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

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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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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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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Correlation Patterns Between DNA Methylation and Gene Expression in The Cancer Genome Atlas

Cancer Informatics ◽

10.1177/1176935119828776 ◽

2019 ◽

Vol 18 ◽

pp. 117693511982877 ◽

Cited By ~ 28

Author(s):

John CG Spainhour ◽

Hong Seo Lim ◽

Soojin V Yi ◽

Peng Qiu

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Promoter Region ◽

The Cancer Genome Atlas ◽

Gene Body ◽

Cpg Sites ◽

Cpg Site ◽

Cancer Genome Atlas ◽

Genome Atlas

Background: DNA methylation is a form of epigenetic modification that has been shown to play a significant role in gene regulation. In cancer, DNA methylation plays an important role by regulating the expression of oncogenes. The role of DNA methylation in the onset and progression of various cancer types is now being elucidated as more large-scale data become available. The Cancer Genome Atlas (TCGA) provides a wealth of information for the analysis of various molecular aspects of cancer genetics. Gene expression data and DNA methylation data from TCGA have been used for a variety of studies. A traditional understanding of the effects of DNA methylation on gene expression has linked methylation of CpG sites in the gene promoter region with the decrease in gene expression. Recent studies have begun to expand this traditional role of DNA methylation. Results: Here we present a pan-cancer analysis of correlation patterns between CpG methylation and gene expression. Using matching patient data from TCGA, 33 cancer-specific correlations were calculated for each CpG site and the expression level of its corresponding gene. These correlations were used to identify patterns on a per-site basis as well as patterns of methylation across the gene body. Using these identified patterns, we found genes that contain conflicting methylation signals beyond the commonly accepted association between the promoter region methylation and silencing of gene expression. Beyond gene body methylation in whole, we examined individual CpG sites and show that, even in the same gene body, some sites can have a contradictory effect on gene expression in cancers. Conclusions: We observed that within promoter regions there was a substantial amount of positive correlation between methylation and gene expression, which contradicts the commonly accepted association. We observed that the correlation between CpG methylation and gene expression does not exhibit in a tissue-specific manner, suggesting that the effects of methylation on gene expression are largely tissue independent. The analysis of correlation associated with the location of the CpG site in the gene body has led to the identification of several different methylation patterns that affect gene expression, and several examples of methylation activating gene expression were observed. Distinctly opposing or conflicting effects were seen in close proximity on the gene body, where negative and positive correlations were seen at the neighboring CpG sites.

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Aberrant DNA Methylation-Mediated FOXF2 Dysregulation Is a Prognostic Risk Factor for Gastric Cancer

Frontiers in Molecular Biosciences ◽

10.3389/fmolb.2021.645470 ◽

2021 ◽

Vol 8 ◽

Author(s):

Cheng Zhang ◽

Yong-Zhi Li ◽

Dong-Qiu Dai

Keyword(s):

Gastric Cancer ◽

Dna Methylation ◽

Western Blot ◽

Methylation Level ◽

Promoter Region ◽

Target Genes ◽

Risk Group ◽

Rna Seq ◽

Qrt Pcr ◽

Aberrant Dna Methylation

Background: The prognosis of gastric cancer (GC) patients is poor. The effect of aberrant DNA methylation on FOXF2 expression and the prognostic role of FOXF2 methylation in GC have not yet been identified.Methods: The RNA-Seq and gene methylation HM450 profile data were used for analyzing FOXF2 expression in GC and its association with methylation level. Bisulfite sequencing PCR (BSP) was performed to measure the methylation level of the FOXF2 promoter region in GC cell lines and normal GES-1 cells. The cells were treated with the demethylation reagent 5-Aza-dC, and the mRNA and protein expression levels of FOXF2 were then measured by qRT-PCR and western blot assays. The risk score system from SurvivalMeth was calculated by integrating the methylation level of the cg locus and the corresponding Cox regression coefficient.Results: FOXF2 was significantly downregulated in GC cells and tissues. On the basis of RNA-Seq and Illumina methylation 450 data, FOXF2 expression was significantly negatively correlated with the FOXF2 methylation level (Pearson’s R = −0.42, p < 2.2e−16). The FOXF2 methylation level in the high FOXF2 expression group was lower than that in the low FOXF2 expression group. The BSP assay indicated that the methylation level of the FOXF2 promoter region in GC cell lines was higher than that in GES-1 cells. The qRT-PCR and western blot assay showed that FOXF2 mRNA and protein levels were increased in GC cells following treatment with 5-Aza-Dc. The methylation risk score model indicated that patients in the high risk group had poorer survival probability than those in the low risk group (HR = 1.84 (1.11–3.07) and p = 0.0068). FOXF2 also had a close transcriptional regulation network with four miRNAs and their corresponding target genes. Functional enrichment analysis of the target genes revealed that these genes were significantly related to several important signaling pathways.Conclusion: FOXF2 was downregulated due to aberrant DNA methylation in GC, and the degree of methylation in the promoter region of FOXF2 was related to the prognosis of patients. The FOXF2/miRNAs/target genes axis may play a vital biological regulation role in GC.

