Refined DNase-seq protocol and data analysis reveals intrinsic bias in transcription factor footprint identification
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Sequencing of DNase I hypersensitive sites (DNase-seq) is a powerful technique for identifying cis-regulatory elements across the genome. We studied the key experimental parameters to optimize performance of DNase-seq. Sequencing short fragments of 50-100 base pairs (bp) that accumulate in long internucleosome linker regions was more efficient for identifying transcription factor binding sites compared to sequencing longer fragments. We also assessed the potential of DNase-seq to predict transcription factor occupancy via generation of nucleotide-resolution transcription factor footprints. In modeling the sequence-specific DNase I cutting bias, we found a strong effect that varied over more than two orders of magnitude. This indicates that the nucleotide-resolution cleavage patterns at many transcription factor binding sites are derived from intrinsic DNase I cleavage bias rather than from specific protein-DNA interactions. In contrast, quantitative comparison of DNase I hypersensitivity between states can predict transcription factor occupancy associated with particular biological perturbations.
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Adding a methyl group to cytosine can affect local DNA shape, as shown by altered DNase I digestion rate and patterns.
“Adding a methyl group to the cytosine could affect the local DNA shape, as evidenced by the altered DNase I digestion rate and patterns70,71.”
From Transcription factors as readers and effectors of DNA methylation (2016) · cites this paper as [70]
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- Authors
- He, H. H., Meyer, C. A., Hu, S. S., Chen, M.-W., Zang, C., Liu, Y., Rao, P. K., Fei, T., Xu, H., Long, H., Liu, X. S., & Brown, M.
- Affiliations
- University Health Network (CA)
- Harvard University (US)
- Dana-Farber Cancer Institute (US)
- Tongji University (CN)
- Corresponding author
- Long, Henry
- Liu, X Shirley
- Brown, Myles
- ORCID
- Venue
- Nature Methods
- Published
- 2013-12-08
- Volume
- 11
- Issue
- 1
- Pages
- 73-78
- ISSN
- 1548-7091 (ISSN-L)
- 1548-7105
- PMC
- PMC4018771
- OpenAlex
- W2009853003
- Cited by
- 218
- References
- 22
- Citations by year
- 2026: 8 · 2025: 4 · 2024: 14 · 2023: 6 · 2022: 10 · 2021: 17 · 2020: 13 · 2019: 30 · 2018: 28 · 2017: 24 · 2016: 26 · 2015: 18 · 2014: 18 · 2013: 1
- FWCI
- 9.41
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- www.springer.com/tdm (tdm)
- Locations
- Nature Methods (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Digital Access to Scholarship at Harvard (DASH) (Harvard University) (submittedVersion, cc-by)
- Funders
- National Human Genome Research Institute (U41HG007000)
- National Cancer Institute (K99CA172948, P50CA090381)
- National Institute of General Medical Sciences (R01GM099409)
- National Institute of Diabetes and Digestive and Kidney Diseases (R01DK074967)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- DNase-seq, DNase I hypersensitive sites, transcription factor footprints, cis-regulatory elements, transcription factor binding sites, DNase I hypersensitivity, transcription factor occupancy, protocol optimization
- MeSH terms
- Binding Sites, Chromatin, Deoxyribonuclease I, Female, Gene Expression Regulation, Humans, Male, Nucleosomes, Nucleotides, Receptors, Androgen, Transcription Factors, Tumor Suppressor Protein p53, Sequence Analysis, DNA, K562 Cells, Amino Acid Motifs, Cell Line, Tumor, Gene Regulatory Networks, MCF-7 Cells
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