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.


Overview

Protocols

This section provides updated ChIPmentation protocols.

Protocol version Updated on Comment
ChIPmentation v1.14 28th September 2016 Step-by-step protocol.
ChIPmentation v1.1 14th October 2015 Tested with: H3K27ac (500k cells), H3K27me3 (500k cells)
CTCF (500k cells), GATA1 (500k cells), PU.1 (500k cells)
ChIPmentation v1.0 (publication) 10th July 2015 Tested with: H3K4me1 (10M cells), H3K4me3 (10-500k cells), H3K27ac (10M cells), H3K27me3 (10k-500k cells), H3K36me3 (10M cells),
CTCF (100k-10M cells), GATA1 (100k-10M cells), PU.1 (500k-10M cells), REST (100k-10M cells)

Publications

Here are some examples of publications using ChIPmentation.

Title Journal DOI Organisms Cell types Antibodies
Epigenome analysis links gene regulatory elements in group 2 innate lymphocytes toasthma susceptibility Journal of Allergy and Clinical Immunology 10.1016/j.jaci.2017.12.1006 Human and Mouse Innate lymphoid cells H3K4me2
Systemic Human ILC Precursors Provide a Substrate for Tissue ILC Differentiation Cell 10.1016/j.cell.2017.02.021 Human Innate lymphoid cells H3K4me2
Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks Nature Communications 10.1038/ncomms11938 Human chronic lymphocytic leukemia H3K4me1, H3K27ac, H3K27me3
The Helicase Aquarius/EMB-4 Is Required to Overcome Intronic Barriers to Allow Nuclear RNAi Pathways to Heritably Silence Transcription Developmental Cell 10.1016/j.devcel.2017.07.002 C. elegans whole animals H3K9me3
Type I interferons and the cytokine TNF cooperatively reprogram the macrophage epigenome to promote inflammatory activation Nature Immunology 10.1038/ni.3818 Human macrophages IRF-1
Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming Nature Genetics 10.1038/s41588-017-0030-7 Mouse B cell progenitors H3K4me2

Genome browser tracks

52 libraries were sequenced for ChIPmentation, 24 libraries for standard ChIP-seq, nine libraries for ChIP-tagmentation, and two libraries for ATAC-seq.

Data

52 libraries were sequenced for ChIPmentation, 24 libraries for standard ChIP-seq, nine libraries for ChIP-tagmentation, and two libraries for ATAC-seq.

Software

To foster reproducibility and facilitate reuse, the source code underlying the analysis is contained in a Git repository at Github.

Citation

If you use these data in your research, please cite:

Christian Schmidl*, André F. Rendeiro*, Nathan C. Sheffield and Christoph Bock. ChIPmentation: fast, robust, low-input ChIP-seq for histones and transcription factors. Nature Methods 12, 963–965 (2015), doi:10.1038/nmeth.3542

* Shared first authors

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