DNaseI Seq or DNase-Seq
DNase l Hypersensitive Sites Sequencing
DNase I footprinting was first published in 1978 (Galas et al., 1978) and predates both Sanger sequencing and NGS. The first published use with NGS was published by Boyle et al. 2008 (Boyle et al., 2008) and later optimized for sequencing (Anderson et al., 1981). A high-sensitivity protocol is also available (scDNase-seq) (Jin et al., 2015).
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 cells (Chumsakul et al., 2013)
Advantages:
- Can detect –open” chromatin (Zentner et al., 2012)
- 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 promoters (Kumar et al., 2013)
Disadvantages:
- DNase l is sequence-specific and hypersensitive sites might not account for the entire genome (Yan et al., 2016)
- DNA loss through the multiple purification steps limits sensitivity (Lu et al., 2016)
- Integration of DNase I with ChIP data is necessary to identify and differentiate similar protein-binding sites
Reagents:
Illumina Library prep and Array Kit Selector
Reviews:
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
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
References:
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
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
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
Badal S. S., Wang Y., Long J., et al. miR-93 regulates Msk2-mediated chromatin remodelling in diabetic nephropathy. Nat Commun. 2016;7:12076
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
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
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
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
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
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
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
Metser G., Shin H. Y., Wang C., et al. An autoregulatory enhancer controls mammary-specific STAT5 functions. Nucleic Acids Res. 2016;44:1052-1063
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
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
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
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
Related
History: DNaseI Seq or DNase-Seq
Revision by sbrumpton on 2017-06-21 09:34:01 - Show/Hide
DNase l Hypersensitive Sites Sequencing
DNase I footprinting was first published in 1978 (Galas et al., 1978) and predates both Sanger sequencing and NGS. The first published use with NGS was published by Boyle et al. 2008 (Boyle et al., 2008) and later optimized for sequencing (Anderson et al., 1981). A high-sensitivity protocol is also available (scDNase-seq) (Jin et al., 2015).
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 cells (Chumsakul et al., 2013)
Advantages:- Can detect –open” chromatin (Zentner et al., 2012)
- 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 promoters (Kumar et al., 2013)
Disadvantages:- DNase l is sequence-specific and hypersensitive sites might not account for the entire genome (Yan et al., 2016)
- DNA loss through the multiple purification steps limits sensitivity (Lu et al., 2016)
- Integration of DNase I with ChIP data is necessary to identify and differentiate similar protein-binding sites
Reagents:Illumina Library prep and Array Kit SelectorReviews: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;55:1-31Yan 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;183:96-109References: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;9:1168-1182Frank 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;9:15Lu F., Liu Y., Inoue A., Suzuki T., Zhao K., et al. Establishing Chromatin Regulatory Landscape during Mouse Preimplantation Development. Cell. 2016;165:1375-1388Badal S. S., Wang Y., Long J., et al. miR-93 regulates Msk2-mediated chromatin remodelling in diabetic nephropathy. Nat Commun. 2016;7:12076Adar 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:E2124-2133Bevington 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;35:515-535Browne 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;425:94-102Chaitankar 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;55:1-31Corces 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;48:1193-1203Georgakilas 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:D190-195Lensing 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;13:855-857Metser G., Shin H. Y., Wang C., et al. An autoregulatory enhancer controls mammary-specific STAT5 functions. Nucleic Acids Res. 2016;44:1052-1063Schmidt 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;16:2359-2372Shin H. Y., Willi M., Yoo K. H., et al. Hierarchy within the mammary STAT5-driven Wap super-enhancer. Nat Genet. 2016;48:904-911Thompson 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:e0148619Yang 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