Mining the Selective Remodeling of DNA Methylation in Promoter Regions to Identify Robust Gene-Level Associations With Phenotype

Epigenetics is an essential biological frontier linking genetics to the environment, where DNA methylation is one of the most studied epigenetic events. In recent years, through the epigenome-wide association study (EWAS), researchers have identified thousands of phenotype-related methylation sites. However, the overlaps of identified phenotype-related DNA methylation sites between various studies are often quite small, and it might be due to the fact that methylation remodeling has a certain degree of randomness within the genome. Thus, the identification of robust gene-phenotype associations is crucial to interpreting pathogenesis. How to integrate the methylation values of different sites on the same gene and to mine the DNA methylation at the gene level remains a challenge. A recent study found that the DNA methylation difference of the gene body and promoter region has a strong correlation with gene expression. In this study, we proposed a Statistical difference of DNA Methylation between Promoter and Other Body Region (SIMPO) algorithm to extract DNA methylation values at the gene level. First, by choosing to smoke as an environmental exposure factor, our method led to significant improvements in gene overlaps (from 5 to 17%) between different datasets. In addition, the biological significance of phenotype-related genes identified by SIMPO algorithm is comparable to that of the traditional probe-based methods. Then, we selected two disease contents (e.g., insulin resistance and Parkinson’s disease) to show that the biological efficiency of disease-related gene identification increased from 15.43 to 44.44% (p-value = 1.20e–28). In summary, our results declare that mining the selective remodeling of DNA methylation in promoter regions can identify robust gene-level associations with phenotype, and the characteristic remodeling of a given gene’s promoter region can reflect the essence of disease.

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Mining the Selective Remodeling of DNA Methylation in Promoter Regions to Identify Robust Gene-Level Associations with Phenotype

10.1101/2020.01.05.895326 ◽

2020 ◽

Cited By ~ 1

Author(s):

Yuan Quan ◽

Fengji Liang ◽

Yuexing Zhu ◽

Ying Chen ◽

Ruifeng Xu ◽

...

Keyword(s):

Dna Methylation ◽

Promoter Region ◽

Biological Significance ◽

Biological Efficiency ◽

Body Region ◽

P Value ◽

Promoter Regions ◽

Exposure Factor ◽

Epigenetic Events ◽

Gene Level

AbstractEpigenetics is an essential biological frontier linking genetics to the environment, where DNA methylation is one of the most studied epigenetic events. In recent years, through the epigenome-wide association study (EWAS), researchers have identified thousands of phenotype-related methylation sites. However, the overlap between identified phenotype-related DNA methylation sites are often quite small, and it might clue to methylation remodeling has a certain degree of randomness within the genome. Thus, the identification of robust gene-phenotype associations is crucial for interpreting pathogenesis. How to integrate the methylation values of different sites on the same gene and to mining the DNA methylation at the gene level remains a challenge. A recent study found that the DNA methylation difference of the gene body and promoter region has a strong correlation with gene expression. In this study, we proposed a Statistical difference of DNA Methylation between Promoter and Other Body Region (SIMPO) algorithm to extract DNA methylation values at the gene level. First, by choosing to smoke as an environmental exposure factor, our method led to significant improvements in gene overlaps (from 5% to 17%) between different datasets. In addition, the biological significance of these genes (∼23%) are significantly better than those identified by traditional probe-based methods (∼18%, P-value = 5.18e-03). Then, we selected two disease content (e.g., insulin resistance and Parkinson’s disease) to show that the biological efficiency of disease-related gene identification increased from 15.43% to 44.44% (P-value = 1.20e-28). Thus, our results declare that mining the selective remodeling of DNA methylation in promoter regions can identify robust gene-level associations with phenotype, and the characteristic remodeling of a given gene’s promoter region can reflect the essence of disease.

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EGFR DNA Methylation Correlates With EGFR Expression, Immune Cell Infiltration, and Overall Survival in Lung Adenocarcinoma

Frontiers in Oncology ◽

10.3389/fonc.2021.691915 ◽

2021 ◽

Vol 11 ◽

Author(s):

Zhanyu Xu ◽

Fanglu Qin ◽

Liqiang Yuan ◽

Jiangbo Wei ◽

Yu Sun ◽

...

