylation levels are shown as average methylation ± SD (control ( n = 5) versus d21 ( n = 6)). Methylation levels were also quantified from d0 to d14 ( n = 2) in order to visualize how methylation patterns were restored following the reactivation of Dnmt1 (C and D). ( C ) Repeat sequences (LINE-1, IAP, SINE) were able to regain most or all of their original methylation levels following the reactivation of Dnmt1 . ( D ) Germline-DMDs (gDMDs) of imprinted genes ( H19, Plag1, Gnas ) did not recover methylation following the reactivation of Dnmt1 . ( E ) Levels of methylation at individual CpG sites in specific imprinted gene ( Peg13, Mest, Kcnq1 ) gDMDs showed similar levels across a number of CpGs. (C–E) Quantified by Sequenom MassArray. Control versus d21 Dnmt1 tet/tet ES cells: *** P < 0.005, ** P < 0.01. See also Supplementary Figures S1 and S2.

Article Snippet: Using quantitative Sequenom MassArray, the methylation status of various REs (LINE-1, IAP, SINE, Minor Satellite and Gamma Satellite) was determined before and following the pharmacological inactivation of Dnmt1 in our ES cell reprogramming model (Figure and ).

Techniques: DNA Methylation Assay, Genome Wide, Methylation, Expressing, Inhibition, Control

Journal: Nucleic Acids Research

Article Title: Transient DNMT1 suppression reveals hidden heritable marks in the genome

doi: 10.1093/nar/gku1386

Figure Lengend Snippet: Regions identified by a combination of MCIp enrichment and array hybridization revealing loss of DNA methylation following the inactivation and reactivation of Dnmt1 in the Dnmt1 tet/tet ES cells. ( A ) Characteristics of top array probes revealing loss of methylation at d21 versus control Dnmt1 tet/tet ES cells. ( B ) Hypomethylated regions quantitatively analyzed for CpG methylation levels. Methylation levels are shown as averages ± SD, Ctrl ( n = 5) versus d21 ( n = 6). Levels of methylation at single CpGs were quantified by Sequenom MassArray. Control versus d21 Dnmt1 tet/tet ES cells: *** P < 0.005. See also Supplementary Figure S4 and Table S2.

Article Snippet: Using quantitative Sequenom MassArray, the methylation status of various REs (LINE-1, IAP, SINE, Minor Satellite and Gamma Satellite) was determined before and following the pharmacological inactivation of Dnmt1 in our ES cell reprogramming model (Figure and ).

Techniques: Hybridization, DNA Methylation Assay, Methylation, Control, CpG Methylation Assay

Journal: BMC Genetics

Article Title: DNA methylation of CpG sites in the chicken KLF7 promoter and Exon 2 in association with mRNA expression in abdominal adipose tissue and blood metabolic indicators

doi: 10.1186/s12863-020-00923-6

Figure Lengend Snippet: DNA methylation analysis of chicken KLF7 in adipose tissues. a . The CpG density of the genomic region of chicken KLF7 analyzed by CpGplot (Version 6.6.0). b . The CpG loci analyzed in the promoter and Exon 2. c . The levels of DNA methylation of CpG loci analyzed. d . The comparison of DNA methylation levels between the promoter and Exon 2. Asterisks indicate a significant difference between the promoter and Exon 2 (Student’s t test, *** P < 0.001)

Article Snippet: The methylation level of individual units was measured by Quantitative Methylation Analysis (MassARRAY EpiTYOER, Sequenom, San Diego, CA).

Techniques: DNA Methylation Assay, Comparison

Journal: BMC Genetics

Article Title: DNA methylation of CpG sites in the chicken KLF7 promoter and Exon 2 in association with mRNA expression in abdominal adipose tissue and blood metabolic indicators

doi: 10.1186/s12863-020-00923-6

Figure Lengend Snippet: Datasets characteristics of DNA methylation of chicken KLF7 in abdominal adipose tissues

Article Snippet: The methylation level of individual units was measured by Quantitative Methylation Analysis (MassARRAY EpiTYOER, Sequenom, San Diego, CA).

Techniques: DNA Methylation Assay

Journal: BMC Genetics

Article Title: DNA methylation of CpG sites in the chicken KLF7 promoter and Exon 2 in association with mRNA expression in abdominal adipose tissue and blood metabolic indicators

doi: 10.1186/s12863-020-00923-6

Figure Lengend Snippet: Association analysis of DNA methylation with KLF7 transcripts and blood metabolic indicators. a . The r value of the Spearman correlation analysis. b . The P value of the Spearman correlation analysis. c . The number of samples used in the Spearman correlation analysis. d . The regression analysis between the DNA methylation of PCpG6 and KLF7 transcripts in chicken adipose tissue

Article Snippet: The methylation level of individual units was measured by Quantitative Methylation Analysis (MassARRAY EpiTYOER, Sequenom, San Diego, CA).

Techniques: DNA Methylation Assay

Journal: BMC Genetics

Article Title: DNA methylation of CpG sites in the chicken KLF7 promoter and Exon 2 in association with mRNA expression in abdominal adipose tissue and blood metabolic indicators

doi: 10.1186/s12863-020-00923-6

Figure Lengend Snippet: Schematic representation of the relationship of DNA methylation, KLF7 transcripts, glycaemia and abdominal fat content in chicken. The negative associations marked red and blue were confirmed by the reference [ , ], respectively

Article Snippet: The methylation level of individual units was measured by Quantitative Methylation Analysis (MassARRAY EpiTYOER, Sequenom, San Diego, CA).

Techniques: DNA Methylation Assay

Journal: BMC Genetics

Article Title: DNA methylation of CpG sites in the chicken KLF7 promoter and Exon 2 in association with mRNA expression in abdominal adipose tissue and blood metabolic indicators

doi: 10.1186/s12863-020-00923-6

Figure Lengend Snippet: Oligonucleotides used in the current study

Article Snippet: The methylation level of individual units was measured by Quantitative Methylation Analysis (MassARRAY EpiTYOER, Sequenom, San Diego, CA).

Techniques: Methylation

Journal: Oncotarget

Article Title: DNA methylation promotes paired box 2 expression via myeloid zinc finger 1 in endometrial cancer

doi: 10.18632/oncotarget.12626

Figure Lengend Snippet: A. Bisulfite sequencing results showed fragment B1 (-764 to -447 bp) of the PAX2 promoter was hypermethylated in endometrial cancer cell lines and tissues: rows represent clones (10 for each sample), columns represent CpG sites. Black squares represent methylated CpGs, and white squares represent unmethylated CpGs. EEC: endometrial epithelial cell. EnCa: endometrial cancer. N: normal. B. MassARRAY results indicate that PAX2 was hypermethylated in endometrial cancer tissues compared with normal endometrial tissues. M1 is an amplicon of a 280-bp fragment from -723 bp to -443 bp; M2 is an amplicon of a 379-bp fragment from -468 bp to -89 bp. Hypermethylated CpG sites were centralized in the 5’ of M1 (CpG 1 to 7).

Article Snippet: The PCR annealing Tm was 56°C, and sample preparation was performed according to “Training Instructions for EpiTYPER Quantitative Methylation Analysis Using MassCLEAVE for MassARRAY” (Sequenom).

Techniques: Methylation Sequencing, Clone Assay, Methylation, Amplification