Mapping genome-wide transcription factor binding sites in frozen tissues
Open accessAbstract
Background: Genome-wide maps of transcription factor binding sites in primary tissues can expand our understanding of genome function, transcriptional regulation, and genetic alterations that contribute to disease risk. However, almost all genome-wide studies of transcription factors have been in cell lines, and performing these experiments in tissues has been technically challenging and limited in throughput. Results: Here we outline a simple strategy for mapping transcription factor binding sites in frozen tissues that utilizes dry pulverization of samples and is scalable for high-throughput analyses. We show that the method leads to accurate and reproducible chromatin immunoprecipitation next-generation sequencing (ChIP-seq) data, and is highly sensitive, identifying high-quality transcription factor binding sites from chromatin corresponding to only 5 mg of liver tissue. Conclusions: The enhanced reproducibility, robustness, and sensitivity of the dry pulverization method, in addition to the ease of implementation and scalability, makes ChIP-seq in primary tissues a widely accessible assay.
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The ChIP-seq protocols used were similar to those previously described by the authors' lab and consistent with ENCODE Consortium recommendations.
“Protocols for ChIP-seq are similar to those for frozen tissue previously described by our lab115,116 and consistent with techniques recommended by the ENCODE Consortium (www.encodeproject.org/documents).”
From Single nucleus multiomics identifies ZEB1 and MAFB as candidate regulators of Alzheimer’s disease-specific cis-regulatory elements (2023) · cites this paper as [115]
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Self-citation
- Authors
- Savic, D., Gertz, J., Jain, P., Cooper, G. M., & Myers, R. M.
- Affiliations
- HudsonAlpha Institute for Biotechnology (US)
- Corresponding author
- Myers, Richard M
- Venue
- Epigenetics & Chromatin
- Published
- 2013-09-16
- Volume
- 6
- Issue
- 1
- Pages
- 30-30
- ISSN
- 1756-8935 (ISSN-L)
- PMC
- PMC3848595
- OpenAlex
- W2124717826
- Cited by
- 31
- References
- 43
- Citations by year
- 2025: 1 · 2024: 1 · 2023: 1 · 2021: 3 · 2020: 3 · 2019: 3 · 2018: 1 · 2017: 7 · 2016: 3 · 2015: 7 · 2013: 1
- FWCI
- 1.64
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Epigenetics & Chromatin (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Funders
- National Institutes of Health
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- transcription factor binding sites, frozen tissue, ChIP-seq, primary tissue, liver, chromatin immunoprecipitation, transcriptional regulation
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