Table 1.

Summary of genes involved in pharynx development

Gene	Homology	M/Z	Expression (initiation)	Pha phenotype	Targets	Binding sequence	Upstream genes	References
ceh-2	Homeobox ems, EMX	Z	I3, NSM, M3, pm2, e2	Poor feeding, M3 defective		?	?	Aspock et al. 2003
ceh-22	Nkx 2.2 Homeobox TF	Z	pm3–5, pm7	Indistinct BM around pharynx	myo-2	CACTTAT	pha-4 ceh-22 ceh-2 pha-2	Kalb et al. 1998, Mango et al. 1994, Okkema & Fire 1994, Okkema et al. 1997
ceh-24	Nkx 2.3 TF	Z	pm8	None	?	?	?	Harfe et al. 1998
ceh-28	Nkx 2 TF	Z	M4	Peristalsis defective, M4 outgrowth				Ray et al. 2008
ceh-43	Distal-less homeobox	Z	Non-pha neurons, epidermis	Pun, anterior leakage				Aspock & Burglin 2001, Burglin & Aspock 1999
daf-12	NHR Zn TF	Z	Broadly	Daf	myo-2 ceh-22	AGTGCA	daf-9	Ao et al. 2004
eya-1	Eyes absent	Z	Broadly ≥ bean	Thin, asymmetric	?	NA	?	Furuya et al. 2005
gei-17	E3 sumo ligase	?	?	Thick isthmus	?	NA	?	Roy Chowdhuri et al. 2006
glp-1	Notch Rcp	M	ABa@4 ABa@12	Aph	ref-1 pha-4	NA	?	Kalb et al. 1998, Mango et al. 1994, Priess et al. 1987
hlh-6	Sage-like	Z	Glands	Loss of some g2 glands, misformed g1 glands, PGM1 activation	phat		lag-1 pha-4	Raharjo & Gaudet 2007, Smit et al. 2008
htz-1	H2A.Z histone variant	Z	Broadly from the 28-cell stage	Delayed activation	myo-2, R07B1.9 many	NA	?	Updike & Mango 2006, Whittle et al. 2008
lag-1	Su(H) TF	M	Broadly	Aph	ref-1 pha-4	RTGGGAA	glp-1	Christensen et al. 1996, Smith & Mango 2007
lin-12	Notch receptor	Z	pm8	pm8 tubulogenesis	lag-1 aff-1 eff-1	NA	lag-2/Delta	Rasmussen et al. 2008
med-1/2	GATA-like Zn TF	M, Z	EMS@4 and maternal	Ppa	tbx-35	RRRAGTATAC	skn-1	Broitman-Maduro et al. 2005, Maduro
myo-2	Myosin heavy chain	Z	pm1–pm8			NA	pha-4 ceh-22 peb-1 daf-12 daf-3	Ao et al.2004, Gaudet & Mango 2002, Mango et al. 1994, Okkema & Fire 1994, Thatcher et al. 2001
peb-1	FLYWCH Zn TF	Z	Broadly	Glands distended	myo-2	YDTGCCRW	?	Beaster-Jones & Okkema 2004, Fernandez et al. 2004, Thatcher et al. 2001
pha-1	Novel	Z	Broadly	Arrested diffn, loss of TF expression	ceh-22 pha-4	NA or ?	?	Fay et al. 2004, Granato et al. 1994, Schnabel & Schnabel 1990
pha-2	Homeobox	Z	pm5, I4, epi	pm4, pm5, morph	ceh-22 ceh-2			Avery 1993, Morck et al. 2004
pha-4	FoxA	Z	ABa@44 MS@28	Pha, adult longevity	many	TRTTKRY	lag-1 tbx-37/38 med-1/2 glp-1 tbx-35, tbx-2	Broitman-Maduro et al. 2006, Gaudet & Mango 2002, Good et al. 2004, Maduro et al. 2005b, Mango et al. 1994, Smith & Mango 2007
ref-1 family	bHLH TF	Z	ABa@26 ABp@4 EMS@24	None	tbx-37 tbx-2	CANNTG	lag-1, glp-1	Neves & Priess 2005, Smith & Mango 2007
skn-1	Zipper TF	M	EMS@4	Pha	ref-1 end-1 med-1, med-2	G/ATCAT + A/T	?	Bowerman et al. 1992, Maduro et al. 2005b, Mango et al. 1994, Neves & Priess 2005
smk-1	PPH phosphatase regulatory subunit	?	Broadly	Adult aging, DNA damage	sod-1, sod-2, sod-3, sod-4, sod-5, ctl-1, lys-8	?	?	Wolff et al. 2006, Panowski et al. 2007
tbx-2	T-box	Z	ABa@8E	ABa muscles absent	pha-4 ceh-22?	?	ref-1 tbx-37/38?	Roy Chowdhuri et al. 2006, Smith & Mango 2007
tbx-37/38	T-box	Z	ABa@24	Aph	pha-4?	?	ref-1 in some cell types	Good et al. 2004
tmy-1	Tropomyosin	Z	Pha muscles pm1, pm3, pm4, pm5, pm7, intestine, gonad	Lethal		NA	pha-4 ceh-22	Anokye-Danso et al. 2008
ubc-9	E2 sumo ligase	?	?	ABa muscles absent	?	NA	?	Roy Chowdhuri et al. 2006
unc-39	Six4/5	Z	Mesoderm arc	Pun metacorpus	?	?	?	Yanowitz et al. 2004

Genes that are implicated in pharynx development are listed from earliest stages of specification to later events. Aph: anterior pharynx absent, Daf: dauer defective, M/Z: maternal or zygotic contribution of RNA or protein, Pha: pharynx absent, pm: pharyngeal muscle, PPa: posterior pharynx absent, Pun: pharynx unattached, Rcp: receptor, TF: transcription factor, Zn: zinc, ?: unknown. Adapted and extended from Mango (2007).