Many of the key cellular processes including establishing the cell's identity are governed by chromatin proteins. Mapping their binding on the level of a single cell would give us important insights into a new dimension of cellular heterogeneity. However, ChIP-seq, the main method to study protein-DNA interaction in the chromatin context, has proven very challenging to scale down. ChIPmentation is a modification of ChIP-seq, in which the Tn5 transposase is used to introduce sequencing adapters in one step. This allows to significantly reduce the required input material. ChIPmentation is a robust and versatile approach and even though it has not yet achieved single-cell resolution, we believe that it is a very promising starting point for further downscaling.
Mapping the genomic locations of chromatin-associated proteins, such as transcription factors and histone modifications, is key to understanding the mechanisms of transcriptional regulation. ChIPmentation offers a simple and robust way of investigating the genomic binding sites of a protein using relatively low-input material. Here, we present a detailed protocol for the key steps that lead to a successful ChIPmentation experiment, as well as a quick analysis pipeline to examine the data.
School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, PR China. Electronic address:
ChIP-seq is widely used for mapping the transcription factor (TF) binding sites throughout the genome in vivo. In this study, we adopted and modified ChIPmentation, a fast, robust, low-input requirement ChIP-seq method, to a transient expression system using soybean protoplasts to expedite the exploration of TF binding sites. To test this new protocol, we expressed a tagged version of a C2H2-type zinc finger TF, JAGGED1 (GmJAG1), in soybean protoplasts and successfully identified its binding sites in the soybean genome.
Many of the key cellular processes including establishing the cell's identity are governed by chromatin proteins. Mapping their binding on the level of a single cell would give us important insights into a new dimension of cellular heterogeneity. However, ChIP-seq, the main method to study protein-DNA interaction in the chromatin context, has proven very challenging to scale down.
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) is widely used to map histone marks and transcription factor binding throughout the genome. Here we present ChIPmentation, a method that combines chromatin immunoprecipitation with sequencing library preparation by Tn5 transposase ('tagmentation'). ChIPmentation introduces sequencing-compatible adaptors in a single-step reaction directly on bead-bound chromatin, which reduces time, cost and input requirements, thus providing a convenient and broadly useful alternative to existing ChIP-seq protocols.
