ChIPmentation:
fast, cheap, low-input ChIP-seq for histones and transcription factors

Supplementary Website

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 (updated 2018/09/25):

Title Journal DOI Cell types Cell number Antibodies
An Integrated and Semiautomated Microscaled Approach to Profile Cis-Regulatory Elements by Histone Modification ChIP-Seq for Large-Scale Epigenetic Studies Methods Mol Biol 10.1007/978-1-4939-7896-0_22 CD4 T cells 100k H3K27ac
Chromatin accessibility maps of chronic lymphocytic leukaemia identify subtype-specific epigenome signatures and transcription regulatory networks Nature Communications 10.1038/ncomms11938 (2016) CLL cells 10k-1M H3K4me1, H3K27ac
Epigenome analysis links gene regulatory elements in group 2 innate lymphocytes to asthma susceptibility J Allergy Clin Immunol 10.1016/j.jaci.2017.12.1006 ILC2 NA H3K4me2
Genome-wide CRISPR screens in T helper cells reveal pervasive cross-talk between activation and differentiation bioRxiv 10.1101/196022 T cells 1M IRF4 (sc-6059), BATF (sc-100974) and FLAG (Sigma M2, #F3165)
High-Throughput ChIPmentation: freely scalable, single day ChIPseq data generation from very low cell-numbers BioRxiv 10.1101/426957 MEC1 cells 100 to 150k H3K27ac, CTCF
HOXA9 cooperates with activated JAK/STAT signaling to drive leukemia development. Cancer Discovery 10.1158/2159-8290.CD-17-0583 ALL-SIL cells 20M-40M H3K27me3 (Millipore 07-449 or Active Motif 39155); H3K4me3 (Active Motif 39159); H3K4me1 (Active Motif 39297); H3K27ac (4729 or Active Motif 39134); STAT5 (Cell Signaling 8363); HOXA9 (Sigma HPA061982)
Integrative multi-omics analysis of intestinal organoid differentiation Mol Sys Biol 10.15252/msb.20188227 Intestinal crypt–villus structure derived organoid culture 80k-150k Hnf4g, H3K27me3, H3K4me3, and H3K27ac
Mutant NPM1 Maintains the Leukemic State through HOX Expression Cancer Cell 10.1016/j.ccell.2018.08.005 OCI-AML3 NA H3K27me3, H3K4me3, and H3K27ac
RNF8 and SCML2 cooperate to regulate ubiquitination and H3K27 acetylation for escape gene activation on the sex chromosomes Plos Genetics 10.1371/journal.pgen.1007233 Spermatocytes and spermatids NA H3K4me2, H3K27ac
Systemic Human ILC Precursors Provide a Substrate for Tissue ILC Differentiation Cell 10.1016/j.cell.2017.02.021 ILCs 20-50k H3K4me2
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 50k H3K9me3
The HoxD cluster is a dynamic and resilient TAD boundary controlling the segregation of antagonistic regulatory landscapes Genes Development 10.1101/gad.307769.117 Limb tissue NA CTCF
The role of TCF3 as potential master regulator in blastemal Wilms tumors Int J Cancer 10.1002/ijc.31834 Xenograft Wilms tumor cell cultures NA H3K4me3, and H3K27ac
The transcription factor Grainy head primes epithelial enhancers for spatiotemporal activation by displacing nucleosomes Nature Genetics 10.1038/s41588-018-0140-x Third-instar larvae NA GFP
Transcription Factors Drive Tet2-Mediated Enhancer Demethylation to Reprogram Cell Fate Cell Stem Cell 10.1016/j.stem.2018.08.016 B cells reprogrammed to iPS cells 100k H3K4me2
Transcription factors orchestrate dynamic interplay between genome topology and gene regulation during cell reprogramming Nature Genetics 10.1038/s41588-017-0030-7 Reprogrammed B cells 100k H3K4me2
Type I interferons and the cytokine TNF cooperatively reprogram the macrophage epigenome to promote inflammatory activation Nature Immunology 10.1038/ni.3818 Macrophages NA IRF1

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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