Epigenetics research is focused on understanding how chromatin structure impacts gene expression, the requirement for this architecture in normal cellular processes, and how aberrant regulation of chromatin relates to human disease. In fact, multiple epigenetic mechanisms have been linked to human cancer, and each have distinct roles in regulating chromatin.
1. DNA methylation: DNA methylation is a process by which a methyl group is directly added to DNA sequences. In mammals, DNA methylation occurs almost exclusively in a CpG dinucleotide context, and high levels of DNA methylation are important for heterochromatin and gene silencing. In fact, DNA methylation has been shown to directly inhibit transcription factor binding, and also promotes the establishment of other repressive chromatin features, such as specific histone post-translational modifications (see below). DNA methylation, or 5mC, is catalyzed by a group of enzymes known as DNA methyltransferases, or DNMTs.
2. Histone post-translational modifications (PTMs) Histone PTMs are another class of epigenetic features that can both positively and negatively affect gene expression. Histone proteins are the building blocks of nucleosomes, and nucleosomes are the fundamental subunit of chromatin structure. Each nucleosome is composed of a histone octamer, wrapped with ~147bp DNA. The tails of histones are decorated with a variety of post-translational modifications, or PTMs, including lysine methylation, acetylation, and phosphorylation, which each have distinct roles in chromatin accessibility. Some PTMs, such as trimethylation on lysine 27 of histone H3 (H3K27me3), are indicative of gene silencing, and result in a more compact chromatin structure at gene promoters. Other PTMs, such as histone acetylation, lead to an opening of chromatin architecture via electrostatic interactions, making chromatin more accessible to transcription factors, chromatin remodelers, and other interacting proteins. And further, some histone PTMs directly interact with multiple chromatin complexes, and facilitate mechanisms that are essential to normal developmental processes.
Because of the significance that epigenetic changes have on gene regulation and the formation of disease, many assays have been developed to profile the localization of chromatin modifications relative to DNA sequence. One assay for chromatin profiling is ChIP-seq, or chromatin immunoprecipitation sequencing, which provides a genome-wide map of histone PTM (or other chromatin interacting protein) localization. . ChIP-seq is used in many studies to determine changes in chromatin structure in disease vs. healthy controls, and can help reveal novel epigenetic mechanisms. Indeed, ChIP-seq data is often critical to epigenetics research, particularly histone PTMs, as their location on chromatin may provide new insights towards disease and reveal novel drug targets or diagnostic indicators.
In ChIP-seq for histone PTMs, highly specific antibodies to the mark of interest are used to enrich and isolate specific subsets of chromatin from large fragmented pools. It is imperative to use highly specific antibodies that exhibit low cross-reactivity, thus preventing contamination of results by off-target PTMs, and ensuring both accurate and reliable sequencing data. EpiCypher has developed a novel process for validating antibodies used in ChIP-seq assays: SNAP-ChIP (Sample Normalization and Antibody Profiling for ChIP). SNAP-ChIP profiles ChIP antibodies against panels of DNA-barcoded modified recombinant nucleosomes (i.e. SNAP-ChIP spike-ins) in situ, thus directly assaying their specificity and efficiency in the context of a ChIP experiment. EpiCypher SNAP-ChIP Certified Antibodies thus represent the most rigorously validated ChIP antibodies for a given histone PTM target.
The use of highly specific antibodies is crucial to generating reliable ChIP-seq data for peer-reviewed publications. To learn more about SNAP-ChIP Certified Antibodies that EpiCypher offers and to see a full list of their products for ChIP-seq, visit their site at EpiCypher.com.
Moosavi A., Motevalizadeh Ardekani A.
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