Journal: Carcinogenesis

Article Title: Estrogen-mediated epigenetic repression of the imprinted gene cyclin-dependent kinase inhibitor 1C in breast cancer cells

doi: 10.1093/carcin/bgr017

Figure Lengend Snippet: 11p15.5 epigenetic and genetic states and expression of CDKN1C in breast cancer cells. (A) The DNA methylation status of the 11p15.5 ICR differentially methylated domain was analyzed by high-resolution bisulfite PCR pyrosequencing in primary tumors (n = 306), breast cancer cell lines (n = 52) and normal breast tissues (n = 19). Methylation levels of individual CpG sites (circles) are shown in a color gradient ranging from 0% (white) to 100% (blue). Left, diagram of CpG sites interrogated by the pyrosequencing assay. Right, results presented in rows of columns. (B) Multiple linear regression analysis of impact of 11p15.5 ICR methylation and genetic status on CDKN1C expression in breast cancer cells. The combined 11p15.5 ICR methylation, copy number and CDKN1C mRNA levels in 16 breast cancer cell lines were assessed by bisulfite PCR pyrosequencing, DNA copy number qPCR and qRT–PCR, respectively. DNA copy number of 11p15.5 ICR was quantified by absolute standard curve of cloned PCR products as described in supplementary Figure S4 (available at Carcinogenesis Online). Relative CDKN1C ΔCt expression values were obtained by normalizing to the 36B4 reference gene. (C) The effect of E2 on CDKN1C expression in breast cancer cells with 11p15.5 ICR hypermethylation. MDA-MB-453 and T47D cells were stimulated with 10 nM E2 or vehicle for 12 h. CDKN1C mRNA levels were assessed as described in Figure 1. Results are the average of two independent experiments. Columns, mean (n = 6); bars, SD.

Article Snippet: Approximately 300 ng of genomic DNA was bisulfite modified with EZ DNA Methylation Kit (Zymo Research, Irivine, CA) according to the manufacturer’s protocol.

Techniques: Expressing, DNA Methylation Assay, Methylation, Pyrosequencing Assay, Quantitative RT-PCR, Clone Assay

Journal: Carcinogenesis

Article Title: Estrogen-mediated epigenetic repression of the imprinted gene cyclin-dependent kinase inhibitor 1C in breast cancer cells

doi: 10.1093/carcin/bgr017

Figure Lengend Snippet: Potential mechanisms causing repression of CDKN1C in breast cancer cells. (A) Proposed model for epigenetic repression of CDKN1C through coordinated loop formation with the 11p15.5 ICR. CTCF binding to the ICR and CDKN1C locus and forms a long-range intrachromosomal loop via dimerization of CTCF. Ligand-bound ERα complex (orange and blue sphere) may mediate silencing through the formation of a secondary loop that serves both to sequester upstream tissue-specific enhancers and to recruit PRC2 and HDAC1 to the 11p15.5 ICR. CTCF serves as a scaffold to secure the PRC2 complex that methylates H3K27, leading to the formation of a repressive chromatin state at the CDKN1C locus. (B) Proposed regulatory mechanism of CDKN1C-AS. The formation of a double-stranded RNA may negatively regulate stability, transport and/or translation of the sense CDKN1C transcript. (C) Summary of three potential mechanisms causing CDKN1C repression in breast cancer cells. DNA methylation status of 11p15.5 ICR is indicated by large oval: white (unmethylated), black (methylated). Upper left, in the normal imprinted domain unmethylated 11p15.5 ICR on the paternal allele (♂) functions as a silencer and a promoter for KCNQ1OT1 transcription, repressing CDKN1C expression. The methylated maternal allele (♀) cannot function as a silencer or a promoter for KCNQ1OT1, thus permitting expression of CDKN1C. Upper right, the CDKN1C-AS transcript represses CDKN1C in trans, potentially through a double-stranded RNA mechanism. Under certain cellular conditions, this may be induced by estrogen-mediated upregulation of CDKN1C-AS. Lower left, DNA hypomethylation resulting from genetic loss of the methylated 11p15.5 ICR allele leads to aberrant domain silencer activity mediated by unrestricted CTCF binding and KCNQ1OT1 transcription, repressing CDKN1C expression. Lower right, estrogen induces KCNQ1OT1 transcription and CTCF recruitment to mediate ICR silencer activity, which in turn direct epigenetic repression of the CDKN1C locus.

