By Ben Butkus
Bio-Rad Laboratories has launched a real-time PCR assay kit that helps researchers assess chromatin structure in cells and correlate it to gene expression more rapidly than current methods, the company said this week.
The kit is expected to provide users with a quick and easy way to correlate epigenetic changes such as DNA methylation and histone modification with gene expression, Viresh Patel, a senior product manager at Bio-Rad, told PCR Insider.
In addition, the product is Bio-Rad's first real-time qPCR-based kit focused on a specific research application, and will likely not be the last, Patel said.
"This would be the first real applications-focused kit that uses qPCR that we've developed and launched," Patel said. "We have some other active areas of development to continue to expand the applications for real-time PCR and provide all-encompassing kits like this, to enable researchers to speed up their time to results for specific applications." Patel did not elaborate on other potential research applications.
The new product, called the EpiQ chromatin analysis kit, is a real-time PCR assay for the rapid quantitative assessment of chromatin structure. Bio-Rad said that it is the first commercial research tool that helps scientists quantify the impact of epigenetic events on gene expression regulation through chromatin state changes.
Epigenetic processes such as DNA methylation and histone modification control gene expression by altering chromatin structure. Genes that are actively transcribed are associated with so-called accessible chromatin regions called euchromatin, while genes that are silenced are often in inaccessible chromatin regions called heterochromatin.
"Typically, researchers studying epigenetic markers such as methylation and histone modification are trying to correlate those marks with expression differences," Patel said. "It can be difficult to make those correlations, as there isn't a clear one-to-one correlation between methylation pattern or density or even a specific histone mark with respect to how that activates or represses gene expression."
As researchers try to understand the mode of regulation and whether chromatin state plays a role in the expression of specific genes of interest — "that's where the EpiQ product provides information. It actually assesses the chromatin state inside cells," Patel said.
Other techniques exist for assessing chromatin state, most notably a "homebrew" approach that involves isolating and purifying nuclei from several million cells before chromatin digestion. This process may take up to two days to complete.
"Time and high cell requirements are kind of plaguing the adoption of that technique," Patel said. The EpiQ kit, he added, streamlines the process in terms of time and cell requirement. According to Bio-Rad, the kit can assess chromatin structure in as few as 50,000 cultured cells in six hours' time.
Bio-Rad has been offering the kit since December and has thus far sold the product to a few laboratories. One of those labs at the University of California, Berkeley, is using the product as part of a study on how sequence diversity in HIV-1 impacts gene expression properties of the virus.
More specifically, the researchers, in David Shaffer's laboratory at UC Berkeley, are studying how sequence diversity in a particular viral protein, which is necessary to activate gene expression from the viral promoter, alters the chromatin around the promoter, Siddharth Day, a graduate student in the lab, wrote in an e-mail to PCR Insider.
In addition, Day and colleagues are investigating how the chromatin environment around the site of HIV-1 integration into the host genome impacts gene expression from the viral promoter.
In both projects, the group has used chromatin immunoprecipitation, or ChIP, along with the EpiQ kit to assess the chromatin environment around the viral promoter.
"The advantage of the EpiQ kit is that it provides a quick overview of the chromatin state," Day said, adding that it takes around a day to get results. "In contrast, it takes a few days to do the ChIP assay, though ChIP can give greater molecular insights. The EpiQ kit could also be convenient if one is interested in looking at the chromatin state around several genes simultaneously."
All told, the EpiQ kit provides "a quick and easy way to study the chromatin and in cases where the results appear interesting, it can be further investigated using assays like ChIP that give greater molecular details," Day said.
The EpiQ kit components include buffers for cell permeabilization and in situ chromatin digestion, optimized nuclease, materials for genomic DNA purification, control assays for chromatin assessment of a reference and control gene, and EpiQ SYBR Green supermix.
Bio-Rad said that the assay can be used on all Bio-Rad real-time PCR instruments, of which there are four; as well as instruments from other suppliers.
Patel said that Bio-Rad decided to launch the EpiQ as its first application-focused kit after "years of research and observations of the growing area of epigenetics" and its increased use in research areas "outside of the typical cancer and developmental biology areas — especially with the recent surge in stem cell research." Further, epigenetics now appears to be an integral part of all gene expression regulation, Patel said.
"The other facet is just wanting to develop tools that would enable epigenetics research to be streamlined, and providing new information that customers don't have access to today," he said.
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