methylation-specific digital karyotyping  (INFINIUM Inc)

Journal: PLoS Genetics

Article Title: Epigenetic Regulation of Cell Type–Specific Expression Patterns in the Human Mammary Epithelium

doi: 10.1371/journal.pgen.1001369

Figure Lengend Snippet: (A) Associations between fraction of genes highly expressed in CD24+ or CD44+ cells and the location of DMRs (p<10 −5 ) in the two cell types relative to TSS. Y-axes show fraction of genes in the four different gene expression groups (i.e. CD24-high, CD44-high, no difference, and not expressed) relative to the location of DMRs hypermethylated in CD24+ (blue line) or CD44+ (red line) cells and all MSDK sites used as control. (B) Differentially (≥2-fold difference) expressed genes are enriched in DMRs. Bar charts show associations between genes with indicated DMR and gene expression patterns as described in panel A. Genes in each gene set have DMR (indicated left side) within promoter region (−5 kb from TSS to +2 kb, left panel) or in gene body (+2 kb to end, right panel). The number of MSDK sites and associated genes in each group is indicated. We used four different cut-offs for DMRs, 2, 5,10, 20 (-log10 p-value) from top to bottom (black triangle). Randomly picked MSDK sites did not show any enrichment pattern. (C) Correlation between mean gene expression levels in relation to promoter and gene body methylation in CD24+ and CD44+ cells. Red stars mark statistically significant differences relative to all MSDK sites. (D) Functional enrichment analysis (left panel) of genes associated with promoter and gene body DMRs in CD24+ and CD44+ cells and the number of overconnected objects in each functional category within each group (right panel). X-axis indicates –log10 p-values for enrichment with the indicated protein class (left panel) and the number of objects (right panel), respectively. Definitions are the same as described in .

Article Snippet: We also adapted MSDK (Methylation-Specific Digital Karyotyping) and SAGE (Serial Analysis of Gene Expression) protocols for the Illumina genome analyzer to enable the integrative analysis of all three types of data using the same platform.

Techniques: Gene Expression, Control, Methylation, Functional Assay

Journal: PLoS Genetics

Article Title: Epigenetic Regulation of Cell Type–Specific Expression Patterns in the Human Mammary Epithelium

doi: 10.1371/journal.pgen.1001369

Figure Lengend Snippet: (A) Genomic regions (+/− 5 kb and +/− 0 kb from DMR for K27 and K4, respectively) associated with DMRs in one cell type (e.g., CD44+ cells) are enriched for K4 or K27 mark in the other (e.g., CD24+ cells). Bar chart shows observed/expected ratio of the indicated MSDK sites with the designated K27 and K4 patterns between CD44+ and CD24+ cells. (B) Associations between gene expression and histone and DNA methylation patterns. Y-axis shows the –log10 p-value of enrichment for genes with the indicated expression and histone modification pattern in gene body and promoter DMRs. Orange line indicates –log10 (p value) of statistical significance, numbers 1–4 mark significantly enriched patterns. (C) Schematic models depicting possible changes in DNA methylation and K27 enrichment during CD44+ to CD24+ cell differentiation and their effect on gene expression based on data presented in panel B. Examples of genes within each group are listed. White (unmethylated) and black (methylated) circles indicate potential DNA methylation sites (i.e., CpG) in the promoter and gene body, blue and orange ovals represent lack and presence of K27 mark, respectively. Red and dashed green arrows indicate increased and decreased gene expression, respectively.

Article Snippet: We also adapted MSDK (Methylation-Specific Digital Karyotyping) and SAGE (Serial Analysis of Gene Expression) protocols for the Illumina genome analyzer to enable the integrative analysis of all three types of data using the same platform.

Techniques: Gene Expression, DNA Methylation Assay, Expressing, Modification, Cell Differentiation, Methylation

Journal: Cold Spring Harbor Perspectives in Biology

Article Title: Chromatin Remodeling in Mammary Gland Differentiation and Breast Tumorigenesis

doi: 10.1101/cshperspect.a004515

Figure Lengend Snippet: Summary of candidate gene and genome-wide techniques for DNA methylation analysis a

Article Snippet: Microarray-based approaches , DMH (differential methylation hybridization): MTA (methylation tissue array); MSO (methylation-specific oligonucleotide); HELP ( Hpa II tiny fragment enrichment by ligation-mediated PCR); AIMS (amplification of intermethylated sites); MSNP (methylation single nucleotide polymorphism chip-based method); MMASS (microarray-based methylation assessment of single sample); PMAD (promoter-associated methylated DNA amplification); MSDK (methylation-specific digital karyotyping) MIAMI (microarray-based integrated analysis of methylation); MCAM (methylated CpG island amplification and microarray); MeDIP-chip (methylated DNA immunoprecipitation on microarray); MIRA-chip (methylated-CpG island recovery assay on microarray); Mcr BC ; MethylScope ; Pharmacologic unmasking analysis ; and Infinium BeadArray.

Techniques: Genome Wide, DNA Methylation Assay, Cloning, Methylation Sequencing, Methylation, Combined Bisulfite Restriction Analysis Assay, Microarray, Hybridization, Ligation, Amplification, DNA Amplification, Methylated DNA Immunoprecipitation, Immunoprecipitation, Next-Generation Sequencing, Methylated DNA Immunoprecipitation Sequencing