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)


  • 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)


  • 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


Illumina Library prep and Array Kit Selector


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