Epigenetic mechanisms are inheritable factors that regulate genetic expression without changing DNA sequence. These factors are manifest as DNA methylation, histone modification, and small regulatory RNAs.
In recent years the field of epigenetics has grown into one of the most exciting and dynamic fields of biological research, and Zymo Research has grown with it, branding ourselves The Epigenetics Company™.
Bisulfite treatment (conversion) for the deamination of (C)ytosine to (U)racil in DNA has remained the "gold standard" for a number of downstream applications developed over recent years to assess DNA methylation status. Most commonly used methods for local and base-pair methylation resolution have traditionally relied upon pretreatment of DNA with bisulfite, which allows for the most specific, nucleotide-level snapshot of methylation status. However, in addition to the standard bisulfite conversion methodology, Zymo recently began to pioneer the field of bisulfite-independent methylation studies. Specifically, we are able to offer streamlined, one-step enzymatic approaches that substantially reduce processing time to provide locus-specific resolution of methylation status.
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). Investigations of 5-hmC are hindered as there exist few methods to distinguish between 5-mC and 5-hmC with fidelity: Bisulfite conversion, the gold standard for methylation detection, cannot distinguish between the two bases. As a result, the validity of preexisting 5-mC mapping data can be compromised.
The ability to fragment and degrade DNA has been available for years. However, with recent discoveries in the field of epigenetics, this technology can be applied in order to determine methylated and hydroxymethylated modifications of sheared DNA, nucleotides or nucleosides. Fragmented and degraded DNA is ideal for a number of downstream applications including Next-Gen sequencing, LC/Mass spectrometry, thin layer chromatography, and immunoprecipitation.
Nucleosome positioning in promoters is a key gene regulatory mechanism. With the EZ Nucleosomal DNA Prep Kit, yeast or mammalian nucleosomal associated DNA can be purified in less than 30 minutes. The EZ Nucleosomal DNA Prep Kit comes with micrococcal nuclease, optimized buffers, and a streamlined procedure to obtain highly pure nucleosome associated DNA.
Chromatin immunoprecipitation (ChIP) is an established and useful technique for characterizing cellular protein/DNA associations including those specific for genomic loci having undergone histone modification. Consequently, the purity of ChIP DNA is essential for successful downstream analyses (e.g., PCR, Southern blotting) and accurate data interpretation. The ChIP DNA Clean & Concentrator™ from Zymo Research has been designed for quick (2-minute) recovery of ultra-pure DNA from any chromatin immunoprecipitation (ChIP) assay, cell lysate, Proteinase K-digested sample, PCR mixture, or other enzymatic reaction.
Several aspects of epigenetics are strongly linked to non-coding RNAs, especially small RNAs that can direct cytosine methylation and histone modifications that are implicated in gene expression regulation in complex organisms. The ZR RNA MicroPrep™ and ZR RNA MiniPrep™ provide quick methods for the isolation of high quality total RNA from small amounts of cells and tissue. Both kits isolate large and small RNAs that can include those non-coding regulatory species that affect gene expression. For high resolution extraction and purification of small RNAs (e.g., miRNA) from polyacrylamide gel slices, the ZR small-RNA™ PAGE Recovery Kit is available.