Epigenomics:

ChIP-Seq

DNase-Seq

DNase-Seq is one of the several approaches in molecular biology useful to identify DNA response elements, or regulatory regions in general, through genome-wide sequencing of regions sensitive to cleavage by DNase I.
A brief outline of the technique is the following:

1. DNA-protein complexes are treated with DNase I;
2. DNA extraction and sequencing are perfomed;
3. Sequences bound by regulatory proteins are protected  from DNase I digestion;
4. Deep sequencing is performed to provide accurate representation of location of regulatory proteins in the genome.
   

Pros

• Can detect open chromatin
• 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

Cons

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

More information can be found at the website:
https://emea.illumina.com/science/sequencing-method-explorer/kits-and-arrays/dnase-seq-dnasel-seq.html
And this is a video made by a Biology Professor at Davidson College, it explains the protocol in really easy terms:

(Emilia Petrachi)

FAIRE

ATAC-Seq

Nucleosome positioning