Technical articles that are geared for researchers in the field.

Sunshine and Epigenetics: Altering Histone Variant H2A.Z Turnover and Gene Expression in Rice Seedlings

March 7, 2017 Sadman Sakib

Have you ever thought of how the day-night cycle can epigenetically affect plants? Latest research from Zhang et al. has shown a possible mechanism of how histone variants can negatively regulate gene expression in day-night cycles of rice seedling tissues. This paves a way for an exciting area of research of how histone variants can be differentially deposited in a very short time span, in order to fine tune the transcription due to the environmental stimuli in plants. Histones variants, [more…]

Introducing WERAM: Find Integrated Info on Your Histone Regulator in Your Favorite Species

January 5, 2017 Blanca Valle

Recently Dr. Yu Xue’s group, at the Huazhong University of Science and Technology in Wuhan, China, developed a database designated as Eukaryotic Writers, Erasers and Readers protein of Histone Acetylation and Methylation system Database (WERAM). WERAM is a comprehensive database containing integrated information on the writers, erasers, and readers of histone acetylation and methylation. Namely writers are the enzymes that catalyze acetylation and methylation, the erasers are the enzymes that remove these marks, and the readers are proteins that recognize and interact [more…]

Editing DNA Methylation Using CRISPR/Cas9

November 29, 2016 Estephany Ferrufino

Gene expression is controlled on several levels from DNA sequence to post-transcriptional changes. Epigenetics demonstrate that gene expression can be controlled by chemical changes in the DNA such as methylation. Since the discovery of epigenetics, researchers have been attempting to produce effective methods to alter the methylation status of select genes. This would enable researchers to effectively turn on or off target genes without affecting the genetic code. Liu et al. (2016) have repurposed the CRISPR/Cas9 system to edit DNA [more…]

The Epigenetic Marks of Circulating Cell-Free DNA (cfDNA)

September 16, 2016 Blanca Valle

Circulating cell-free DNA (cfDNA) are small DNA fragments found circulating in plasma or serum, as well as other bodily fluids. The cfDNA isolated from plasma usually contains fragments of about ~170-500 bp, mostly corresponding to ~170 bp mononucleosomal and ~300 bp dinucleosomal DNA fragments [1,2], thought to arise mostly from apoptotic cells. In addition, larger fragments (>1,000 bp) are often detected, thought to arise mostly from necrotic cells. In healthy individuals, the levels of cfDNA in plasma/serum are generally low, ranging between [more…]

Histone variant H2A.Z underlies inactivation of activity-dependent gene expression in learned behavior

August 23, 2016 Caitlin Aamodt

Over the past decade discoveries about the role of epigenetic mechanisms in learning and memory have changed the way scientists think about cognition 1. The most well characterized to date are histone acetylation and DNA methylation, but more recently discovered epigenetic mechanisms are continuing to shape researchers’ understandings of transcriptional regulation in post-mitotic neurons. Chromatin is made up of nucleosomes, which are 147 base pairs of DNA wrapped around a histone octomer. The canonical histones that organize DNA at the [more…]

New Method Simultaneously Profiles Methylome and Transcriptome in the Same Single Cell

April 7, 2016 Marisa Mariani

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…]

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…]

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