Keyword(s):

Dna Methylation ◽

Protein Expression ◽

Lung Adenocarcinoma ◽

Methylation Level ◽

Promoter Region ◽

Body Region ◽

Gene Body ◽

Immune Infiltration ◽

Cpg Sites ◽

Gene Body Region

BackgroundThe epidermal growth factor receptor (EGFR) is a primary target of molecular targeted therapy for lung adenocarcinoma (LUAD). The mechanisms that lead to epigenetic abnormalities of EGFR in LUAD are still unclear. The purpose of our study was to evaluate the abnormal methylation of EGFR CpG sites as potential biomarkers for LUAD.MethodsTo assess the differentially methylation CpG sites of EGFR in LUAD, we used an integrative study of Illumina HumanMethylation450K and RNA-seq data from The Cancer Genome Atlas (TCGA). We evaluated and compared EGFR multiple-omics data to explore the role of CpG sites located in EGFR promoter regions and gene body regions and the association with transcripts, protein expression levels, mutations, and somatic copy number variation. We calculated the correlation coefficients between CpG sites of EGFR and immune infiltration fraction (by MCPcounter and ESTIMATE) and immune-related pathways in LUAD. Finally, we validated the differential methylation of clinically and prognostically relevant CpG sites using quantitative methylation-specific PCR (qMSP).ResultsWe found that the methylation level of many EGFR CpGs in the promoter region was negatively correlated with the transcription level, protein expression, and SCNV, while the methylation at the gene body region was positively correlated with these features. The methylation level of EGFR CpGs in the promoter region was positively correlated with the level of immune infiltration and IFN-γ signature, while the opposite was found for methylation of the gene body region. The qMSP results showed that cg02316066 had a high methylation level, while cg02166842 had a low methylation level in LUAD. There was a high degree of co-methylation between cg02316066 and cg03046247.ConclusionOur data indicate that EGFR is an epigenetic regulator in LUAD acting through DNA methylation. Our research provides a theoretical basis for the further detection of EGFR DNA methylation as a predictive biomarker for LUAD survival and immunotherapy.

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Deficiency in Vitamin B12 and Ferritin Is Associated With Epigenetic Alterations in Cancer Patients

10.21203/rs.3.rs-251474/v1 ◽

2021 ◽

Author(s):

Khaled A. Elawdan ◽

Sabah Farouk ◽

Salah Araf ◽

Hany Khalil

Keyword(s):

Dna Methylation ◽

Vitamin B12 ◽

Cancer Patients ◽

Promoter Region ◽

Dna Methyltransferases ◽

Epigenetic Alterations ◽

Promoter Regions ◽

Methylation Sensitive Restriction Enzyme ◽

Low Levels ◽

Dna Methylation Analysis

Abstract Background: Cancer is the second-leading cause of death worldwide, caused by several mutations in DNA within the cells including epigenetic alteration. The epigenetic changes are external modifications to the DNA that switch “on” or “off” gene expression. The present study was conducted to investigate the epigenetic modifications and its correlation with the levels of vitamin B12 and ferritin in cancer patients with hepatocellular carcinoma (HCC), breast cancer (BC), lung cancer (LC), or colon cancer (CC). Methods and Results: A total of 200 blood samples were obtained from cancer patients and healthy individuals. The relative expression of DNA methyltransferases (DNMTs), Ten-Eleven translocation (TET), and methionine synthase (MS) was evaluated in patients with the normal level of vitamin B12/ferritin and patients with the deficient levels of them. DNA methylation within the promoter regions was investigated of each indicated genes using the methylation-sensitive restriction enzyme HpaII and bisulfite PCR. Interestingly, the expression of DNMT1, DNMT3a, and DNMT3b was increased in patients with low levels of vitamin B12 and ferritin, while the expression of MS, TET1, and TET3 was significantly decreased. DNA methylation analysis in patients with deficient levels of vitamin B12/ferritin showed a methylated-cytosine within the location 318/CG and 385/CG in the promoter region of TET1 and TET3, respectively. Moreover, the bisulfite PCR assay further confirmed the methylation changes in the promoter region of TET1 and TET3 at the indicated locations. Conclusion: These data indicate that the deficiency in vitamin B12 and ferritin in cancer patients plays a key role in the epigenetic exchanges during cancer development.

