Aberrant silencing of the CpG island-containing human O6-methylguanine DNA methyltransferase gene is associated with the loss of nucleosome-like positioning.

Tumor-associated aberrant silencing of CpG island-containing genes has been correlated with increased cytosine methylation, a "closed" chromatin structure, and exclusion of transcription factor binding in the CpG island/promoter regions of affected genes. Given the lack of understanding of what constitutes a closed chromatin structure in CpG islands, however, it has been difficult to assess the relationship among cytosine methylation, chromatin structure, and inappropriate gene silencing. In this study, nuclease accessibility analysis was used to more clearly define the chromatin structure in the CpG island of the human O6-methylguanine DNA methyltransferase (MGMT) gene. Chromatin structure was then related to in vivo DNA-protein interactions and cytosine methylation status of the MGMT CpG island in human glioma cells varying in MGMT expression. The results of these studies indicated that the "open" chromatin structure associated with the MGMT CpG island in MGMT+ cells consisted of an approximately 250-bp transcription factor-binding, nuclease-accessible, nucleosome-free region of DNA, whose formation was associated with at least four flanking, precisely positioned nucleosome-like structures. In MGMT- cells, this precise nucleosomal array was lost and was replaced by randomly positioned nucleosomes (i.e., the closed chromatin structure), regardless of whether methylation of the CpG island was spread over the entire island or limited to regions outside the transcription factor binding region. These results suggest that CpG islands facilitate the expression of housekeeping genes by facilitating nucleosomal positioning and that the conditions that alter the formation of this array (such as perhaps methylation) may indirectly affect CpG island-containing gene expression.

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Subtype-associated epigenomic landscape and 3D genome structure in bladder cancer

Genome Biology ◽

10.1186/s13059-021-02325-y ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Tejaswi Iyyanki ◽

Baozhen Zhang ◽

Qixuan Wang ◽

Ye Hou ◽

Qiushi Jin ◽

...

Keyword(s):

Bladder Cancer ◽

Transcription Factor ◽

Cancer Cell ◽

Genome Structure ◽

Transcription Factor Binding ◽

Specific Gene ◽

Open Chromatin ◽

Factor Binding ◽

3D Genome ◽

Genome Wide

Abstract Muscle-invasive bladder cancers are characterized by their distinct expression of luminal and basal genes, which could be used to predict key clinical features such as disease progression and overall survival. Transcriptionally, FOXA1, GATA3, and PPARG are shown to be essential for luminal subtype-specific gene regulation and subtype switching, while TP63, STAT3, and TFAP2 family members are critical for regulation of basal subtype-specific genes. Despite these advances, the underlying epigenetic mechanisms and 3D chromatin architecture responsible for subtype-specific regulation in bladder cancer remain unknown. Result We determine the genome-wide transcriptome, enhancer landscape, and transcription factor binding profiles of FOXA1 and GATA3 in luminal and basal subtypes of bladder cancer. Furthermore, we report the first-ever mapping of genome-wide chromatin interactions by Hi-C in both bladder cancer cell lines and primary patient tumors. We show that subtype-specific transcription is accompanied by specific open chromatin and epigenomic marks, at least partially driven by distinct transcription factor binding at distal enhancers of luminal and basal bladder cancers. Finally, we identify a novel clinically relevant transcription factor, Neuronal PAS Domain Protein 2 (NPAS2), in luminal bladder cancers that regulates other subtype-specific genes and influences cancer cell proliferation and migration. Conclusion In summary, our work identifies unique epigenomic signatures and 3D genome structures in luminal and basal urinary bladder cancers and suggests a novel link between the circadian transcription factor NPAS2 and a clinical bladder cancer subtype.

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DNA Methylation of Human Choline Kinase Alpha Promoter-Associated CpG Islands in MCF-7 Cells

Genes ◽

10.3390/genes12060853 ◽

2021 ◽

Vol 12 (6) ◽

pp. 853

Author(s):

Siti Aisyah Faten Mohamed Sa’dom ◽

Sweta Raikundalia ◽

Shaharum Shamsuddin ◽

Wei Cun See Too ◽

Ling Ling Few

Keyword(s):

