Evolution of Epigenetic Research Methods

2004: ChIC

ChIC (chromatin immunocleavage) consists of tethering the fusion protein pA-MN (protein A fused to micrococcal nuclease) to antibodies that in turn are specifically bound to a chromatin protein.

2006: MNase-seq

MNase-seq, short for micrococcal nuclease digestion with deep sequencing, relies on the use of the non-specific endo-exonuclease micrococcal nuclease, to bind and cleave protein-unbound regions of DNA on chromatin. The uncut DNA is then purified from the proteins and sequenced through one or more of the various Next-Generation sequencing (NGS) methods.

2007: ChIP-seq

ChIP-sequencing, also known as ChIP-seq, combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins. It can be used to map global binding sites precisely for any protein of interest.

2010: FAIRE-seq

FAIRE-Seq stands for Formaldehyde-Assisted Isolation of Regulatory Elements. The FAIRE-Seq protocol doesn't require the permeabilization of cells or isolation of nuclei, and can analyse any cell type. It is followed by non-directed chromatin fragmentation and subssequent NGS.

2013: ATAC-seq

ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) identifies accessible DNA regions by probing open chromatin with hyperactive mutant Tn5 Transposase that inserts sequencing adapters into open regions of the genome. It is an alternative advanced method for MNase-seq, FAIRE-Seq and DNase-Seq providing increased sensitivity.

2017: CUT&RUN

ab-directed MNase chromatin fragmentation + NGS PMID 2807901

2018: AutoCUT&RUN

automated CUT&RUN PMID 30577869

2019 CUT&Tag

ab-directed Tn5 chromatin fragmentation PMID 31036827

2019: uli.CUT&RUN

CUT&RUN on low cell numbers PMID 30955888

2021: scCUT&Tag

single cell CUT&Tag PMID 33846645

2022: CUT&RUN LoV-U

low volume CUT&RUN and in situ protein denaturation DOI 10.1101/2022.07.06.498999

2022: CUT&Tag2for1

H3K27me3 and Pol2 CUT&Tag PMID 35300717