Table 1 |
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Strategies for epigenome mapping |
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|
Method |
Strategy |
Features |
Base-pair resolution possible? |
Reference |
|
|
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|
MNase digestion |
Digests non-occluded DNA |
Maps nucleosomes, other DNA-occluding particles |
[11] |
|
|
DNase I hypersensitivity |
Digests non-occluded DNA and nucleosomes with 10 bp periodicity |
Maps 'open' chromatin |
[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] |
|
|
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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. |
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Zentner and Henikoff Genome Biology 2012 13:250 doi:10.1186/gb-2012-13-10-250 |
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