Efficient low-cost chromatin profiling with CUT&Tag
- 10 September 2020
- journal article
- research article
- Published by Springer Science and Business Media LLC in Nature Protocols
- Vol. 15 (10), 3264-3283
- https://doi.org/10.1038/s41596-020-0373-x
Abstract
We recently introduced Cleavage Under Targets & Tagmentation (CUT&Tag), an epigenomic profiling strategy in which antibodies are bound to chromatin proteins in situ in permeabilized nuclei. These antibodies are then used to tether the cut-and-paste transposase Tn5. Activation of the transposase simultaneously cleaves DNA and adds adapters (‘tagmentation’) for paired-end DNA sequencing. Here, we introduce a streamlined CUT&Tag protocol that suppresses DNA accessibility artefacts to ensure high-fidelity mapping of the antibody-targeted protein and improves the signal-to-noise ratio over current chromatin profiling methods. Streamlined CUT&Tag can be performed in a single PCR tube, from cells to amplified libraries, providing low-cost genome-wide chromatin maps. By simplifying library preparation CUT&Tag requires less than a day at the bench, from live cells to sequencing-ready barcoded libraries. As a result of low background levels, barcoded and pooled CUT&Tag libraries can be sequenced for as little as $25 per sample. This enables routine genome-wide profiling of chromatin proteins and modifications and requires no special skills or equipment.Keywords
Funding Information
- Details of the funding program are found here: https://chanzuckerberg.com/rfa/seed-networks-for-the-human-cell-atlas/https://chanzuckerberg.com/rfa/seed-networks-for-the-human-cell-atlas/
- U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (R01 GM108699)
This publication has 40 references indexed in Scilit:
- Use Model-Based Analysis of ChIP-Seq (MACS) to Analyze Short Reads Generated by Sequencing Protein–DNA Interactions in Embryonic Stem CellsPublished by Springer Science and Business Media LLC ,2014
- Impact of sequencing depth in ChIP-seq experimentsNucleic Acids Research, 2014
- High-resolution mapping of transcription factor binding sites on native chromatinNature Methods, 2013
- Chromatin ImmunoprecipitationPublished by Springer Science and Business Media LLC ,2013
- Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome positionNature Methods, 2013
- ChIP-seq guidelines and practices of the ENCODE and modENCODE consortiaGenome Research, 2012
- Fast gapped-read alignment with Bowtie 2Nature Methods, 2012
- BEDTools: a flexible suite of utilities for comparing genomic featuresBioinformatics, 2010
- ChIC and ChEC: Genomic Mapping of Chromatin ProteinsMolecular Cell, 2004
- Formaldehyde-mediated DNA-protein crosslinking: a probe for in vivo chromatin structures.Proceedings of the National Academy of Sciences of the United States of America, 1985