ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements
Abstract
Gene expression is controlled by dynamic localization of thousands of regulatory proteins to precise genomic regions. Understanding this cell type-specific process has been a longstanding goal yet remains challenging because DNA–protein mapping methods generally study one protein at a time. Here, to address this, we developed chromatin immunoprecipitation done in parallel (ChIP-DIP) to generate genome-wide maps of hundreds of diverse regulatory proteins in a single experiment. ChIP-DIP produces highly accurate maps within large pools (>160 proteins) for all classes of DNA-associated proteins, including modified histones, chromatin regulators and transcription factors and across multiple conditions simultaneously. First, we used ChIP-DIP to measure temporal chromatin dynamics in primary dendritic cells following LPS stimulation. Next, we explored quantitative combinations of histone modifications that define distinct classes of regulatory elements and characterized their functional activity in human and mouse cell lines. Overall, ChIP-DIP generates context-specific protein localization maps at consortium scale within any molecular biology laboratory and experimental system.
Copyright and License
2024, The Author(s), under exclusive licence to Springer Nature America, Inc.
Acknowledgement
We thank S. Hiley for editing. We thank I.-M. Strazhnik and A. Koivula for illustrations and formatting the figures. This work was funded by grants from the NIH (R01 HG012216, R01 DA053178, U01 DK127420 to M.G.), the Chan Zuckerberg Initiative Ben Barres Early Career Acceleration Award, the NIH UCLA-Caltech Medical Scientist Training Program (T32GM008042, I.N.G. and B.T.Y.), NCI F30CA278005 (J.K.G.) and the University of Southern California MD/PhD program (J.K.G.). Sequencing was performed at the Millard and Muriel Jacobs Genetics and Genomics facility at Caltech with support from I. Antoshechkin and at the Broad Institute Genomics Platform.
Contributions
These authors contributed equally: Andrew A. Perez, Isabel N. Goronzy.
A.A.P., M.R.B. and M.G. conceived ChIP-DIP; A.A.P. and M.R.B. developed ChIP-DIP; A.A.P., I.N.G. and J.K.G. optimized ChIP-DIP; A.A.P. and I.N.G. generated the data presented in this paper; C.S.L., O.E. and A.B. cultured, collected and treated cells; I.N.G. developed the computational pipeline; B.T.Y. generated the GitHub repository for the pipeline; I.N.G. performed data analysis and visualization; A.A.P., I.N.G. and M.G. generated figures and wrote the paper.
Conflict of Interest
M.G., A.A.P., M.R.B., I.N.G. and J.K.G. are inventors of a submitted patent covering the ChIP-DIP method. The other authors declare no competing interests.
Supplemental Material
Supplementary Information: Supplementary Figs. 1–13, Notes 1–3, Methods and Tables 1–5.
Supplementary Data 1: Antibody ID oligonucleotide sequences.
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Additional details
- National Institutes of Health
- R01 HG012216
- National Institutes of Health
- R01 DA053178
- National Institutes of Health
- U01 DK127420
- National Institutes of Health
- NIH UCLA-Caltech Medical Scientist Training Program T32GM008042
- National Institutes of Health
- NCI F30CA278005
- Chan Zuckerberg Initiative (United States)
- Ben Barres Early Career Acceleration Award -
- Accepted
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2024-10-21Accepted
- Available
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2024-11-25Published online
- Caltech groups
- Division of Biology and Biological Engineering
- Publication Status
- Published