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A role for poly(ADP-ribosyl)ation in DNA methylation

Biochemistry and Cell Biology ◽

10.1139/o03-050 ◽

2003 ◽

Vol 81 (3) ◽

pp. 197-208 ◽

Cited By ~ 10

Author(s):

Giuseppe Zardo ◽

Anna Reale ◽

Giovanna De Matteis ◽

Serena Buontempo ◽

Paola Caiafa

Keyword(s):

Dna Methylation ◽

Gene Silencing ◽

Control Mechanism ◽

Epigenetic Modification ◽

Housekeeping Genes ◽

Promoter Regions ◽

Epigenetic Events ◽

Aberrant Dna Methylation ◽

Methylation Patterns ◽

Histone Methylation And Acetylation

The aberrant DNA methylation of promoter regions of housekeeping genes leads to gene silencing. Additional epigenetic events, such as histone methylation and acetylation, also play a very important role in the definitive repression of gene expression by DNA methylation. If the aberrant DNA methylation of promoter regions is the starting or the secondary event leading to the gene silencing is still debated. Mechanisms controlling DNA methylation patterns do exist although they have not been ultimately proven. Our data suggest that poly(ADP-ribosyl)ation might be part of this control mechanism. Thus an additional epigenetic modification seems to be involved in maintaining tissue and cell-type methylation patterns that when formed during embryo development, have to be rigorously conserved in adult organisms.Key words: DNA methylation, chromatin, poly(ADP-ribosyl)ation.

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Association of Breastfeeding Duration with Susceptibility to Allergy, Influenza, and Methylation Status of TLR1 Gene

Medicina ◽

10.3390/medicina55090535 ◽

2019 ◽

Vol 55 (9) ◽

pp. 535

Author(s):

Ma’mon M. Hatmal ◽

Nada N. Issa ◽

Walhan Alshaer ◽

Hamzeh J. Al-Ameer ◽

Omar Abuyaman ◽

...

Keyword(s):

Dna Methylation ◽

Promoter Region ◽

Methylation Status ◽

Breastfeeding Duration ◽

Toll Like Receptor ◽

Chain Reaction ◽

Blood Samples ◽

Three Samples ◽

Gene Level ◽

Polymerase Chain

Background and Objectives: This study aimed to investigate the possible association between exclusive breastfeeding duration during early infancy and susceptibility to allergy and influenza in adulthood. Furthermore, we also investigated the association of breastfeeding duration with DNA methylation at two sites in the promoter of the toll-like receptor-1 (TLR1) gene, as well as the association between DNA methylation of the toll-like receptor-1 (TLR1) gene and susceptibility to different diseases. Materials and Methods: Blood samples were collected from 100 adults and classified into two groups according to breastfeeding duration (<6 months and ≥6 months) during infancy. Subjects were asked to complete a questionnaire on their susceptibilities to different diseases and sign a consent form separately. Fifty-three samples underwent DNA extraction, and the DNA samples were divided into two aliquots, one of which was treated with bisulfite reagent. The promoter region of the TLR1 gene was then amplified by polymerase chain reaction (PCR) and sequenced. Results: We found a significant association between increased breastfeeding duration and a reduction in susceptibility to influenza and allergy, as well asa significant reduction in DNA methylation within the promoter of the TLR1 gene. No association was found between DNA methylation and susceptibility to different diseases. Conclusions: The findings demonstrate the significance of increased breastfeeding duration for improved health outcomes at the gene level.