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223 ABERRENT TIMP-2 GENE EXPRESSION IN CLONED BOVINE NEONATAL PLACENTA IS DUE TO ABNORMAL EPIGENETIC MODIFICATIONS

Reproduction Fertility and Development ◽

10.1071/rdv17n2ab223 ◽

2005 ◽

Vol 17 (2) ◽

pp. 262

Author(s):

H.R. Kim ◽

J.K. Kang ◽

J.T. Yoon ◽

J.K. Jung ◽

H.H. Seong ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Histone Modification ◽

Promoter Region ◽

Tissue Remodeling ◽

Protein Patterns ◽

Cpg Sites ◽

Cloned Bovine ◽

Actin Protein ◽

Normal Placenta

A global proteomics approach by 2-D gel electrophoresis and mass spectrometry was used to analyze the differential protein patterns of three placentae obtained after postnatal death of fetuses from SCNT of Korean Native cattle and three normal placentae obtained after birth of AI fetuses, as previously reported (Kim et al. 2004 Reprod. Fertil. Develop. 16, 145). One differentially up-regulated proteins in SCNT placenta was identified as TIMP-2 protein that is related to extracellular matrix degradation and tissue remodeling processes. To ensure that the identified protein was truly up-regulated in SCNT placenta, a small portion of the protein lysates were subjected to Western blotting with the antibodies against TIMP-2 and β-actin protein. Band images were scanned with a GT-6000 Scanner (Epson-Seiko, Suwa, Nagano, Japan) and densitometric analyses were performed using NIH Image (version 1.56). Proteins were normalized against the levels of β-actin protein. Indeed, Western blot analysis revealed a significant increase in TIMP-2 protein level (about 5-fold) in SCNT placenta compared with normal. Epigenetic programming of the genome by DNA methylation and histone modification ensures proper gene expression during development. To examine how the TIMP-2 gene was programmed to be active in SCNT placenta, we first investigated the status of DNA methylation in the promoter region of the TIMP-2 gene. Sodium bisulfite mapping revealed that most CpG sites in SCNT placenta cells were unmethylated in agreement with expression of TIMP-2 compared with those in normal placenta cells, suggesting that TIMP-2 gene programming by hypomethylation of CpG sites in the promoter region was responsible for the expression in SCNT placenta. We then examined histone modification of the nucleosome in the coding region of the TIMP-2 gene of SCNT placenta cells and normal placenta cells. Chromatin immunoprecipitation (ChIP) assay revealed that H3-K9/K14 acetylation of the TIMP-2 locus in SCNT placenta cells was about 2-fold higher than in normal placenta cells. Therefore, it is postulated that the SCNT placenta at the end of gestation seems to be unusual in tissue remodeling via improper expression of TIMP-2 by abnormal epigenetic modification, and that may affect placental abnormality such as enlarged and dysfunctional placentae as reported in cloned bovine and mouse.

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Evaluation of acute myeloid leukemia blast percentage on MethylC-Capture Sequencing results

Experimental Hematology and Oncology ◽

10.1186/s40164-021-00219-0 ◽

2021 ◽

Vol 10 (1) ◽

Author(s):

Erna Yang ◽

Desheng Gong ◽

Wei Guan ◽

Jieying Li ◽

Xuefeng Gao ◽

...

Keyword(s):

Dna Methylation ◽

Bone Marrow ◽

Acute Myeloid Leukemia ◽

Methylation Level ◽

Myeloid Leukemia ◽

Promoter Regions ◽

Aberrant Dna Methylation ◽

Next Generation Sequencing Ngs ◽

Capture Sequencing ◽

Acute Myeloid

AbstractAberrant DNA methylation is often related to the diagnosis, prognosis, and therapeutic response of acute myeloid leukemia (AML); however, relevant studies on the relationship between bone marrow myeloblast percentage and the DNA methylation level in AML have not been reported. We evaluated the effects of AML blast percentage on DNA methylation level using the MethylC-capture sequencing (MCC-Seq) approach based on next-generation sequencing (NGS) and found that the methylation level of both genome-wide and promoter regions significantly increased when the percentage of AML blasts reached ≥ 40%, indicating that an accurate DNA methylation level in cancer cells can be obtained when the bone marrow samples of AML patients have more than 40% myeloblasts.

