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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New SMRT-BS Method to Revolutionize Quantitative, Multiplexed Targeted Bisulfite Sequencing for Methylation Analysis

August 4, 2015 Bailey Kirkpatrick

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…]

Collecting & Analyzing Libraries For Chromatin Immunoprecipitation (ChIP)

March 10, 2015 David Esopi

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…]

A Starter Chromatin Immunoprecipitation (ChIP) Protocol

February 10, 2015 David Esopi

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…]

Preparation for Chromatin Immunoprecipitation (ChIP)

February 3, 2015 David Esopi

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…]

Simple Tweak Could Make Post-Bisulfite Library Preparation Suitable for RRBS

January 13, 2015 M.C. Williams

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…]

Introducing O-GlcNAc – The Latest Addition to the Orchestra of Epigenetic Modifications

December 15, 2014 Sam Keating

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…]

Advancements in DNA Methylation Analysis Technologies

October 21, 2014 Bailey Kirkpatrick

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…]

A Researcher’s Guide to Successful DNA Bisulfite Conversion

October 14, 2014 Milka Rodriguez

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…]

New Single-Cell Bisulfite Sequencing Technique Boosts Epigenetic Research

July 30, 2014 Bailey Kirkpatrick

A new single-cell bisulfite sequencing (scBS-seq) technique that can advance epigenetic experiments has been developed by researchers from BSRC-funded Babraham Institute and the Wellcome Trust Sanger Institute Single Cell Genomics Centre. Using this powerful technique, all epigenetic marks on the DNA within a single cell can be mapped out. This novel method could enhance our understanding of embryonic development and holds promise for improving clinical applications such as fertility treatments and cancer therapy. It may also reduce the amount of [more…]

Global DNA Methylation Analysis: The Best Assay You Haven’t Done Yet

July 24, 2014 Milka Rodriguez

Over the past decade significant advances have been made in methylation profiling technology allowing for highly specific and accurate information about the epigenome of various species. Because the 5mC and 5hmC modifications are widespread with possibly different functions, further insight into their distribution is important. Traditional methylation analysis methods such as mass spec, HPLC and TLC allow high accuracy but also require sophisticated equipment, are not high through-put and most importantly are expensive. Likewise more modern applications such as next [more…]

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