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DNA methylation subpatterns at distinct regulatory regions in human early embryos

Open Biology ◽

10.1098/rsob.180131 ◽

2018 ◽

Vol 8 (10) ◽

pp. 180131 ◽

Cited By ~ 5

Author(s):

Rongsong Luo ◽

Chunling Bai ◽

Lei Yang ◽

Zhong Zheng ◽

Guanghua Su ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Correlation Analysis ◽

Promoter Region ◽

Promoter Regions ◽

Regulate Gene Expression ◽

Early Embryos ◽

Candidate Promoter ◽

Single Base Resolution ◽

Genomic Regions

DNA methylation has been investigated for many years, but recent technologies have allowed for single-cell- and single-base-resolution DNA methylation datasets and more accurate assessment of DNA methylation dynamics at the key genomic regions that regulate gene expression in human early embryonic development. In this study, the region from upstream 20 kb to downstream 20 kb of RefSeq gene was selected and divided into 12 distinct regions (up20, up10, up5, up2, 5'UTR, exon, intron, 3'UTR, down2, down5, down10 and down20). The candidate promoter region (TSS ± 2 kb) was further divided into 20 consecutive subregions, which were termed ‘bins’. The DNA methylation dynamics of these regions were systematically analysed along with their effects on gene expression in human early embryos. The dynamic DNA methylation subpatterns at the distinct genomic regions with a focus on promoter regions were mapped. For the 12 distinct genomic regions, up2 and 5'UTR had the lowest DNA methylation levels, and their methylation dynamics were different with other regions. The region 3'UTR had the highest DNA methylation levels, and the correlation analysis with gene expression proved that it was a feature of transcribed genes. For the 20 bins in promoter region, the CpG densities showed a normal distribution pattern, and the trend of the methylated CpG counts was inverse with the DNA methylation levels, especially for the bin 1 (downstream 200 bp of the TSS). Through the correlation analysis between DNA methylation and gene expression, the current study finally revealed that the region bin −4 to 6 (800 bp upstream to 1200 bp downstream of the TSS) was the best candidate for the promoter region in human early embryos, and bin 1 was the putative key regulator of gene activity. This study provided a global and high-resolution view of DNA methylation subpatterns at the distinct genomic regions in human early embryos.

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Association of Aberrant DNA Methylation Level in the CD4 and JAK-STAT-Pathway-Related Genes with Mastitis Indicator Traits in Chinese Holstein Dairy Cattle

Animals ◽

10.3390/ani12010065 ◽

2021 ◽

Vol 12 (1) ◽

pp. 65

Author(s):

Tahir Usman ◽

Nawab Ali ◽

Yachun Wang ◽

Ying Yu

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Dairy Cattle ◽

Methylation Level ◽

Promoter Region ◽

Promoter Regions ◽

Cpg Sites ◽

Cell Counts ◽

Aberrant Dna Methylation ◽

Stat Pathway

The present study was designed to evaluate the gene expression and DNA methylation level in the promoter region of the CD4 and the JAK-STAT-pathway-related genes. A total of 24 samples were deployed in the gene expression and 118 samples were used in the DNA methylation study. Student’s t-tests were used to analyze the gene expression and DNA methylation. The evaluation of DNA methylation in promoter regions of JAK2 and STAT5A revealed hypo-methylation levels of CpG sites and higher gene expression in cows diagnosed with mastitis as compared to the healthy control, and vice versa in those with CD4. DNA methylation was negatively correlated with gene expression in JAK2, STAT5A, and CD4 genes. Six, two, and four active transcription factors were identified on the CpG sites in the promoter regions of JAK2, STAT5A, and CD4 genes, respectively. Regarding correlation analysis, the DNA methylation levels of CD4 showed significantly higher positive correlations with somatic cell counts (p < 0.05). Findings of the current study inferred that aberrant DNA methylation in the CpG sites at the 1 kb promoter region in JAK2, STAT5A, and CD4 genes due to mastitis in cows can be used as potential epigenetic markers to estimate bovine mastitis susceptibility in dairy cattle.

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Deficiency in vitamin B12 and ferritin is associated with epigenetic alterations in cancer patients

10.21203/rs.3.rs-249193/v1 ◽

2021 ◽

Author(s):

Khaled A. Elawdan ◽

Sabah Farouk ◽

Salah Araf ◽

Hany Khalil

Keyword(s):

Dna Methylation ◽

Vitamin B12 ◽

Cancer Patients ◽

Promoter Region ◽

Dna Methyltransferases ◽

Epigenetic Alterations ◽

Promoter Regions ◽

Methylation Sensitive Restriction Enzyme ◽

Low Levels ◽

Dna Methylation Analysis

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Induction of IGFBP-1 Expression by cAMP Is Associated with Histone Acetylation Status of the Promoter Region in Human Endometrial Stromal Cells

Endocrinology ◽

10.1210/en.2012-1420 ◽

2012 ◽

Vol 153 (11) ◽

pp. 5612-5621 ◽

Cited By ~ 31

Author(s):

Isao Tamura ◽

Hiromi Asada ◽

Ryo Maekawa ◽

Manabu Tanabe ◽

Lifa Lee ◽

...