Dna Methylation ◽

Transcription Factor ◽

Binding Site ◽

Promoter Activity ◽

Cytosine Methylation ◽

Cpg Island ◽

Cpg Islands ◽

Site Directed Mutagenesis ◽

Choline Kinase ◽

Mcf 7

Choline kinase (CK) is the enzyme catalyzing the first reaction in CDP-choline pathway for the biosynthesis of phosphatidylcholine. Higher expression of the α isozyme of CK has been implicated in carcinogenesis, and inhibition or downregulation of CKα (CHKA) is a promising anticancer approach. This study aimed to investigate the regulation of CKα expression by DNA methylation of the CpG islands found on the promoter of this gene in MCF-7 cells. Four CpG islands have been predicted in the 2000 bp promoter region of ckα (chka) gene. Six CpG island deletion mutants were constructed using PCR site-directed mutagenesis method and cloned into pGL4.10 vectors for promoter activity assays. Deletion of CpG4C region located between –225 and –56 significantly increased the promoter activity by 4-fold, indicating the presence of important repressive transcription factor binding site. The promoter activity of methylated full-length promoter was significantly lower than the methylated CpG4C deletion mutant by 16-fold. The results show that DNA methylation of CpG4C promotes the binding of the transcription factor that suppresses the promoter activity. Electrophoretic mobility shift assay analysis showed that cytosine methylation at MZF1 binding site in CpG4C increased the binding of putative MZF1 in nuclear extract. In conclusion, the results suggest that DNA methylation decreased the promoter activity by promoting the binding of putative MZF1 transcription factor at CpG4C region of the ckα gene promoter.

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Bioinformatics Analysis of SNPs in IL-6 Gene Promoter of Jinghai Yellow Chickens

Genes ◽

10.3390/genes9090446 ◽

2018 ◽

Vol 9 (9) ◽

pp. 446 ◽

Cited By ~ 3

Author(s):

Shijie Xin ◽

Xiaohui Wang ◽

Guojun Dai ◽

Jingjing Zhang ◽

Tingting An ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Binding Sites ◽

Promoter Region ◽

Bioinformatics Analysis ◽

Cpg Islands ◽

Regulatory Region ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Factor Binding

The proinflammatory cytokine, interleukin-6 (IL-6), plays a critical role in many chronic inflammatory diseases, particularly inflammatory bowel disease. To investigate the regulation of IL-6 gene expression at the molecular level, genomic DNA sequencing of Jinghai yellow chickens (Gallus gallus) was performed to detect single-nucleotide polymorphisms (SNPs) in the region −2200 base pairs (bp) upstream to 500 bp downstream of IL-6. Transcription factor binding sites and CpG islands in the IL-6 promoter region were predicted using bioinformatics software. Twenty-eight SNP sites were identified in IL-6. Four of these 28 SNPs, three [−357 (G > A), −447 (C > G), and −663 (A > G)] in the 5′ regulatory region and one in the 3′ non-coding region [3177 (C > T)] are not labelled in GenBank. Bioinformatics analysis revealed 11 SNPs within the promoter region that altered putative transcription factor binding sites. Furthermore, the C-939G mutation in the promoter region may change the number of CpG islands, and SNPs in the 5′ regulatory region may influence IL-6 gene expression by altering transcription factor binding or CpG methylation status. Genetic diversity analysis revealed that the newly discovered A-663G site significantly deviated from Hardy-Weinberg equilibrium. These results provide a basis for further exploration of the promoter function of the IL-6 gene and the relationships of these SNPs to intestinal inflammation resistance in chickens.

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Fetal growth restriction alters transcription factor binding and epigenetic mechanisms of renal 11β-hydroxysteroid dehydrogenase type 2 in a sex-specific manner

AJP Regulatory Integrative and Comparative Physiology ◽

10.1152/ajpregu.00122.2010 ◽

2010 ◽

Vol 299 (1) ◽

pp. R334-R342 ◽

Cited By ~ 54

Author(s):

Mariana Baserga ◽

Rajwinderjit Kaur ◽

Merica A. Hale ◽

Allyson Bares ◽

Xing Yu ◽

...

