Methidiumpropyl Ethylenediaminetetraacetic Acid (EDTA) Sequencing MPE-seq is a method for the genome-wide characterization of chromatin that involves the treatment of nuclei with a complex of methidiumpropyl-EDTA (MPE) and ferrous iron. The MPE-Fe(II) complex binds to DNA via intercalation of the methidium moiety and then generates […]

Micrococcal Nuclease Sequencing / Micrococcal Nuclease_Assisted Isolation of Nucleosomes / Isolated Nucleosome Sequencing / Isolated Nucleosome Sequencing Micrococcal nuclease (MNase) is derived from Staphylococcus aureus, and its first use to determine chromatin structure dates back to 1975, when the method was called, variously, staphylococcal nuclease […]

Mapping in Vivo Nascent Chromatin with EdU MINCE-seq was developed to characterize the genome-wide location of nucleosomes and other chromatin proteins behind replication forks at high temporal and spatial resolution (Ramachandran et al., 2016). In this method, newly replicated DNA is labeled with the nucleotide […]

High-Throughput Sequencing With Fluorescent Ligand Interaction Profiling HiTS-FLIP is a technique for measuring quantitative protein-DNA binding affinity at unprecedented depth. In this approach, the optics built into a high-throughput sequencer are used to visualize in vitro binding of a protein to sequenced DNA in a […]

Fixed-Tissue Chromatin Immunoprecipitation Sequencing FiT-seq is a method to extract soluble chromatin from FFPE tissue samples for the detection of histone-binding sites (Cejas et al., 2016). The distinguishing feature of this method is a proteinase K digestion step to reverse the effects of heavily crosslinked […]

Formaldehyde-Assisted Isolation of Regulatory Elements / Sonication of Crosslinked Chromatin FAIRE-seq (Giresi et al., 2009) (Hogan et al., 2006) and Sono-Seq (Auerbach et al., 2009) are based on differences in crosslinking efficiencies between DNA and nucleosomes or sequence-specific DNA-binding proteins. In this method, DNA-protein complexes […]

DNase I Simplified in-Nucleus Method for plants This method is a simplified DNase I protocol specifically intended for plants(Cumbie et al., 2015). It contains an additional step of nuclei purification in Percoll gradients prior to DNase I digestion, in order to remove cellular debris and […]

DNA Adenine Methyltransferase Interaction Detection DamID allows the identification of protein-binding sites in living cells without the need for crosslinking or immunoprecipitation. It was developed in 2006 as a microarray method before it was adapted to NGS (Vogel et al., 2006). DamID involves the low-level […]

Chromatin Immunoprecipitation Sequencing / High-Throughput ChIP / Exonuclease trimmed ChIP / Multiplexed ChIP ChIP-Seq is a well-established method to map specific protein-binding sites (Solomon et al., 1988). It has given rise to a vast number of derivatives, such as AHT-ChIP-Seq (Aldridge et al., 2013), BisChIP-Seq […]

Chromatin Immunoprecipitation with Sequencing Library Preparation by Tn5 Transposase ChIPmentation combines ChIP with sequencing library preparation by Tn5 transposase (tagmentation) (Schmidl et al., 2015). Both ATAC-seq and ChIPmentation can be combined usefully in the same experiment to assay open chromatin and protein binding, respectively (Chaitankar […]