Table 1.

In vivo and in vitro methods to identify TF-DNA binding sites.

Method	Input	TF source	Time	Relative cost	Advantages	Disadvantages	References
ChIP-seq	Cross-linked chromatin	Endogenous or in vivo expressed recombinant protein	4–5 days	medium	Can be applied for a wide range of organisms	Low resolution of binding site maps; prone to false positive and false negative errors; low signal-to-noise ratio peaks	[25–27]
ChIP-exo	Cross-linked chromatin	Endogenous or in vivo expressed recombinant protein	4–5 days	high	High resolution of binding site maps	High technical complexity	[28, 34]
ChIP-nexus	Cross-linked chromatin	Endogenous or in vivo expressed recombinant protein	4–5 days	high	High resolution of binding site maps	High technical complexity	[28, 33]
CUT&RUN	Native chromatin	Endogenous or in vivo expressed recombinant protein	2 days	medium	High resolution of binding site maps; high signal-to-noise ratio peaks	No published report for plant TFs	[30]
CUT&Tag	Native chromatin	Endogenous or in vivo expressed recombinant protein	2 days	medium	High resolution of binding site maps; high signal-to-noise ratio peaks	No published report for plant TFs	[31]
DamID	Native chromatin	In vivo expressed recombinant protein	4–5 days	high	Identification of transient TF-DNA interactions	Low resolution of binding site maps	[29, 32]
scCC	RNA	In vivo expressed recombinant protein	2 days	medium	Simultaneous measure of transcriptome and TF binding profiles at the single-cell level	Low resolution of binding site maps; possible modification or silencing of target gene expression due to transposon integration	[43]
nextPBM	Randomized synthetic DNA	Endogenous or in vivo expressed recombinant protein	2-3 days	medium	Captures the effect of TF-protein interactions and post-translational modifications on DNA binding specificity and affinity	Lack of endogenous genome sequence and chromatin context	[41]
PBM	Randomized synthetic DNA	In vitro or nonnative cell expressed recombinant protein	2 days	low	Identifies binding sequence motifs in a high-throughput manner	Lack of endogenous genome sequence and chromatin context	[15, 38]
SELEX-seq	Randomized synthetic DNA	In vitro or nonnative cell expressed recombinant protein	2 days	low	Identifies binding sequence motifs in a high-throughput manner	Lack of endogenous genome sequence and chromatin context	[15, 35]
DAP-seq	Genomic DNA	In vitro or nonnative cell expressed recombinant protein	2 days	low	High resolution of binding site maps in endogenous genome context; high signal-to-noise ratio peaks; can be easily performed in a high-throughput manner; can be used to dissect the direct and indirect binding sites and disentangle the cooperative action of TFs	Lack of chromatin context	[15, 36, 39]
Multi-DAP-seq	Genomic DNA	In vitro or nonnative cell expressed recombinant protein	2 days	low	Can be applied to non-model organisms; high resolution of binding site maps in endogenous genome context; high signal-to-noise ratio peaks; can be easily performed in a high-throughput manner	Lack of chromatin context; potential modification of DNA binding specificity and/or affinity due to incorporation of biotinylated lysine into the TF protein sequence	[37]