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.

Genome-Wide DNA Methylation Analysis in Autism
Xi-Yu Jia, Xueguang Sun, Eliza Bacon, Adam Peterson, TzuHung Chung

Lacking consistent genetic mutation data in autism and increased risk of prenatal /maternal factors for disease development suggest a possible epigenetic mechanism for the disease development. DNA methylation is one of the major epigenetic regulators and its importance in development and disease is well established. Using next generation sequencing in combination with bisulfite-based DNA methylation detection, genome-wide 5-methylcytosine (5-mC) were investigated in autism blood samples from monozygotic twins. Our results indicate that “epimutations” are present in the affected children's blood DNA and these epigenetic changes were in agreement with other published biochemical data implicating epigenetics as a key element in the development of the disease.

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Genome-Wide DNA Methylation Analysis In Plants and Animals
Xueguang Sun, TzuHung Chung, Eliza Bacon, Ron Leavitt, Nikolas Isely, Marc Van Eden & Xi-Yu Jia

DNA methylation is a highly conserved epigenetic mark present in many eukaryotic organisms including plants, animals, and fungi. It plays an important role in the regulation of gene expression. A number of studies have shown its involvement in plant and animal growth and reproduction primary through the processes of genomic imprinting, X-chromsome inactivation, and the silencing of transposons and other repetitive DNA elements. As such, the understanding of DNA methylation has become a major focus of the research conducted during the “post-genomics” era. However, the precise determination of a DNA's methylation pattern on a genomic scale has posed a challenge especially for those complex genomes. Combining well-established bisulfite conversion chemistry with NextGen sequencing, we have established a robust service platform for analyzing DNA methylation with single base resolution at the genomic scale. The service features a streamlined workflow coupled with a comprehensive bioinformatics pipeline to provide both a consolidated and cost-effective solution for epigenetic analysis of plant and animal genomes. This technology has been used successfully for the analysis of methylomes from many organisms including soybean, mouse, and chicken. Additional analyses of other species are ongoing. Those data should provide a means to understanding how environment as well as other factors may alter an organism's fitness through heritable changes in epigenetic gene expression.

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Genome-Wide Human Brain DNA 5-hmC Profiling Using a Novel Sequence- and Strand-Specific Method
Xueguang Sun, Adam Petterson, Tzu Hung Chung, Xi Yu Jia, Pu Zhang

5-Hydroxymethylcytosine (5-hmC) is an epigenetic hallmark which has recently become central in mapping and sequencing work. While the exact function of this base is not fully understood, it is likely to regulate gene expression as a member of active DNA demethylation pathways. The levels of 5-hmC in genomic DNA vary significantly depending on the cell type, though the highest levels are found in cells of the central nervous system (CNS): These findings suggest importance of 5- hmC in gene regulation within the CNS. While several methods have been developed to profile 5-hmC at genomic scale, most are enrichment-based, utilize large amounts of genomic DNA input, and have relatively low resolution. Although efforts have been made to detect 5hmC at single-site resolution, the methods described to date still require several micrograms of DNA, require parallel or subtractive sequencing, and employ successive chemical treatments that degrade the DNA and hinder sequencing. By combining modification-sensitive restriction enzymes with massively parallel (“next-generation”) sequencing approaches, we developed a novel Reduced Representation Hydroxymethylation Profiling (RRHP) method for genome-wide 5-hmC mapping at single-site resolution from low (100 ng) DNA inputs. Importantly, the method can detect strand polarity of 5-hmC modifications, and also enables the direct identification of single nucleotide polymorphisms (SNPs) within sequencing reads. Due to the fragmentation approach, data can be directly compared with single-base DNA methylation data from Reduced Representation Bisulfite Sequencing (RRBS). Human brain 5-hmC mapping generated with this method, combined with DNA methylation profiling data, indicates unique distributions of 5-hmC modification: We confirm that several important neuronal loci, such as BDNF, NLGN2, CES1, and TAF1, demonstrate extensive 5-hmC modification. This new method of detection and mapping is a powerful tool in enhancing our understanding of the interplay of genetic and epigenetic regulations in neurobiology and other diverse biological fields

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Genome-Wide Human Brain DNA 5-hmC Profiling Using a Novel Sequence- and Strand-Specific Method
Xueguang Sun, Adam Petterson, Tzu Hung Chung, Marc E. Van Eden, and Xi Yu Jia

5-Hydroxymethylcytosine (5-hmC) is an epigenetic hallmark rapidly gaining much interest within mapping and sequencing disciplines. While the precise role of 5-hmC is not fully understood, it is implicated in regulation of gene expression via active DNA demethylation pathways. Previous studies demonstrate that it plays a role in cell differentiation and carcinogenesis: Cells that are more stem- and progenitor-like have greatly reduced levels of 5-hmC compared with more differentiated cells. Similarly, tumor cells display less 5-hmC than their normal counterparts independent of either grade or stage, suggesting that global loss of 5-hmC may be an early event in carcinogenesis. Several methods have been described to profile 5-hmC at the genomic level: Most are enrichment-based via immunoprecipitation or other bioorthogonal labeling schemes, and several conversion methods have also been described that exploit selective oxidation. Here we employ a new method which combines modification-sensitive restriction enzymes with next-generation sequencing approaches to allow genome-wide 5-hmC mapping at single-site resolution in several families of carcinomas. This new method should provide a unique tool in enhancing our understanding of the interplay of genetic and epigenetic regulations in carcinogenesis.

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Genomic Approach for DNA Methylation and Hydroxymethylation Analysis
M. Krispin, X. Sun, R. Leavitt, D. Butler, W. Pirovano, B. Reichert, T. Chung, E. Bacon, A. Petterson, M. Van Eden, X. Jia

DNA methylation and hydroxymethylation are some of the most important epigenetic modifications that can occur in the human genome. For instance, DNA methylation plays a vital role in the regulation of gene expression in normal cell development and aging, and also in the formation and progression of cancer and other diseases. Large scale identification of putative epigenetic biomarker candidates is now achievable with the ability to profile DNA methylation and hydroxymethylation at the genomic level. Once validated, specific biomarkers could be applied to clinical and molecular diagnostic fields. Due to the increased availability of Next-Gen sequencing technology, a number of new technologies have been developed for interrogating DNA methylation and hydroxymethylation at the genomic scale. Zymo Research has recently perfected sample prep and bioinformatics analysis as part of its new DNA Methylation and Hydroxymethylation Profiling Services. These epigenetic services combine next-generation sequencing with Zymo's well-established epigenetic technologies and innovative bioinformatics algorithms for the most streamlined, comprehensive genome scale data generation to date. With these new services, hundreds of epigenomic biomarker candidates can be discovered simultaneously. Furthermore, Zymo Research offers services for validation of biomarker candidates via targeted sequencing or qPCR. abstract Introduction

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