Scientific Posters

Zymo Research's scientific posters highlight the latest breakthroughs in molecular biology, showcasing innovations spanning from epigenetics to microbiomics. We are proud to present insights from our collaborations with leading scientists and institutions worldwide, with more contributions to the field of life science on the horizon.

A Novel Method for Locus Specific Detection of 5-Hydroxymethylcytosine
James L. Yen, Stella Choi, Marc Van Eden, & Xi Yu Jia

Epigenetic misregulation leading to diseases, such as cancer, has classically been understood in terms of aberrant DNA methylation patterns. For decades, 5-methylcytosine (5mC) has been the focus of epigenetic DNA modification studies. But recently, a novel epigenetic DNA modification, 5-hydroxymethylcytosine (5hmC), has been shown to be present at high levels in mammalian brain and ES cells. 1,2 It has also been found at appreciable levels in many normal and diseased tissues. DNA methylation (5-methylcytosine) plays a major role in gene regulation. Promoters of many genes are methylated for regulated gene silencing. When this set DNA methylation pattern is undermined, the risk of acquiring diseases may increase. It has been well documented that many diseases (e.g. cancer, neurodegenerative diseases, etc.) have epigenetic roots. Many of these misregulated epigenetic alterations have proven to be reliable markers of disease or of disease progression. The role of the newly discovered, “6 th base” (5- hydroxymethylcytosine) is less clear. Unlike methylation, 5hmC has been shown to be found predominantly within gene bodies as well as non-promoter regions. Its role in biology has been speculated to be involved in DNA demethylation (active and passive) as well as in poising genes for later activation. Current tools available to map DNA methylation (e.g. bisulfite conversion) cannot distinguish between 5mC and 5hmC. 3 Here we describe the first method for locus specific interrogation of 5hmC within DNA by use of our Quest 5-hmC Detection Kit™.

View Poster
A Novel One-Step Method for Rapid and Accurate DNA Methylation Quantification
Onyi Chima , Lam Nguyen , Michelle Rabot & Xi Yu Jia

DNA methylation plays a central role in widespread biological phenomena. Current methods used to evaluate DNA methylation such as Bisulfite Sequencing and Methylation Specific PCR present a number of problems as they are expensive, lengthy and involve multiple steps that increase chances of contamination. Therefore, we sought to develop a one-step system for rapid and accurate DNA methylation quantification. Here, we describe a simple method that exploits the specificity of Methylation Specific Restriction Enzymes (MSRE) to digest unmethylated CpG dinucleotides juxtaposed to real-time PCR for the selective amplification of methylated DNA. Thus, integration of the multiple steps of traditional procedures into one simple step decreases chances of contamination and allows for rapid and accurate DNA methylation percentage quantification. Our one-step MSRE-qPCR system selectively amplified methylated DNA and accurately measured methylation profiles of known DNA methylated standards. Methylation percentages of blind controls determined by the one-step system closely coincided with actual methylation percentages. This assay has proven to be a cost-effective assay for accurate region-specific methylation status quantification and will be a valuable tool in research and diagnostics

View Poster
A Novel Sequencing Method for Genome-Wide Profiling of 5-Hydroxymethylcytosine With Single-Base Resolution
Darany Tan, TzuHung Chung, Xueguang Sun & Xi-Yu Jia

5-hydroxymethylcytosine (5hmC) is an epigenetic mark abundant in embryo stem cells and brain tissues. The exact biological functions of 5hmC are still under close investigation although several lines of evidence have indicated it could be involved in active DNA demethylation. Meanwhile, extensive studies have been carried out to determine its genomic distribution. A number of approaches have been developed using either affinity based enrichment, such as hMeDIP, that rely on antibody and other specific binding proteins to target 5hmC, or modified bisulfite sequencing, namely oxidative bisulfite sequencing (OxBS) and TET assisted bisulfite sequencing (TAB-sequencing). However, all those methods have limitations which hamper their application. For example, affinity based methods lack single base resolution while modified bisulfite sequencing methods require efficient chemical or enzymatic oxidation which cannot be easily achieved or guaranteed. As an alternative, we have developed a novel genome-wide sequencing method that utilizes an enzyme based modification approach coupled with bisulfite-sequencing for detecting 5hmC. This methodology allows quantification of 5hmC levels with single CpG resolution and can also be employed for locus-specific assays. Using this method, we were able to map and quantify 5hmC sites at the genomic scale for several different biological samples. This novel method can determine the exact location and abundance of 5hmC, which will facilitate our understanding of 5hmC in regulating gene expression in different biological contexts.

View Poster
A Urine-Based DNA Methylation Test to Detect Upper Tract Urothelial Carcinoma: Results from a Prospective Pilot Study
Paolo Piatti, Alireza Ghoreifi, Sanam Seyedian, Yap Ching Chew, Benjamin Jara, Lucy Sanossian, Jeffrey Bhasin, Michael Basin, Taikun Yamada, Gerhard Fuchs, Sumeet Bhanvadia, Rene Sotelo, Andrew Hung, Monish Aron, Mihir Desai, Inderbir Gill, Siamak Daneshmand, Gangning Liang, Hooman Djaladat

Upper Tract Urothelial Carcinoma (UTUC) is an uncommon, yet lethal malignancy of the urinary tract. Diagnosis and preoperative risk stratification of UTUC patients present distinct challenges given the limitations of currently available tools such as urine cytology, endoscopic biopsy, and cross-sectional imaging. Decision-making and prognosis of UTUC relies heavily on TNM stage and pathological grade, which are is not accurately available until RNU is performed.

View Poster
Accelerated Epigenetic Aging in Bladder Cancer Patients
Yap Ching Chew, Wei Guo, Xiaojing Yang, Paolo Piatti, Mingda Jin, Keith Booher, Michiko Suwoto, and Xi Yu Jia

Aging represents the most important risk factor for many chronic diseases including cardiovascular diseases, diabetes, and cancer, therefore understanding the mechanisms of aging is a fundamental step for designing new treatments for chronic diseases. DNA methylation is the most reliable and accurate molecular marker for aging quantification, however, genome-wide DNA methylation profiling techniques, such as reduced representative bisulfite sequencing and illumina Bead Array that are widely used in aging research are prohibitively expensive and have poor data quality at low-read coverage sites. Here we report a robust targeted bisulfite sequencing approach, called SWARM (Simplified Whole-panel Amplification Reaction Method), for the accurate biological age determination. SWARM is flexible and low cost, requires relatively low DNA starting material, allows the simultaneous amplification and sequencing of hundreds of loci, and has shown to increase sample throughput. Using the SWARM approach, we were able to analyze the methylation level of several hundreds of age-associated loci including the published Horvath Clock sites. Gender-specific age-predictive models were built using the elastic net regression of DNA methylation levels of the loci and chronological age of urine DNA samples of over 300 healthy subjects of 18 to 88 years old. Urine samples from bladder cancer patients exhibit significant age acceleration, with an average of >10 years. In brief, our gender-specific urine DNAge analysis is a tool for the precise biological aging quantification and can be used to address questions in aging and urinary tract health.

View Poster

Want to get in touch with our Scientists? Send us a message!

Need help? Contact Us