Keyword(s):

Transcription Factor ◽

Chromatin Structure ◽

Methylation Status ◽

Hydroxysteroid Dehydrogenase ◽

Transcription Factor Binding ◽

Growth Restriction ◽

Artery Ligation ◽

Factor Binding ◽

Specific Manner

Intrauterine growth restriction (IUGR) increases the risk of serious adult morbidities such as hypertension. In an IUGR rat model of hypertension, we reported a persistent decrease in kidney 11β-hydroxysteroid dehydrogenase type 2 (11β-HSD2) mRNA and protein levels from birth through postnatal (P) day 21. This enzyme deficiency can lead to hypertension by limiting renal glucocorticoid deactivation. In the present study, we hypothesized that IUGR affects renal 11β-HSD2 epigenetic determinants of chromatin structure and alters key transcription factor binding to the 11β-HSD2 promoter in association with persistent downregulation of its mRNA expression. To test this hypothesis, we performed bilateral uterine artery ligation on embryonic day 19.5 pregnant rats and harvested kidneys at day 0 (P0) and P21. Key transcription factors that can affect 11β-HSD2 expression include transcriptional enhancers specificity protein 1 (SP1) and NF-κB p65 and transcriptional repressors early growth response factor (Egr-1) and NF-κB p50. Our most important findings were as follows: 1) IUGR significantly decreased SP1 and NF-κB (p65) binding to the 11β-HSD2 promoter in males, while it increased Egr-1 binding in females and NF-κB (p50) binding in males; 2) IUGR increased CpG methylation status, as well as modified the pattern of methylation in several CpG sites of 11β-HSD2 promoter at P0 also in a sex-specific manner; and 3) IUGR decreased trimethylation of H3K36 in exon 5 of 11β-HSD2 at P0 and P21 in both genders. We conclude that IUGR is associated with altered transcriptional repressor/activator binding in connection with increased methylation in the 11β-HSD2 promoter region in a sex-specific manner, possibly leading to decreased transcriptional activity. Furthermore, IUGR decreased trimethylation of H3K36 of the 11β-HSD2 gene in both genders, which is associated with decreased transcriptional elongation. We speculate that alterations in transcription factor binding and chromatin structure play a role in in utero reprogramming.

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TET2 Mutations Affect Non-CpG Island DNA Methylation at Enhancers and Transcription Factor–Binding Sites in Chronic Myelomonocytic Leukemia

Cancer Research ◽

10.1158/0008-5472.can-14-0739 ◽

2015 ◽

Vol 75 (14) ◽

pp. 2833-2843 ◽

Cited By ~ 55

Author(s):

Jumpei Yamazaki ◽

Jaroslav Jelinek ◽

Yue Lu ◽

Matteo Cesaroni ◽

Jozef Madzo ◽

...

Keyword(s):

Dna Methylation ◽

Transcription Factor ◽

Binding Sites ◽

Cpg Island ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Chronic Myelomonocytic Leukemia ◽

Factor Binding ◽

Myelomonocytic Leukemia

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Effects of cytosine methylation on transcription factor binding sites

BMC Genomics ◽

10.1186/1471-2164-15-119 ◽

2014 ◽

Vol 15 (1) ◽

pp. 119 ◽

Cited By ~ 128

Author(s):

Yulia A Medvedeva ◽

Abdullah M Khamis ◽

Ivan V Kulakovskiy ◽

Wail Ba-Alawi ◽

Md Shariful I Bhuyan ◽

...

Keyword(s):

Transcription Factor ◽

Binding Sites ◽

Cytosine Methylation ◽

Transcription Factor Binding Sites ◽

Transcription Factor Binding ◽

Factor Binding

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Epigenetics and expression of key genes associated with cardiac fibrosis: NLRP3, MMP2, MMP9, CCN2/CTGF and AGT

Epigenomics ◽

10.2217/epi-2020-0446 ◽

2021 ◽

Vol 13 (3) ◽

pp. 219-234

Author(s):

Sruti Chandra ◽

Kenneth C Ehrlich ◽

Michelle Lacey ◽

Carl Baribault ◽

Melanie Ehrlich

Keyword(s):

Transcription Factor ◽

Cardiac Fibrosis ◽

Expression Profiles ◽

Transcription Factor Binding ◽

Open Chromatin ◽

Dna Hypomethylation ◽

Silent Gene ◽

Specific Expression ◽

Tissue Specific ◽

Factor Binding

Aims: Excessive inflammatory signaling and pathological remodeling of the extracellular matrix drive cardiac fibrosis and require changes in gene expression. Materials and methods: Using bioinformatics, both tissue-specific expression profiles and epigenomic profiles of some genes critical for cardiac fibrosis were examined, namely, NLRP3, MMP2, MMP9, CCN2/CTGF, AGT (encodes angiotensin II precursors) and hsa-mir-223 (post-transcriptionally regulates NLRP3). Results: In monocytes, neutrophils, fibroblasts, venous cells, liver and brain, enhancers or super-enhancers were found that correlate with high expression of these genes. One enhancer extended into a silent gene neighbor. These enhancers harbored tissue-specific foci of DNA hypomethylation, open chromatin and transcription factor binding. Conclusions: This study identified previously undescribed enhancers containing hypomethylated transcription factor binding subregions that are predicted to regulate expression of these cardiac fibrosis-inducing genes.

