Successful application of novel plant ChIP-seq technology results in high quality sequencing data from Arabidopsis thaliana seedling cells

In the recent years massively parallel sequencing (also known as Next Generation Sequencing or NGS) has become the dominant method for sequencing, and the decreasing costs and increasing yields transformed biosciences. Due to greater accessibility and higher throughput, NGS is also highly utilized in epigenetic or epigenomic studies, most widely in ChIP-seq. NGS is the detection method of choice for ChIP, which gives an accurate qualitative and quantitative insight into protein-DNA interactions, such as binding events and sites of transcription factors or chromatin modi cations including methylation and acetylation.

In addition to the widespread use of ChIP-seq and other NGS-related techniques, another major trend is the increasing use of limited amounts of starting material (e.g. due to ancient fossil samples, forensic samples, or limitations on amounts of material generated cells). In some instances, samples such as may not yield enough material for a regular ChIP-seq as in the case of embryonic tissues, the few cell layers of a speci c zone in the apical meristem, etc. In other studies the researcher might be simply interested in the epigenetic events in a single cell.

Plant researchers also have a need for ChIP-seq from limited amounts of material, but their needs are rarely met. There are not many commercial solutions available that are dedicated to plant research, and usually these are not designed for low cell number experiments.

In this study, we show a successful and reliable ChIP-seq technology using limited amounts of plant material, with speci c reagents and protocols, supported by strict bioinformatic QC analysis.