Why should you care about epigenetics? Why do some foods cause health problems and others make us healthy? How does stress impact our long-term well-being? Why is it that the older we get, the more likely it is that age-related illness will strike us? Unlocking the secrets behind these and other questions has the potential to revolutionize life as we know it. The emerging field of epigenetics is aiming to do just that. The importance of nature versus nurture has long been disputed. It cannot be denied that environment greatly influences how a child grows and develops, nor can it be denied that our DNA is the blueprint that makes us who we are. Epigenetics merges these two seemingly contradictory lines of thought to explain how environmental factors cause physical modifications to DNA and its associated structures, which result in altered functions. The most commonly known epigenetic modification is DNA methylation. Although many technologies have been developed in the past to characterize genomic DNA methylation, none of them has been able to efficiently determine DNA methylation patterns on a genomic scale. Until now. What’s the easiest way to discover your next biomarker? Rapid advances in bisulfite chemistries, library methods, and sequencing platforms have revolutionized the field of biomarker discovery and analysis. Zymo Research is proud to offer the first consolidated service for tackling the exciting challenge of epigenetic biomarker discovery. EpiQuest™ Services are a customizable family of processes tailored to the individual researcher, allowing for more robust analysis of the methylome than ever before. Highlights of these services include…  Next-Gen bisulfite sequencing platforms for genome-wide and whole-genome DNA methylation analysis  Low DNA input (< 500 ng genomic DNA)  Applicable to a broad range of sample sources (human, mouse, rat, plant, etc.)  Streamlined workflows with comprehensive bioinformatic analysis and high NH2 NH2 N N H C Cytosine OH N O N H 5m quality publishable data delivery NH2  Customizable, rapid turnaround at an affordable cost EpiQuest™ Workflow N O C 5-Methylcytosine N H 5hm O C Genomic DNA DNA fragmentation, end modification, adaptor addition, size selection, bisulfite conversion, limited amplification 5-Hydroxymethylcytosine Library Construction What’s the future of epigenetic research? Next-Gen Sequencing To date, epigenetic modification of DNA has been most closely associated with detection and quantitation of 5-methylcytosine (5-mC). The so-called “fifth base” has become a springboard for the study of the closely related 5-hydroxymethylcytosine (5-hmC). The modified base is speculated to be an intermediate in oxidative demethylation pathways, but could itself constitute a new layer of epigenetic regulation, gaining attention in recent years as a potential epigenetic factor in fields ranging from ES-cell renewal and cell mass specification (Ito et al, 2010) to several myelodysplastic pathologies (Lorsbach et al, 2003). Bioinformatic Processing Publishable Data Learn more at www.zymoresearch.com THE Epigenetics COMPANY™ How does epigenetics play a key role in your research? Development & Stem Cells Cancer Aging The development of an organism is dictated by precise gene expression. Epigenetics, especially DNA methylation, is a critical factor in the development process. Following fertilization of the egg, a wave of DNA demethylation is followed by remethylation events to “reprogram” the maternal and paternal genomes for proper zygote development. Accordingly, misregulation of these epigenetic factors can result in developmental abnormalities. Therefore, research focused on the mechanisms and roles of DNA methylation/ hydroxymethylation in development should be essential for understanding developmental and stem cell biology. Cancer has conventionally been considered a genetic disorder. However, recent research has demonstrated epigenetic factors to be important in cancer biology. Aberrant DNA methylation (5-mC) and potentially hydroxymethylation (5-hmC) can result in the misregulation of gene expression (e.g., silencing of tumor suppressors and activating oncogenes), chromosomal instability, and mutations. A better understanding of the relationship between epigenetic regulation and cancer will be necessary for greater advances in the understanding of both processes and in the development of cancer therapies. Aging is an inevitable part of life. DNA methylation patterns are known to change with age. Recent research has found that methylation at specific loci can be used as a predictor of a patient’s age. Also, age associated diseases (e.g., cancer, Alzheimer’s, etc.) can be correlated with shifts in DNA methylation. An understanding of how DNA methylation and age are correlated should give insight into the processes of aging and disease. The search for epigenetic modifiers... Methylated DNA (5-mC) Enrichment Select & enrich specific regions of the genome based on 5-mC content. Global 5-mC Quantification Rapidly quantitate global levels of 5-mC in DNA from any tissue or sample source. Locus-Specific 5-mC Analysis Interrogate a gene(s) 5-mC. Genome-wide 5-mC DNA Analysis Determine genomic 5-mC content Tools & Solutions MeDIP1 MethylCap Methylated-DNA IP Kit: Features a highly specific anti-5mC monoclonal antibody for enrichement of methylated DNA from any pool of fragmented genomic DNA. 1 LC/MS2 ELISA* HPLC2 DNA Degradase™ & DNA Degradase Plus™ Enzymes: For preparation of DNA prior to composition analysis by LC/MS, TLC, and HPLC. 2 Bisulfite Sequencing3 MSRE-qPCR5 Next-Gen Bisulfite Sequencing4 Methylation Array EZ DNA Methylation™ family of bisulfite kits: The most cited chemistries for rapid, complete conversion of DNA for methylation analysis. Spin column and 96-well plate formats allow for various sample inputs (DNA, cells, blood, etc.). Converted DNA is ideal for PCR, bisulfite and pyro-sequencing, library prep, and other analytical procedures. 3 EpiQuest™ Services: Streamlined sample prep, Next-Gen sequencing, and unique bioinformatic workflows for consolidated genomic DNA methylation analysis. Flexible: broad range of sample sources/organisms, customizable, and affordable. 4 NH2 N N H 5m Hydroxymethyl DNA (5-hmC) Enrichment Select & enrich specific regions of the genome based on 5-hmC content. 5-Methylcytosine (5-mC) O C A epigenetic This “classical” DN ociated with modification is ass found in en wh ng nci sile gene s. promoter ytosine 5-hydroxymethylc (5-hmC) covered DNA This newly dis ion is found cat difi mo tic epigene the brain as hin wit els at high lev ct function exa e Th well as ESC’s. ered… cov dis be to s ain rem OH Global 5-hmC Quantification Rapidly quantitate global levels of 5-hmC in DNA from any tissue or sample source. Locus-Specific 5-hmC Analysis Interrogate a gene(s) 5-hmC content. NH2 OneStep qMethyl™ Kit: Single step, qPCR procedure for bisulfite-free determination of DNA methylation status. Ideal for rapid screening of single- and multi-locus DNA methylation. 5 HMeDIP* 5-hmC Cap* LC/MS2 TLC2 HPLC2 ELISA* Quest 5-hmC Detection Kit™: For 5-hmC identification in sequence- and locusspecific context within DNA. Single tube reaction format for convenient DNA analysis using real-time PCR. 6 7 Restriction Digestion/qPCR6 N N H 5hm O C Genome-wide 5-hmC Analysis Enrich and quantify 5-hmC in genomic DNA. HMeDIP-Seq 5-hmC Cap-Seq7 Services for 5-hmC analysis: Please inquire, [email protected] * Coming soon. 7 Tel: (949) 679-1190 | Toll Free: (888) 882-9682 www.zymoresearch.com | [email protected]