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Presetting of chromatin structure and transcription factor binding poise the human GADD45 gene for rapid transcriptional up-regulation

Nucleic Acids Research ◽

10.1093/nar/27.19.3881 ◽

1999 ◽

Vol 27 (19) ◽

pp. 3881-3890 ◽

Cited By ~ 20

Author(s):

D. Graunke

Keyword(s):

Transcription Factor ◽

Chromatin Structure ◽

Transcription Factor Binding ◽

Factor Binding

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Inhibitors of Histone Deacetylase and DNA Methyltransferase Synergistically Activate the Methylated Metallothionein I Promoter by Activating the Transcription Factor MTF-1 and Forming an Open Chromatin Structure

Molecular and Cellular Biology ◽

10.1128/mcb.22.23.8302-8319.2002 ◽

2002 ◽

Vol 22 (23) ◽

pp. 8302-8319 ◽

Cited By ~ 116

Author(s):

Kalpana Ghoshal ◽

Jharna Datta ◽

Sarmila Majumder ◽

Shoumei Bai ◽

Xiaocheng Dong ◽

...

Keyword(s):

Transcription Factor ◽

Histone Deacetylase ◽

Chromatin Structure ◽

Dna Methyltransferase ◽

Combined Treatment ◽

Hdac Inhibitors ◽

Prolonged Treatment ◽

Open Chromatin ◽

Chip Assay

ABSTRACT Inhibitors of DNA methyltransferase (Dnmt) and histone deacetylases (HDAC) synergistically activate the methylated metallothionein I gene (MT-I) promoter in mouse lymphosarcoma cells. The cooperative effect of these two classes of inhibitors on MT-I promoter activity was robust following demethylation of only a few CpG dinucleotides by brief exposure to 5-azacytidine (5-AzaC) but persisted even after prolonged treatment with the nucleoside analog. HDAC inhibitors (trichostatin A [TSA] and depsipeptide) either alone or in combination with 5-AzaC did not facilitate demethylation of the MT-I promoter. Treatment of cells with HDAC inhibitors increased accumulation of multiply acetylated forms of H3 and H4 histones that remained unaffected after treatment with 5-AzaC. Chromatin immunoprecipitation (ChIP) assay showed increased association of acetylated histone H4 and lysine 9 (K9)-acetyl H3 with the MT-I promoter after treatment with TSA, which was not affected following treatment with 5-AzaC. In contrast, the association of K9-methyl histone H3 with the MT-I promoter decreased significantly after treatment with 5-AzaC and TSA. ChIP assay with antibodies specific for methyl-CpG binding proteins (MBDs) demonstrated that only methyl-CpG binding protein 2 (MeCP2) was associated with the MT-I promoter, which was significantly enhanced after TSA treatment. Association of histone deacetylase 1 (HDAC1) with the promoter decreased after treatment with TSA or 5-AzaC and was abolished after treatment with both inhibitors. Among the DNA methyltransferases, both Dnmt1 and Dnmt3a were associated with the MT-I promoter in the lymphosarcoma cells, and association of Dnmt1 decreased with time after treatment with 5-AzaC. Treatment of these cells with HDAC inhibitors also increased expression of the MTF-1 (metal transcription factor-1) gene as well as its DNA binding activity. In vivo genomic footprinting studies demonstrated increased occupancy of MTF-1 to metal response elements of the MT-I promoter after treatment with both inhibitors. Analysis of the promoter by mapping with restriction enzymes in vivo showed that the MT-I promoter attained a more open chromatin structure after combined treatment with 5-AzaC and TSA as opposed to treatment with either agent alone. These results implicate involvement of multifarious factors including modified histones, MBDs, and Dnmts in silencing the methylated MT-I promoter in lymphosarcoma cells. The synergistic activation of this promoter by these two types of inhibitors is due to demethylation of the promoter and altered association of different factors that leads to reorganization of the chromatin and the resultant increase in accessibility of the promoter to the activated transcription factor MTF-1.

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