Posts Tagged ‘epigenetics’

The First Epigenetics Tool that Quantifies Chromatin State for Gene Expression Studies

 :: Posted by American Biotechnologist on 02-15-2011

Bio-Rad Laboratories, Inc.’s new EpiQ chromatin analysis kit is a real-time PCR assay for the rapid quantitative assessment of chromatin structure. Complementing existing epigenetic assays such as DNA methylation and chromatin immunoprecipitation, the EpiQ kit is the first commercial research tool that helps scientists quantify the impact of epigenetic events on gene expression regulation through chromatin state changes.

“The EpiQ chromatin analysis kit provides researchers with an easy and fast way to quantify a gene’s chromatin state,” said Viresh Patel, Bio-Rad Marketing Manager for PCR reagents. “Using the kit, cancer, developmental, and stem cell biology researchers are able to glean direct information regarding the chromatin state that’s associated with epigenetic marks such as DNA methylation and histone modifications for the first time.”

Epigenetic processes such as DNA methylation and histone modification control gene expression by altering chromatin structure. Genes that are actively transcribed are associated with “accessible” chromatin regions called euchromatin, while genes that are transcriptionally silent are often in “inaccessible” chromatin regions called heterochromatin. The EpiQ kit can provide quantitative information about chromatin accessibility, which correlates very strongly with gene expression.

Reduces Analysis Time from Days to Hours
Until now, the only way to quantitatively probe the status of chromatin structure was through the use of homebrew methods, first described in 2001 (Rao, et. al., J. Immunol.). This approach requires the isolation and purification of nuclei from several millions cells prior to chromatin digestion and takes more than two days to complete. With the EpiQ kit, chromatin structure data can be obtained within six hours from as few as 50,000 cultured cells, without the need for nuclei isolation.

Key benefits of the EpiQ chromatin analysis kit include:

  • Assessment of chromatin structure in cultured cells within six hours
  • Requirement of relatively few cells (as few as 50,000) to perform analysis
  • Generation of quantitative chromatin structure information for multiple genomic elements

How It Works
The Chromatin state of a gene can be identified in situ based on its sensitivity to the action of the nuclease in the EpiQ kit. In heterochromatin, genomic DNA is inaccessible to nuclease digestion and remains available for subsequent qPCR. Analysis of heterochromatin using the EpiQ kit reveals a minimal quantification cycle (Cq) shift between digested and undigested samples. In contrast, DNA in euchromatin is susceptible to nuclease digestion and is unavailable for qPCR. Analysis of euchromatin using the EpiQ kit shows a large Cq shift between digested and undigested samples.

What Is Included in the EpiQ Kit
EpiQ kit components include buffers for cell permeabilization and in situ chromatin digestion, optimized nuclease, materials for genomic DNA purification, control assays (qPCR primers) for chromatin assessment of a reference (epigenetically silenced) and control (constitutively expressed) gene, and EpiQ™ Chromatin SYBR® Green Supermix, a real-time PCR reagent designed to amplify genomic DNA. The supermix can be used on all Bio-Rad real-time PCR instruments and on those from other suppliers; some instruments may require slight modifications to the supermix.

For more information about the EpiQ chromatin analysis kit, visit www.bio-rad.com/epiq.

For a layman’s guide to epigenetics see epigenetics for friends and family.

Epigenetics for friends and family

 :: Posted by American Biotechnologist on 02-09-2011

I often find it difficult explaining to friends and family exactly what I do in the lab. In fact, before I started my graduate work, concepts such as DNA, protein, electrophoresis and gene transfer all seemed to esoteric and foreign. That’s why, whenever I come across an article or video that helps clarify our field of work to the layman, I am inclined to share.

In honor of the 10 year anniversary of the sequencing of the human genome, Joe Kloc of Mother Jones has put together a simple yet elegant explanation of epigenetics.

Check it out by clicking on The Illustrated Guide to Epigenetics.

Feeling Good About Being A Molecular Biologist

 :: Posted by American Biotechnologist on 09-12-2010

Here’s an inspirational story that played on CBS describing how epigenetic therapy rescued firefighter Jerry Morton from the deathly clutches of lung cancer. Epigenetics involves changes in gene expression without an associated change in the underlying DNA sequence. Examples of epigenetic processes include: bookmarking, gene silencing and X chromosome inactivation. Many cancer treatments fail because while trying to kill cancer cells, the treatment destroys many healthy cells as well. According to the CBS report “in epigenetic therapy, instead of actually trying to kill the cancer cells, they try to change their behavior so they don’t act like cancer.”

Stories such as these should provide us with the inspiration we need to continue slaving away in the lab day in and day out. As molecular biologists we are the key to the future of medicine. I once read an interview of a senior investigator at a prominent university who said that he would rather be a scientist than a medical doctor. In his words, “while doctors are members of the orchestra, scientists are the conductors.”