Journal: Cancers

Article Title: Impact of Physical Activity on DNA Methylation Signatures in Breast Cancer Patients: A Systematic Review with Bioinformatic Analysis

doi: 10.3390/cancers16173067

Figure Lengend Snippet: Effects of PA on DNA methylation patterns in BC populations. Table summarising the study design and results of interest from all selected articles that evaluated the effects of PA on DNA methylation signatures in BC patients. DNA methylation results are presented using the gene codes of the genes associated and/or affected by the PA-induced methylation changes reported by the original authors.

Article Snippet: The authors also analysed global DNA methylation in white blood cell DNA [ , ] using the luminometric methylation assay (LUMA), a quantitative measurement of genome-wide DNA methylation, as described by Bjornsson et al. [ ], and LINE-1, where four CpG sites in the promoter region of LINE-1 were assessed using a validated pyrosequencing-based methylation assay [ ].

Techniques: DNA Methylation Assay, Methylation, Control

Journal: Scientific Reports

Article Title: DNA methylation and hydroxymethylation analyses of the active LINE-1 subfamilies in mice

doi: 10.1038/s41598-017-14165-7

Figure Lengend Snippet: Pyrosequencing-based DNA methylation assay of the active LINE-1 subfamilies in mice. ( a ) Schematic representation of 5′-UTR of the active LINE-1 (TfI, A, and GfII) in mice, drawn from previous studies , . Designed primers and examined CpG sites are indicated. 5′-UTR of the active LINE-1 subfamilies generally consists of a variable number of monomers and truncated monomers as well as a nonmonomer region upstream of ORF1. Definitions of monomers and nonmonomers were determined previously , . Numbers in brackets indicate the total copy number of full length elements, and rough age of the subfamily . Myr, million years; ORF, open reading frame; F, forward primer; R, reverse primer; S, sequence primer. ( b ) Alignment of the nonmonomer sequences of TfI, A, and GfII. Nonconserved sequences among these subfamilies are highlighted in black. The analyzed CpGs within the nonmonomer sequences (TfI_CpG#1, TfI_CpG#2, A, and GfII_CpG#3) are boxed. Note that GfII_CpG#1 and GfII_CpG#2 are located in the truncated monomer sequence. ( c ) Agarose gel electrophoresis analysis of the PCR amplicons. The expected amplicon sizes of TfI, A, and GfII are 261 bp, 129 bp, and 244 bp, respectively. A 100-bp DNA ladder (TakaraBio) was used. Arrows indicate respective sizes of bands. ( d ) A representative pyrogram in pyrosequencing analysis (TfI_CpG#2). The pyrosequencing reaction starts with an input of enzyme (E) followed by substrates (S). The sequence after S is as listed as dispensation order in Table . The shaded site is the cytosine analyzed in this study.

Article Snippet: Figure 1 Pyrosequencing-based DNA methylation assay of the active LINE-1 subfamilies in mice. ( a ) Schematic representation of 5′-UTR of the active LINE-1 (TfI, A, and GfII) in mice, drawn from previous studies , .

Techniques: DNA Methylation Assay, Sequencing, Agarose Gel Electrophoresis, Amplification

Journal: Scientific Reports

Article Title: DNA methylation and hydroxymethylation analyses of the active LINE-1 subfamilies in mice

doi: 10.1038/s41598-017-14165-7

Figure Lengend Snippet: mC and hmC levels of the active LINE-1 subfamilies in the adult mouse brain regions. For TfI, two CpG sites located within the nonmonomer region; for A, one CpG site located within the nonmonomer region; and for GfII, three CpG sites (two located within the truncated monomer, and one within the nonmonomer region) were analyzed. Three samples were available for analysis for each CpG site, except for the samples indicated by # symbol, for which only two were available. Values are given as mean ± standard deviation. mC, DNA methylation; hmC, hydroxymethylation; FC, frontal cortex; Hp, hippocampus; Cb, cerebellum; BG, basal ganglia.

Article Snippet: Figure 1 Pyrosequencing-based DNA methylation assay of the active LINE-1 subfamilies in mice. ( a ) Schematic representation of 5′-UTR of the active LINE-1 (TfI, A, and GfII) in mice, drawn from previous studies , .

Techniques: Standard Deviation, DNA Methylation Assay

Journal: Scientific Reports

Article Title: DNA methylation and hydroxymethylation analyses of the active LINE-1 subfamilies in mice

doi: 10.1038/s41598-017-14165-7

Figure Lengend Snippet: mC and hmC levels of the active LINE-1 subfamilies in the brain and nonbrain tissues. The data from four brain regions were averaged and treated as a single tissue, Brain (AVE). Three samples were available for analysis for each CpG site, except for the samples indicated by # symbol, for which only two were available. Values are given as mean ± standard deviation. *Statistically significant (ANOVA followed by Tukey’s test, P < 0.05). mC, DNA methylation; hmC, hydroxymethylation.

