Table 1.

Experimental approaches to define pioneer function

Pioneera	Domain	Method	References
OCT4 (POU5F1)	POU, homeodomain	ChIP-seq, Cut-and-tag SeEN-seq, Cryo-EM, EMSA	(Meers et al., 2019; Michael et al., 2020; Echigoya et al., 2020; Soufi et al., 2015)
SOX2	HMG	ChIP-seq, Cut-and-tag SeEN-seq, EMSA	(Meers et al., 2019; Michael et al., 2020; Soufi et al., 2015)
MYOD1 (MYF3)	bHLH	ChIP-seq, endonuclease assays	(Gerber et al., 1997; Bergstrom et al., 2002)
GATA3	HMG	ChIP-seq, ATAC-seq, EMSA, Cryo-EM	(Tanaka et al., 2020)
GATA4	HMG	Cut-and-tag, EMSA, nucleosome arrays	(Meers et al., 2019; Cirillo et al., 2002; Fernandez Garcia et al., 2019)
PU.1 (SPI1)	ETS, winged-helix	EMSA	(Feng et al., 2008; Fernandez Garcia et al., 2019)
EOMES	HMG	Cut-and-tag	(Meers et al., 2019)
PAX6 (FVH1)	Paired box, homeodomain	ChIP-seq, ectopic expression	(Sun et al., 2015; Halder et al., 1995)
PAX7 (HUP1)	Paired box, homeodomain	ATAC-seq, FAIRE-seq, ChIP-seq	(Budry et al., 2012; Mayran et al., 2018)
ASCL1	bHLH	EMSA, ChIP-seq, DNase-seq	(Fernandez Garcia et al., 2019; Raposo et al., 2015)
FOXA1 (HNF3A)	Winged-helix	EMSA, nucleosome arrays	(Cirillo et al., 2002)
FOXA2 (HNF3B)	Winged-helix	Cut-and-tag	(Meers et al., 2019)
FOXD3 (HFH2)	Winged-helix	ChIP-seq	(Xu et al., 2009; Krishnakumar et al., 2016)
FOXO1 (FKHR)	Winged-helix	DNase1-footprinting, Nucleosome arrays	(Hatta and Cirillo, 2007)
CEBPα CEBPβ	bZIP	ChIP-reChIP, EMSA	(Iwafuchi-Doi et al., 2016; Fernandez Garcia et al., 2019)
Rap1	Myb-type	smTIRF	(Mivelaz et al., 2020)
Reb1	Basic patch, HTH	PIFE, FRET, EMSA, degron alleles	(Hartley and Madhani, 2009; Donovan et al., 2019)
Cbf1	bHLH	PIFE, FRET, EMSA	(Donovan et al., 2019)

These factors are featured, with central attributes of pioneer function defined from the literature, along with domains and the relevant methods for characterization.

^aIndicates 2 or more of the 4 essential characteristics of pioneer function described in this manuscript.