Article Snippet: Approximately 300 ng of genomic DNA was bisulfite modified with EZ DNA Methylation Kit (Zymo Research, Irivine, CA) according to the manufacturer’s protocol.

Techniques: Binding Assay, DNA Methylation Assay, Methylation, Expressing, Activity Assay

Journal: Gastroenterology and Hepatology From Bed to Bench

Article Title: The epigenetic influence of diet-induced gut microbiome changes in precision nutrition – a systematic review

doi: 10.22037/ghfbb.v18i3.3136

Figure Lengend Snippet: Epigenetic Changes in Gene Expression — This figure illustrates two key epigenetic mechanisms that regulate gene expression: DNA methylation and histone modifications. DNA methylation involves the addition of methyl groups to the promoter region of a gene, inhibiting transcription and leading to gene silencing. Histone modifications, including acetylation and methylation, alter chromatin structure and gene accessibility; acetylation relaxes chromatin, promoting gene activation, while methylation can either enhance or suppress transcription depending on its context. These epigenetic modifications are dynamic and influenced by environmental factors, such as diet, with implications for metabolism, inflammation, and disease susceptibility.

Article Snippet: Sun, et al. (21) , DNA methylation analysis (DREAM sequencing, bisulfite pyrosequencing, qRT-PCR) in a microbiota-inflammation model. , Difficulty separating inflammation’s role in epigenetic changes. , Microbiota and inflammation influenced DNA methylation at CpG sites. , DNA methylation at CpG sites. , Not assessed. , Multi-model approach, deep-sequencing of methylation changes. , Moderate , 2023.

Techniques: Gene Expression, DNA Methylation Assay, Methylation, Activation Assay

Journal: Gastroenterology and Hepatology From Bed to Bench

Article Title: The epigenetic influence of diet-induced gut microbiome changes in precision nutrition – a systematic review

doi: 10.22037/ghfbb.v18i3.3136

Figure Lengend Snippet: Epigenetic Modifications in Metabolic Health and Disease Prevention – This figure illustrates the impact of diet-induced changes in gut microbiome composition on epigenetic modifications and their subsequent effects on metabolic health. The dietary components, such as fiber-rich, polyphenol-rich, and high-fat diets, are shown to influence microbiome diversity and promote the production of metabolites like short-chain fatty acids (SCFAs), which modulate epigenetic markers (e.g., DNA methylation, histone modifications) and gene expression related to inflammation, metabolism, and disease susceptibility. Diets rich in fiber and polyphenols are associated with beneficial microbiome shifts and favorable epigenetic modifications that support metabolic health and reduce the risk of metabolic diseases like obesity and insulin resistance. In contrast, Western-style diets high in fat and processed foods contribute to dysbiosis, inflammation, and adverse epigenetic changes, which may increase the risk of developing chronic metabolic disorders, including obesity and type 2 diabetes.

Article Snippet: Sun, et al. (21) , DNA methylation analysis (DREAM sequencing, bisulfite pyrosequencing, qRT-PCR) in a microbiota-inflammation model. , Difficulty separating inflammation’s role in epigenetic changes. , Microbiota and inflammation influenced DNA methylation at CpG sites. , DNA methylation at CpG sites. , Not assessed. , Multi-model approach, deep-sequencing of methylation changes. , Moderate , 2023.

Techniques: DNA Methylation Assay, Gene Expression, Western Blot