Article Snippet: Figure 1 Pyrosequencing-based DNA methylation assay of the active LINE-1 subfamilies in mice. ( a ) Schematic representation of 5′-UTR of the active LINE-1 (TfI, A, and GfII) in mice, drawn from previous studies , .

Techniques: Standard Deviation, DNA Methylation Assay

Journal: Scientific Reports

Article Title: DNA methylation and hydroxymethylation analyses of the active LINE-1 subfamilies in mice

doi: 10.1038/s41598-017-14165-7

Figure Lengend Snippet: Correlation of actual mC levels between different two CpG sites. Pairs of ( a ) GfII_CpG#1 and GfII_CpG#2, and ( b ) A and GfII_CpG#3 were the only ones that showed significant correlations ( P < 0.05 after Bonferroni correction). Each symbol represents data from one individual tissue ( N = 12 for brain regions and N = 3 each for other tissues, except for the ovary tissue in GfII_CpG#3, for which only two were available). Symbols with * on the right corner indicate that two samples are overlapped on each other in the graph, because they showed the same DNA methylation levels.

Article Snippet: Figure 1 Pyrosequencing-based DNA methylation assay of the active LINE-1 subfamilies in mice. ( a ) Schematic representation of 5′-UTR of the active LINE-1 (TfI, A, and GfII) in mice, drawn from previous studies , .

Techniques: DNA Methylation Assay

Journal: Cancers

Article Title: Impact of Physical Activity on DNA Methylation Signatures in Breast Cancer Patients: A Systematic Review with Bioinformatic Analysis

doi: 10.3390/cancers16173067

Figure Lengend Snippet: Research queries used on each respective database.

Article Snippet: McCullough et al., 2015 (global) [ ] , Population-based-case–control study , Postmenopausal female first primary BC ( n = 1300) (20–98 years of age) , Blood sample , Postmenopausal RPA , LUMA global DNA methylation assay: LUMA Pyrosequencing-based methylation assay: LINE-1 , Global DNA methylation.

Techniques: Activity Assay, DNA Methylation Assay, Methylation

Journal: Cancers

Article Title: Impact of Physical Activity on DNA Methylation Signatures in Breast Cancer Patients: A Systematic Review with Bioinformatic Analysis

doi: 10.3390/cancers16173067

Figure Lengend Snippet: Effects of PA on DNA methylation patterns in BC populations. Table summarising the study design and results of interest from all selected articles that evaluated the effects of PA on DNA methylation signatures in BC patients. DNA methylation results are presented using the gene codes of the genes associated and/or affected by the PA-induced methylation changes reported by the original authors.

Article Snippet: McCullough et al., 2015 (global) [ ] , Population-based-case–control study , Postmenopausal female first primary BC ( n = 1300) (20–98 years of age) , Blood sample , Postmenopausal RPA , LUMA global DNA methylation assay: LUMA Pyrosequencing-based methylation assay: LINE-1 , Global DNA methylation.

Techniques: DNA Methylation Assay, Methylation, Control

Journal: Cancers

Article Title: Impact of Physical Activity on DNA Methylation Signatures in Breast Cancer Patients: A Systematic Review with Bioinformatic Analysis

doi: 10.3390/cancers16173067

Figure Lengend Snippet: Histograms showing the results of the functional pathway enrichment analysis, conducted using g:profiler, of the genes with a significantly modulated DNA methylation status due to PA in BC populations. ( A ) Top significantly enriched molecular functions, ( B ) top 25 significantly enriched biological processes, ( C ) top 25 significantly enriched Reactome pathways, ( D ) top significantly enriched KEEG pathways, ( E ) and top 25 significantly enriched tissues reflected by the Human Protein Atlas.

Article Snippet: McCullough et al., 2015 (global) [ ] , Population-based-case–control study , Postmenopausal female first primary BC ( n = 1300) (20–98 years of age) , Blood sample , Postmenopausal RPA , LUMA global DNA methylation assay: LUMA Pyrosequencing-based methylation assay: LINE-1 , Global DNA methylation.

Techniques: Functional Assay, DNA Methylation Assay

Journal: Cancers

Article Title: Impact of Physical Activity on DNA Methylation Signatures in Breast Cancer Patients: A Systematic Review with Bioinformatic Analysis

doi: 10.3390/cancers16173067

Figure Lengend Snippet: Hypothetical mechanisms underlying PA-induced DNA methylation. SAM, S-Adenosyl methionine; DNMTs, DNA methyltransferases; TET, ten-eleven translocation enzymes; ROS, reactive oxygen species; Nrf2, nuclear factor erythroid 2-related factor 2; TDG, thymine-DNA glycosylase.

Article Snippet: McCullough et al., 2015 (global) [ ] , Population-based-case–control study , Postmenopausal female first primary BC ( n = 1300) (20–98 years of age) , Blood sample , Postmenopausal RPA , LUMA global DNA methylation assay: LUMA Pyrosequencing-based methylation assay: LINE-1 , Global DNA methylation.

Techniques: DNA Methylation Assay, Translocation Assay