If you run enough tedious ChIP experiments, it feels like you might as well be panning for gold back in the 1800s; doing a lot of work for a few nuggets of data. Luckily some technological wizards at Cornell University have your back and are working on a new system called SCAN (Single Chromatin Analysis at the Nanoscale) that will let you survey multiple histone marks simultaneously.
Paul Soloway, who helped lead the development team, explains how SCAN uses multicolor fluorescence microscopy to identify DNA and histones. “When we set up a SCAN experiment, we direct chromatin through the device using a voltage gradient. As a molecule flows though the inspection volume, it is excited by lasers and we detect the intensity of any emitted light. We collect all the data during the run time and process them off line.”
Not to sound like an infomercial, but the SCAN device has some great features:
- Looks at multiple epigenetic marks at once
- Provides genome-wide analysis, but assays single molecules
- Saves sample compared to running multiple ChIPs
- Fast throughput of about 10Mbp/min in a single channel
- Able to study DNA methylation status as well as chromatin
Sounds impressive, right? Well hold on, because according to Dr. Soloway there are a few more tweaks to be made before the SCAN device is ready for prime-time.
“To increase throughput, we’re working on different optics that can analyze multiple parallel nanofluidic channels at one time. The data we published came from analysis of chromatin flowing through a single channel, but the device on which the analysis was done contained 432 channels.” Soloway explains. “Also, we can run channels at a higher voltage than we used in our initial analysis, this too will improve throughput.”
Another big upgrade would combine their system with downstream sequencing. “…we are modifying the existing device to include sorting capability so that we can recover chromatin fragments with defined epigenetic states and perform SCAN-seq.” says Soloway.
Stay tuned, we’re sure to hear more about SCAN soon. Check out more about how SCAN can streamline your chromatin prospecting at Analytical Chemistry, March 2010.