Editing Functional genomics (section)

===At the DNA level===

====Genetic interaction mapping====
{{Main|Epistasis}}
Systematic pairwise deletion of genes or inhibition of gene expression can be used to identify genes with related function, even if they do not interact physically. [[Epistasis]] refers to the fact that effects for two different gene knockouts may not be additive; that is, the phenotype that results when two genes are inhibited may be different from the sum of the effects of single knockouts.

====DNA/Protein interactions====
{{Main|ChIP sequencing}}
Proteins formed by the translation of the mRNA (messenger RNA, a coded information from DNA for protein synthesis) play a major role in regulating gene expression. To understand how they regulate gene expression it is necessary to identify DNA sequences that they interact with. Techniques have been developed to identify sites of DNA-protein interactions. These include [[ChIP-sequencing]], [[CUT&RUN sequencing]] and Calling Cards.<ref>{{cite journal | vauthors = Wang H, Mayhew D, Chen X, Johnston M, Mitra RD | title = Calling Cards enable multiplexed identification of the genomic targets of DNA-binding proteins | journal = Genome Research | volume = 21 | issue = 5 | pages = 748–55 | date = May 2011 | pmid = 21471402 | doi = 10.1101/gr.114850.110 | pmc = 3083092 }}</ref>

====DNA accessibility assays====
Assays have been developed to identify regions of the genome that are accessible. These regions of accessible chromatin are candidate regulatory regions. These assays include [[ATAC-seq]], [[DNase-Seq]] and [[FAIRE-Seq]].