What is Epigenetics technical articles are geared towards epigenetic research techniques, news, and trends in the field of epigenetics, written by scientists from universities and institutions including UCLA, Hofstra, NIH, Johns Hopkins, and more.
Explore in detail new epigenetic research techniques and tips for topics like next-generation sequencing (NGS) in epigenetics, m6A RNA methylation, CRISPR/Cas9 system epigenetic editing, chromatin immunoprecipitation (ChIP) protocol optimization, and single-cell epigenomics methods.
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Every epigenetics scientist knows that chromatin immunoprecipitation (ChIP) is a valuable technique for studying protein-DNA interactions. They also know that antibodies used in ChIP to capture the DNA/protein complex must be reliable and specifically recognize the fixed protein that is bound to the chromatin complex. But how can a researcher be certain that the antibodies they are using work well in ChIP? For many researchers it is not always the case to be “blessed” with a quality ChIP-grade antibody and, unfortunately, [more…]
Researchers rely on high quality antibodies to perform successful chromatin immunoprecipitation (ChIP) experiments. When investigating the protein-DNA interaction of interest, valid and reliable results simply cannot be attained using nonspecific and inefficient antibodies. If the antibody doesn’t come “ChIP-qualified” or “ChIP-grade” from the supplier, there are several tips you can follow to determine if it’s likely to perform well in ChIP and won’t pull down distracting material to get in the way of a successful study. Carry out the standard [more…]
The following histone extraction protocol was written by scientists at Epigentek and is a recommended and optimized procedure for their histone modification assays, successfully utilized by many research labs. Use these easy to follow steps to ensure proper isolation of histone proteins. For tissues (treated and untreated), weigh the sample and cut the sample into small pieces (1-2 mm3) with a scalpel or scissors. Transfer tissue pieces to a Dounce homogenizer. Add TEB buffer (PBS containing 0.5% Triton X 100, 2 [more…]
Hematopoietic stem cells (HSCs) are rare bone marrow cells that have self-renewal capability and are multipotent. Upon differentiation, HSCs become progressively lineage-committed and give rise to different mature blood cells. This process involves extrinsic and intrinsic signals that are strongly influenced by the stem cell microenvironment. Furthermore, differentiation involves silencing of self-renewal genes and induction of a specific transcriptional program. It is not known how epigenetic modifications influences stem cell differentiation and commitment and what specific role these modifications may [more…]
Messenger RNA (mRNA) is a single-stranded RNA molecule that is essential in mediating the transfer of genetic information from DNA by serving as a template for protein synthesis. There are several mechanisms involved in regulating the stability of messenger RNA to influence the level and timing of protein production. Such mechanisms include regulatory elements such as sequence elements or structural motifs that can target mRNA for degradation. Furthermore, post-transcriptional modifications such as dynamic methylation of mRNA could also be involved [more…]
In eukaryotic RNA, the methylation of adenosine at the N6 position to form N6-methyladenosine (m6A) is the most common and abundant postsynthesis modification known. Until recently, the biological significance of this RNA modification has remained unclear due to technical and experimental limitation. These include: detection methods that are mostly limited to immunoprecipitation; low resolution mapping of m6A around methylation sites which cause precise locations to be unclear; and the lack of an experimental model for depletion of the methylation complex [more…]
Scientists at Stanford University School of Medicine have developed a rapid and sensitive method for integrative epigenomic analysis called assay for transposase-accessible chromatin using sequencing (ATAC-seq).This assay is based on direct in vitro transposition of sequencing adaptors into native chromatin, which captures open chromatin sites using a simple two-step protocol with 500–50,000 cells and reveals the interplay between genomic locations of open chromatin, DNA-binding proteins, individual nucleosomes and chromatin compaction at nucleotide resolution. By using ATAC-seq, the scientists discovered classes of DNA-binding [more…]
Researchers at Epigentek recently developed a new and breakthrough approach to identify the “fifth base” of RNA, N6-methyladenosine (m6A) to efficiently study RNA methylation in a practical and cost-effective manner. The technology is based on a high throughput and strip-well microplate format and is made commercially available as the EpiQuik m6A RNA Methylation Quantification Kit, the first of its kind. It was commonly believed that messenger RNA (mRNA) contains four nucleobases — guanine, adenine, uracil, and cytosine. However in 2012, [more…]
The scientists at MIT describe an approach for efficient targeted demethylation of specific CpGs in human cells using fusions of engineered transcription activator–like effector (TALE) repeat arrays and the TET1 hydroxylase catalytic domain. Using these TALE-TET1 fusions, they demonstrated that modification of critical methylated promoter CpG positions can lead to substantial increases in the expression of endogenous human genes. Genome-wide studies have defined cell type–specific patterns of DNA methylation that are important for regulating gene expression in both normal development2 [more…]
5-methylcytosine is found in the context of paired symmetrical methylation of a CpG site. In normal somatic cells, most CpG sites are heavily methylated, while CpG islands (sites of CpG clusters) in germ-line tissues and located near promoters, remain unmethylated thus allowing gene expression to occur. When a CpG island in the promoter region of a gene is methylated, expression of the gene is repressed. The addition of methyl groups is controlled at several different levels in cells and is [more…]