DNase-Seq/DNasel-Seq

DNase-Seq/DNasel-Seq

DNase I footprinting was first published in 1978 and predates both Sanger sequencing and NGS. The first published use with NGS was published by Boyle et al. and later optimized for sequencing¹. A high-sensitivity protocol is also available (scDNase-seq)².

In this method, DNA-protein complexes are treated with DNase l, followed by DNA extraction and sequencing. Sequences bound by regulatory proteins are protected from DNase l digestion. Deep sequencing provides accurate representation of the location of regulatory proteins in the genome. In a variation on this approach, the DNA-protein complexes are stabilized by formaldehyde crosslinking before DNase I digestion. The crosslinking is reversed before DNA purification. In an alternative modification, called GeF-seq, both the crosslinking and the DNase I digestion are carried out in vivo, within permeabilized cells³.

Pros:

• Can detect “open” chromatin⁴
• No prior knowledge of the sequence or binding protein is required
• Compared to formaldehyde-assisted isolation of regulatory elements and sequencing (FAIRE-seq), has greater sensitivity at promoters⁵

Cons:

• DNase l is sequence-specific and hypersensitive sites might not account for the entire genome⁶
• DNA loss through the multiple purification steps limits sensitivity⁷
• Integration of DNase I with ChIP data is necessary to identify and differentiate similar protein-binding sites

• DNase-Seq: Boyle A. P. et al. (2008) High-resolution mapping and characterization of open chromatin across the genome. Cell 132: 311-322
• 1. Anderson S. Shotgun DNA sequencing using cloned DNase I-generated fragments. Nucleic Acids Res. 1981;9:3015-3027
• 2. Jin W., Tang Q., Wan M., et al. Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples. Nature. 2015;528:142-146
• 3. Chumsakul O., Nakamura K., Kurata T., et al. High-resolution mapping of in vivo genomic transcription factor binding sites using in situ DNase I footprinting and ChIP-seq. DNA Res. 2013;20:325-338
• 4. Zentner G. E. and Henikoff S. Surveying the epigenomic landscape, one base at a time. Genome Biol. 2012;13:250
• 5. Kumar V., Muratani M., Rayan N. A., et al. Uniform, optimal signal processing of mapped deep-sequencing data. Nat Biotechnol. 2013;31:615-622
• 6. Yan H., Tian S., Slager S. L., Sun Z. and Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol. 2016;183:96-109
• 7. Lu F., Liu Y., Inoue A., Suzuki T., Zhao K. and Zhang Y. Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development. Cell. 2016;165:1375-1388

1. Chaitankar V., Karakulah G., Ratnapriya R., Giuste F. O., Brooks M. J., et al. Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. Prog Retin Eye Res. 2016;55:1-31
2. Yan H., Tian S., Slager S. L., Sun Z. and Ordog T. Genome-Wide Epigenetic Studies in Human Disease: A Primer on -Omic Technologies. Am J Epidemiol. 2016;183:96-109

1. Qiu Z., Li R., Zhang S., et al. Identification of Regulatory DNA Elements Using Genome-wide Mapping of DNase I Hypersensitive Sites during Tomato Fruit Development. Mol Plant. 2016;9:1168-1182
2. Frank C. L., Manandhar D., Gordan R. and Crawford G. E. HDAC inhibitors cause site-specific chromatin remodeling at PU.1-bound enhancers in K562 cells. Epigenetics Chromatin. 2016;9:15
3. Lu F., Liu Y., Inoue A., Suzuki T., Zhao K., et al. Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development. Cell. 2016;165:1375-1388
4. Badal S. S., Wang Y., Long J., et al. miR-93 regulates Msk2-mediated chromatin remodelling in diabetic nephropathy. Nat Commun. 2016;7:12076
5. Adar S., Hu J., Lieb J. D. and Sancar A. Genome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis. Proc Natl Acad Sci U S A. 2016;113:E2124-2133
6. Bevington S. L., Cauchy P., Piper J., Bertrand E., Lalli N., et al. Inducible chromatin priming is associated with the establishment of immunological memory in T cells. EMBO J. 2016;35:515-535
7. Browne J. A., Yang R., Eggener S. E., Leir S. H. and Harris A. HNF1 regulates critical processes in the human epididymis epithelium. Mol Cell Endocrinol. 2016;425:94-102
8. Chaitankar V., Karakulah G., Ratnapriya R., Giuste F. O., Brooks M. J., et al. Next generation sequencing technology and genomewide data analysis: Perspectives for retinal research. Prog Retin Eye Res. 2016;55:1-31
9. Corces M. R., Buenrostro J. D., Wu B., Greenside P. G., Chan S. M., et al. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nat Genet. 2016;48:1193-1203
10. Georgakilas G., Vlachos I. S., Zagganas K., et al. DIANA-miRGen v3.0: accurate characterization of microRNA promoters and their regulators. Nucleic Acids Res. 2016;44:D190-195
11. Lensing S. V., Marsico G., Hansel-Hertsch R., Lam E. Y., Tannahill D. and Balasubramanian S. DSBCapture: in situ capture and sequencing of DNA breaks. Nat Methods. 2016;13:855-857
12. Metser G., Shin H. Y., Wang C., et al. An autoregulatory enhancer controls mammary-specific STAT5 functions. Nucleic Acids Res. 2016;44:1052-1063
13. Schmidt S. F., Madsen J. G., Frafjord K. O., Poulsen L., Salo S., et al. Integrative Genomics Outlines a Biphasic Glucose Response and a ChREBP-RORgamma Axis Regulating Proliferation in beta Cells. Cell Rep. 2016;16:2359-2372
14. Shin H. Y., Willi M., Yoo K. H., et al. Hierarchy within the mammary STAT5-driven Wap super-enhancer. Nat Genet. 2016;48:904-911
15. Thompson B., Varticovski L., Baek S. and Hager G. L. Genome-Wide Chromatin Landscape Transitions Identify Novel Pathways in Early Commitment to Osteoblast Differentiation. PLoS One. 2016;11:e0148619
16. Yang R., Kerschner J. L., Gosalia N., et al. Differential contribution of cis-regulatory elements to higher order chromatin structure and expression of the CFTR locus. Nucleic Acids Res. 2016;44:3082-3094