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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A new single-cell genomics protocol that is potentially transformative for epigenetics research has been developed by scientists in the UK and Belgium. Applying this method, it is now possible to study the epigenome and transcriptome of a single cell at the same time. This novel approach could enhance our understanding of the link between gene expression and DNA methylation in single cells. Also, the knowledge of this relationship may clarify the mechanisms underlying normal development, and changes that occur with [more…]
Planaria, or flatworms, are often used as a model organism to investigate the fascinating process of how tissues and organs can regenerate. The flatworm has numerous stem cells called neoblasts and, when it’s injured, this intriguing creature can actually restore its own body parts. Researchers conducted the study at the Stowers Institute for Medical Research in the lab of Alejandro Sánchez Alvarado, Ph.D., a Howard Hughes Medical Institute investigator. In two related studies, they examined stem cell differentiation and the [more…]
Bisulfite sequencing offers researchers a profound look into the epigenome and the methylation status of genes. A significant driving force in the development of epigenetic research since 1992, the detection of CpG methylation and methylation abnormalities in DNA via bisulfite sequencing has become overwhelmingly popular – and interest continues to grow. The unparalleled power of next-generation sequencing (NGS) platforms provides researchers with new insights into the nuances of gene expression and countless other critical cellular processes. Still, bioinformatics expertise, cost, [more…]
Editor’s Note: At the author’s request on August 20th, 2015, revisions to this article were made following careful consideration. All changes are denoted in red. In the previous post of this ChIP series, we left off with your samples rotating at four degrees overnight, to give the antibodies plenty of time to bind and the beads plenty of time to block. In this final post, we will finish the assay and provide advice on how to QC and analyze your libraries. [more…]
Editor’s Note: At the author’s request on August 20th, 2015, revisions to this article were made following careful consideration. All changes are denoted in red. In the first post of this ChIP series, we introduced the reader to the general concept and workflow of chromatin immunoprecipitation (ChIP), and provided advice on planning a ChIP experiment and preparing the necessary reagents. In this post, we will go through a more detailed protocol that we have used in our lab with success that [more…]
Editor’s Note: At the author’s request on August 20th, 2015, revisions to this article were made following careful consideration. All changes are denoted in red. Since its introduction in the 1980s, chromatin immunoprecipitation (ChIP) has become one of the most important and powerful techniques in the field of genetics, allowing researchers to characterize a given protein’s binding sites across the genome. With the advent of next-generation sequencing and whole genome analysis, a single ChIP can deliver gigabytes of information, including not [more…]
The concept of DNA library preparation after bisulfite conversion of DNA was originally introduced by Miura et al. (Nucleic Acids Res. 2012) and commercial products for post-bisulfite library preparation were first developed by Epigentek (EpiNext kit) and Epicentre (EpiGnome kit) in 2013, in order to increase sensitivity and reduce sample loss. The major application of post-bisulfite library preparation is whole genome bisulfite sequencing (WGBS) but, with just a slight change to the protocol, this method could also be used for reduced representation [more…]
Post-translational modifications are well known for their influence on protein stability, enzymatic functions, as well as protein:protein interactions. At the level of gene expression, acetylation, methylation, phosphorylation, ADP-ribosylation, ubiquitination and SUMOylation are some of the most prevalent chemical modifications that regulate transcription factors and the chromatin template (the complex of DNA and histone proteins) alike. In particular, the manifold modifications occurring on the histone proteins that closely associate with DNA are proposed to constitute a gene-regulating code (the histone code). [more…]
Recent developments in DNA methylation analysis technologies have made it crucial for researchers to understand which tool is optimal for their epigenetic research. These new methods pose exciting opportunities never before imagined, allowing for epigenetic variation to be connected to phenotypic consequences on a much grander scale and at single-base resolution. In a recent issue of an epigenetics newsletter, The Decoder, scientists at Epigentek discuss the latest progress made in profiling genome-wide and region-specific DNA methylation and offer suggestions on [more…]
DNA bisulfite conversion is a unique tool used to discriminate between methylated and unmethylated cytosines for DNA methylation studies. Only bisulfite modification of DNA followed by sequencing yields reliable information on the methylation states of individual cytosines at single base resolution. The bisulfite modification technique uses bisulfite salt to deaminate cytosine residues on single-stranded DNA, converting them to uracil while leaving 5-methylcytosine unchanged (Figure 1). To effectively and efficiently prepare converted DNA for use in various downstream analyses, an ideal [more…]