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Publications of the Week

PIXUL-ChIP: Integrated High-Throughput Sample Preparation and Analytical Platform for Epigenetic Studies

By April 15, 2019No Comments

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This week we profile a recent publication in Nucleic Acids Research from the laboratories of Dr. Karol Bomsztyk (left)
at UW Medicine SLU, and Dr. Tom Matula (right) at the UW Center for Industrial and Medical Ultrasound.

Can you provide a brief overview of your lab’s current research focus?

Dr. Bomsztyk’s lab has been developing high throughput technologies, such as Fast and Matrix ChIP, and computational tools to tackle molecular complexities of disease with the focus on epigenetic alterations in organ injury, diabetes and cancer. Dr. Matula’s lab at CIMU develops advanced ultrasound technologies for industrial and medical applications.

What is the significance of the findings in this publication?

Chromatin immunoprecipitation (ChIP) is the most widely used approach for identification of genome-associated proteins and their modifications. Over the more than 30 years ChIP assays have become faster, more sensitive and can be carried out in high throughput fashion, for example using microplates as in Matrix ChIP. These advances in ChIP assays have made it possible to better define transcription and chromatin processes and have played a key role in driving the field of epigenetics, discovery of biomarkers and drug targets. However, even with microplate ChIP assays, sample preparation and chromatin fragmentation (which is required to map genomic locations) remains a major bottleneck. We have developed a novel technology (termed “PIXUL” for PIXulated ULtrasound) utilizing an array of ultrasound transducers for simultaneous shearing of samples in standard 96-well microplates. We integrated PIXUL instrument with Matrix ChIP (“PIXUL-ChIP”), that allows for fast, reproducible, low-cost and high throughput sample preparation and ChIP analysis of 96 samples (cell culture or tissues) in as little as one day using cost saving of the shelf microplates. The high throughput capacity of PIXUL-ChIP provides the means to carry out ChIP-qPCR (site specific) or ChIP-seq (genome-wide) experiments involving dozens of samples at time (for example multiple organs or tumors). Further, data are presented to show that the PIXUL instrument can be used as a multipurpose high throughout sample preparation platform for multiomics applications.

What are the next steps for this research?

PIXUL technology was licensed out of the University of Washington to Matchstick Technologies Inc, a UW spin off co-founded by Drs. Bomsztyk and Matula to commercialize PIXUL and bring it to the research market. PIXUL and PIXUL-ChIP technology is expected to have wide application in the field of transcription and chromatin biology as well as epigenetics to advance our understanding these pathways in health and disease, discovery of biomarkers as well as facilitate screening of epigenetic drugs.

This research was funded by:

NIH R33CA191135, R21GM111439, R01DK103849 and Life Sciences Discovery Fund (LSDF) of State of Washington #12330479.

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