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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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EPIGENETIC ALTERATIONS ASSOCIATED WITH PREMATURE OVARIAN FAILURE

Clinical & Investigative Medicine ◽

10.25011/cim.v31i4.4804 ◽

2008 ◽

Vol 31 (4) ◽

pp. 11

Author(s):

Manda Ghahremani ◽

Courtney W Hannah ◽

Maria Peneherrera ◽

Karla L Bretherick ◽

Margo R Fluker ◽

...

Keyword(s):

Dna Methylation ◽

Premature Ovarian Failure ◽

Promoter Region ◽

Gene Promoter ◽

Ovarian Failure ◽

P Value ◽

Epigenetic Alterations ◽

Methylation Array ◽

Cpg Sites ◽

Deficient Mice

Background/Purpose: Premature ovarian failure (POF) affects 1% of women with a largely idiopathic and poorly understood etiology. The objective of this study was to identify specific epigenetic alterations by measuring DNA methylation of gene regulatory regions in women with POF vs. controls. Methods: Blood samples were collected from idiopathic POFpatients (Amenorrhea for at least 3 months and 2 serum FSH levels of > 40mIU/ml obtained > 1 month apart prior to age 40) and control women (CW) (healthy pregnancy after age 37 with out a pregnancy loss). Genomic DNA was extracted from EDTA anticoagulated blood and bisulfite converted for analysis using the Illumina Golden Gate Methylation Panel which measures DNA methylation at 1506 CpG sites in the promoter regions of 807 genes in 10 POF and 12 CW. Candidate genes with altered epigenetic marks between POF and CW at a nominal P-value < 0.05 were identified using a t-testcomparison within the Illumina bead studio software. Genes of interest were further analyzed for quantitative methylation at specific CpG sites using pyrosequencing in 30 POF and 30 CW. Results: Comparison of DNA methylation profiles of our initial POF and CW groups identified several genes with statistically significanthyper- or hypo- methylation in the POF group (P < 0.05), including the Androgen Receptor (AR)promoter region, which was significantly hypermethylated. To further validate these results, DNA methylation of the AR gene promoter was quantified bypryosequencing in a larger group of POF and CW. Pyrosequencing further confirmed a significantly higher DNA methylation of the AR promoter region inPOF vs. CW (P=0.007). Conclusions: This is a novel study identifying epigenetic alterations in POF. The hypermethylation of the AR gene in POF patients may cause decreased level of the AR in these women. This is especially interesting given a recent report of induced POF in AR deficient mice^1. Specific epigenetic markers, as identified by DNA methylation array profiling in blood, may serve as useful biomarkers for POF and other fertility disorders. However, it will need to be determined if these methylation changes are present prior to diagnosis, or are a consequence of menopause itself. Reference: 1.Hiroko S. et al. Premature ovarian failure in androgenreceptor deficient mice. PNAS;103:224-9

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Age-related differences in monocyte DNA methylation and immune function in healthy Kenyan adults and children

Immunity & Ageing ◽

10.1186/s12979-021-00223-2 ◽

2021 ◽

Vol 18 (1) ◽

Author(s):

Katherine R. Dobbs ◽

Paula Embury ◽

Emmily Koech ◽

Sidney Ogolla ◽

Stephen Munga ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Young Adults ◽

Expression Profiles ◽

Gene Expression Profiles ◽

Innate Immune ◽

Inflammatory Gene Expression ◽

Cpg Sites ◽

Age Related ◽

Adults And Children

Abstract Background Age-related changes in adaptive and innate immune cells have been associated with a decline in effective immunity and chronic, low-grade inflammation. Epigenetic, transcriptional, and functional changes in monocytes occur with aging, though most studies to date have focused on differences between young adults and the elderly in populations with European ancestry; few data exist regarding changes that occur in circulating monocytes during the first few decades of life or in African populations. We analyzed DNA methylation profiles, cytokine production, and inflammatory gene expression profiles in monocytes from young adults and children from western Kenya. Results We identified several hypo- and hyper-methylated CpG sites in monocytes from Kenyan young adults vs. children that replicated findings in the current literature of differential DNA methylation in monocytes from elderly persons vs. young adults across diverse populations. Differentially methylated CpG sites were also noted in gene regions important to inflammation and innate immune responses. Monocytes from Kenyan young adults vs. children displayed increased production of IL-8, IL-10, and IL-12p70 in response to TLR4 and TLR2/1 stimulation as well as distinct inflammatory gene expression profiles. Conclusions These findings complement previous reports of age-related methylation changes in isolated monocytes and provide novel insights into the role of age-associated changes in innate immune functions.

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