Table 1

Strategies for epigenome mapping

Method

Strategy

Features

Base-pair resolution possible?

Reference


MNase digestion

Digests non-occluded DNA

Maps nucleosomes, other DNA-occluding particles

Yes [20,23]

[11]

DNase I hypersensitivity

Digests non-occluded DNA and nucleosomes with 10 bp periodicity

Maps 'open' chromatin

Yes [30,44]

[12]

Salt fractionation

Extracts chromatin from intact nuclei with increasing salt concentrations

Maps 'active' and 'nuclear matrix' chromatin

Yes, in combination with MNase digestion

[45]

ChIP

Affinity purification of specific chromatin fragments

Maps protein binding sites

Yes (see ChIP-exo)

[46]

DamID

DNA marking by tethered Dam methyltransferase

In vivo marking of protein-DNA interactions

No

[47]

FAIRE

Differential solubility of 'open' and nucleosomal chromatin by sonication and phenol/chloroform extraction

Maps 'open' chromatin

Maybe

[38]

Sono-seq

Differential solubility of 'open' and nucleosomal chromatin by sonication and phenol/chloroform extraction

Maps 'open' chromatin

Maybe

[39]

CATCH-IT

Metabolic labeling of histones

Measures nucleosome turnover

Maybe

[48]

Genome-wide psoralen crosslinking

Treatment of DNA with the intercalating agent psoralen

Measures helical tension of DNA

No

[49]

ChIP-exo

ChIP followed by exonuclease digestion of immunoprecipitated DNA

Removes non-occluded flanking DNA

Yes

[35]

Targeted chemical cleavage

Targeted chemical cleavage of DNA wrapped around modified nucleosomes

Maps nucleosome positions

Yes

[37]


Methods are listed in chronological order of their first published use in mapping epigenomic features to specific genomic locations. CATCH-IT, covalent attachment of tags to capture histones and identify turnover; ChIP, chromatin immunoprecipitation; ChIP-exo, chromatin immunoprecipitation with exonuclease digestion and high-throughput sequencing; DamID, DNA adenine methyltransferase identification; DNase I, deoxyribonuclease I; FAIRE, formaldehyde-assisted isolation of regulatory elements; MNase, micrococcal nuclease; Sono-seq, sonication of DNA and high-throughput sequencing.

Zentner and Henikoff Genome Biology 2012 13:250   doi:10.1186/gb-2012-13-10-250