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Austrian Team Develops 'ChIPmentation' Protocol to Simplify ChIP-seq

NEW YORK (GenomeWeb) – Scientists from the Research Center for Molecular Medicine at the Austrian Academy of Sciences have developed a ChIP-seq protocol that makes use of transposase tagmentation for library construction. Dubbed ChIPmentation, the researchers published the details of it today in Nature Methods.

The method relies on coupling transposase tagmentation with chromatin immunoprecipitation followed by next-generation sequencing to reduce the time, complexity, and input requirements of standard of ChIP-seq protocols.

The method is "an attractive alternative for essentially all users of ChIP-seq, given its speed, robustness, cost-effectiveness, and simplicity," Christoph Bock, principal investigator at CeMM and senior author of the study, said in a statement. ChIPmentation "makes it easier to process a large number of rare cell types using a standardized workflow," he added, which could make it useful for large-scale projects such as the BLUEPRINT consortium, the International Human Epigenome Consortium, and the International Cancer Genome Consortium.

The transposase tagmentation method was originally described by researchers from the University of Washington, the Marine Biological Laboratory in Woods Hole, BGI, and Epicentre Biotechnologies in a study published in Genome Biology. The library construction method is now sold as an Illumina Nextera kit.

While the method has been adapted for a number of sequencing applications, it had not yet been combined with ChIP-seq. The Austrian team was looking for a way to improve on ChIP-seq methods, which tend to be "tedious, time-consuming, and costly," the authors wrote, and decided to try and combine the tagmentation process with ChIP-seq.

In an initial experiment, they first performed standard chromatin immunoprecipation and then used the tagmentation library prep on the resulting purified chromatin immunoprecipitated DNA, but that approach was "difficult to standardize across samples and across antibodies," they wrote.

Next, the researchers sought to perform tagmentation directly on the immunoprecipated and bead-bound chromatin. Looking across five metrics — measured library size distribution, size distribution inferred from paired-end sequencing reads, read mapping, concordance between sequencing profiles, and signal correlation — the method was robust across a 25-fold difference in transposase concentration. In addition, the method did not result in sequencing adaptor dimers and only required one DNA purification step before library amplification.

The team validated the method for five different histone marks and four transcription factors, and found that in each case the ChIPmentation profiles were high quality and correlated with standard ChIP-seq profiles.

The method also enabled less input material. The researchers were able to obtain accurate ChIPmentation profiles for the histone marks H3K4me3 and H3K27me3 using just 10,000 cells and for transcription factors GATA1 and CTCF using 100,000 cells.

In addition, they found patterns in the spacing of tagmentation events that appeared to be related to "the wrapping of DNA around nucleosomes." They also found patterns around the center of nucleosomes that indicated increased transposase insertion frequency, suggesting that "ChIPmentation data may be useful for inferring transcription factor footprints, nucleosome stability, and nucleosome positioning," the authors wrote.

In a statement, co-lead author, André Rendeiro, explained that the method reveals chromatin structure because tagmentation is performed on chromatin with proteins still bound to the DNA. The group is now "working on computational methods to better understand the biological relevance of these high-resolution patterns," he said.