Methods for Identifying Transcription Factor Binding Sites

Displayed below is the list of methods used for identifying the transcription factor binding sites included in TRANSFAC.

Footprinting reactions

DNase I footprinting

genomic in situ DNAse I footprinting

competitive DNAse I footprint


methidiumpropyl-EDTA.Fe(II) in nuclei

DNase II

hydroxyl radicals

photofootprinting in vivo

copper/phenanthroline footprinting

copper/phenanthroline footprinting in situ

neocarzinostatin footprinting

micrococcal nuclease

micrococcal nuclease in situ

nuclease P1 footprinting

in vivo DMS footprinting

Exonuclease digests

exonuclease III

genomic/in vivo exonuclease III digest

competition exonuclease III digest

lambda exonuclease

T7 gene exonuclease

Gel retardation

direct gel shift

supershift (antibody binding)

gel shift competition

DNA modification reactions

methylation protection

in vivo/genomic methylation protection

methylation interference

Dam methylation

ethylation protection

ethylation interference

DEPC interference

KMnO4 modification

genomic demethylation

uracil interference

depurination interference

missing base interference

carboxymethylation interference

carboxyethylation interference

depyrimidination interference

cytosine and adenine interference

Primer extension footprint

Avidin-biotin complex DNA binding assay

Filter binding assays

southwestern blotting/filter binding

nitrocellulose filter binding

southwestern blotting



genomic UV-photofootprint

UV/primer extension


Affinity chromatography


Electron microscopy

Chromatin immunoprecipitation procedure

Yeast one hybrid system

Functional analysis

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