New Quantitative Method to Apply Tagmentation Technology to ChIP-Seq

Web Published:

Princeton Docket # 16-3268


Chromatin immunoprecipitation (ChIP) is an affinity assay for detecting the interaction between a particular protein and DNA in cells. Using a protein-specific antibody, DNA bound by that protein can be isolated and identified using high throughput sequencing (ChIP-seq). One desirable way to prepare a DNA library for sequencing is known as tagmentation, where a high-activity transposase is used to fragment and tag DNA with sequencing adapters. Researchers in the Lewis-Sigler Institute for Integrative Genomics at Princeton University have developed a greatly improved method to apply tagmentation technology to ChIP-seq called ChIP-SMITH (Simple Multiplexing Index by Transposase with High-resolution ChIP).


One major limitation of current ChIP-seq protocols is the difficulty in normalizing across multiple samples. ChIP-SMITH solves this issue by tagmenting individual samples with barcoded sequencing adaptors after cell lysis, and then multiplexing them for subsequent ChIP and sequencing steps. This allows quantitative comparison across samples, and minimizes loss associated with low levels of starting material. These barcodes also contain randomized dNTP unique molecular identifier tags to distinguish true reads from over-amplified DNA. One major application for ChIP-seq is to identify the exact DNA sequence or “footprint” that binds to a target protein. ChIP-SMITH uses several additional steps to provide higher-resolution binding footprint than previously used techniques like ATAC-Seq. Finally, this invention improves on existing tagmentation technology by utilizing a single transposase design to recover up to 50% more sequences in the final library than current methods.


This technology has immediate application as a kit to apply Tn5-based tagmentation technology to ChIP-seq. As outlined above, it is a significant improvement over other existing methods designed for this purpose.



•       Identification of Protein-DNA binding sequences.

•       DNA library preparation for Next-Generation Sequencing



•       Quantitative multiplexing

•       Pre-ChIP tagmentation

•       Precise footprinting

•       Up to 50% more sequence recovery

•       Controls for PCR bias


Stage of Development

The method has been validated on both histone-modification and Pol II ChIP-seq libraries. Preliminary data indicate increased coverage and sensitivity vs standard techniques.



Kai Chen, Ph.D. is a post-doc researcher in Prof. Mike Levine’s Lab at Princeton University studying functional genomics during early embryogenesis. He is actively involved in developing new genomics assays, especially in Next-Generation Sequencing (NGS), to address the unmet needs in life science research. In addition to independent work in the Levine lab, Kai has worked closely with other laboratories and the Genomics Core Facility in the Lewis Sigler Institute to solve sequencing challenges. During his graduate studies in the Zeitlinger Lab at Stowers Institute for Medical Research, he developed his own high-sensitive ChIP-Seq method for Drosophila embryos. In addition, he gave critical suggestions for developing the ChIP-NEXUS protocol.


Mike Levine, Ph.D. is the Director of the Lewis-Sigler Institute for Integrative Genomics at Princeton University and a world leader in the study of gene-network regulation during development. He is a member of the National Academy of Sciences and has won many awards including the 1996 NAS Molecular Biology Award, the 2009 Wilbur Cross Medal from Yale, and the 2015 EG Conklin Medal from the Society of Development Biology. Levine was a Professor of Genetics at UC Berkeley from 1996-2015 and Chairman of the Chancellor’s Advisory Council for Biology from 2012-2015. He was Head of the Division of Genetics, Genomics and Development from 2007-2011 and served as Acting Director of the Functional Genomics Program at the Joint Genome Institute (DOE) in 2001. Prior to that he held faculty positions at Columbia University and UCSD, and was a Visiting Professor of Zoology at the University of Zurich from 1999-2000.


Intellectual Property Status

Patent protection is pending.


Princeton is currently seeking commercial partners for the further development and commercialization of this opportunity.



Chris Wright

Princeton University Office of Technology Licensing • (609) 258-5579•


Patent Information:
For Information, Contact:
Chris Wright
Licensing Associate
Princeton University
Michael Levine
Kai Chen