Keyword(s):

Dna Methylation ◽

Histone Acetylation ◽

Stromal Cells ◽

Promoter Region ◽

Binding Protein ◽

Methylation Status ◽

Cell Types ◽

Promoter Regions ◽

Endometrial Stromal Cells ◽

Acetylation Status

Abstract Many genes are up- or down-regulated in human endometrial stromal cells (ESCs) undergoing decidualization. IGF-binding protein-1 (IGFBP-1) and prolactin (PRL) are preferentially expressed during decidualization and are recognized as specific markers of decidualization. This study investigated the involvement of epigenetic mechanisms in the regulation of IGFBP-1 and PRL induction by decidualization in ESCs. ESCs isolated from the proliferative phase endometrium were incubated with cAMP to induce decidualization. Human dermal fibroblasts (HDFs) were used as a nonendometrial control. cAMP induced the expressions of both genes in ESCs but induced the expression of only PRL in HDFs. Histone acetylation levels of the IGFBP-1 promoter region evaluated by chromatin immunoprecipitation assay were higher in ESCs than in HDFs. The IGFBP-1 promoter regions in the two cell types showed similar levels of DNA hypomethylation. The histone acetylation levels and DNA methylation status of the PRL promoter and enhancer regions were similar in the two cell types. cAMP had no significant effects on the histone acetylation levels and DNA methylation status of the IGFBP-1 promoter and the PRL promoter and enhancer regions in ESCs. Cotreatment of HDF with cAMP and histone deacetylase inhibitors induced IGFBP-1 expression, which was accompanied by an increased histone acetylation level and recruitment of CCAAT/enhancer-binding protein-β to the promoter region. These results show that, during decidualization in ESCs, high histone acetylation status of the promoter regions of IGFBP-1 and PRL is associated with the induction of the IGFBP-1 and PRL genes by making the promoter regions accessible to transcriptional factors.

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Exposure to PM2.5 during pregnancy or lactation increases methylation while reducing the expression of Pdx1 and NEUROG3 in mouse pancreatic islets

10.1101/852509 ◽

2019 ◽

Author(s):

Raquel Patricia Ataíde Lima ◽

Vitor Ferreira Boico ◽

Guilherme Francisco Peruca ◽

Kellen Cristina da Cruz Rodrigues ◽

Victor Yuji Yariwake ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Air Pollution ◽

Pancreatic Islets ◽

Promoter Region ◽

Negative Impact ◽

Expression Patterns ◽

Maternal Exposure ◽

Promoter Regions ◽

Mouse Pancreatic Islets

ABSTRACTAir pollution is comprised of several substances, including particulate matter (PM). Exposure to air pollution may trigger alterations in DNA methylation thus modifying gene expression patterns. This phenomenon is likely to mediate the relationship between exposure to air pollution and adverse health effects. The purpose of this study was analyzing the effects of exposure to PM2.5 during pregnancy or lactation and whether it would cause multigenerational epigenetic alterations in the promoter region of the genes Pdx1 and NEUROG3 within mouse pancreatic islets. Our results show that maternal exposure to PM2.5 led to an elevation in blood glucose levels within the two following generations (F1 and F2). There was also an increase in DNA methylation in the aforementioned promoter regions accompanied by reduced gene expression in generations F1 and F2 upon F0 exposure to PM2.5 during pregnancy. These data suggest that maternal exposure to PM2.5 from air pollution, particularly during pregnancy, may lead to a multigenerational and lifelong negative impact on glucose homeostasis mediated by an increase in DNA methylation within the promoter region of the genes Pdx1 and NEUROG3 in pancreatic islets.

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