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List of intestinal epithelial differentiation genes

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Table of genes implicated in development and differentiation of the intestinal epithelium{{Cite journal

The table listed below is a running comprehensive list of all intestinal differential genes that have been reported in the literature. The PMID is the pubmed identification number of the papers that support the summarized information in the table corresponding to each row.

Official	Common	Function/phenotype	PMID
APC		Conditional deletion promotes Paneth cell differentiation at the expense of enterocyte, goblet and enteroendocrine cell differentiation. Negative regulator of beta-catenin	15716339 {{Cite journal
ATOH1	Math1, HATH1	Commitment to secretory lineage	20691176{{Cite journal
BLIMP1	PRDM1	Postnatal epithelial maturation; suckling/weaning transition	21878906 {{Cite journal
BMPR1A		Involved in terminal differentiation of secretory cells	17678919 {{Cite journal
CBFA2T2	Mtgr1	Required for maintenance of secretory lineage	16227606 {{Cite journal
CDH1	E-cadherin	Required for maturation/localization of Paneth and goblet cells	21179475 {{Cite journal
CDX1	Cdx1	Induced expression promoted enterocyte differentiation in IEC6 cells	19059241 {{Cite journal
CDX2	Cdx2	Involves in epithelial cell maturation as well as goblet and Paneth cell differentiation. Required for the small intestinal identity during development. In IEC-6 cells, conditional expression induced enterocyte and goblet like cells	21081128{{Cite journal
CTNNB1	Catenin, beta	Paneth cell differentiation. Essential for stem cell/crypt maintenance. Villus and crypt morphogenesis with Tcf3 via c-Myc	18948094{{Cite journal
DLL1		Functions as a cis acting element and required for goblet cell differentiation in the Notch inactive colonic epithelia. Notch ligand in intestine. Required for the maintenance of stem and progenitors	20170633{{Cite journal
DLL4		Notch ligand in intestine. Required for the maintenance of stem and progenitors	21238454
ELF3	ESE-1	Terminal differentiation of absorptive enterocytes	19801644 {{Cite journal
EPHB3		Localization of Paneth cells to crypt base	12408869 {{Cite journal
FGF7	KGF	Regulate epithelial growth and promote differentiation	19326389 {{Cite journal
FGFR3		Paneth cell specification through beta-catenin/Tcf4 dependent and independent pathway. Significant reduction in Paneth cell in knockout mice. Involved in crypt development and stem cell expansion	19407216 {{Cite journal
FOXA1	HNF3A	Involved in goblet cell differentiation and enteroendocrine differentiation	19737569 {{Cite journal
FOXA2	HNF3B	Involved in goblet cell differentiation and enteroendocrine differentiation	19737569
FZD5		Required for Paneth cell maturation. Loss of Paneth cell genes after conditional deletion	15778706 {{Cite journal
GADD45GIP1	Crif1	Essential Elf3 coactivator in differentiation of absorptive enterocytes	19801644
GATA6		Regulates proximal-distal identity in the intestines	21262227 {{Cite journal
GATA4		Required for proximal intestinal identity	16940177 {{Cite journal
GFI1		Required for proper allocation of secretory lineage	16230531 {{Cite journal
HES1	Hes1	Commitment to absorptive lineage	10615124 {{Cite journal
HNF1A	HNF1-α	Regulates terminal differentiation of enterocytes and secretory cells potentially by direct regulation of Atoh1	20133952 {{Cite journal
HNF1B	HNF1-β	Regulates terminal differentiation of enterocytes and secretory cells potentially by direct regulation of Atoh1	20133952 20388655
IHH		Colonocytes differentiation	14770182 {{Cite journal
KLF4	GKLF	Promotes goblet cell differentiation in colon	21070761{{Cite journal
LGR4	GPR48	Promotes Paneth cell differentiation and crypt cell proliferation. Along with LGR5, acts as the receptor for R-Spondin, a WNT co-ligand that amplifies WNT signaling	21508962 21909076
LGR5	GPR49	Premature paneth cell differentiation in fetal intestine. Intestinal stem cell marker. Along with LGR4, acts as the receptor for R-Spondin, a WNT co-ligand that amplifies WNT signaling	19394326 21727895
MMP9		Negatively regulates terminal differentiation of goblet cells in colon	17484881
MSI1		Suppress paneth cell differentiation independent of Notch and Wnt signaling pathways	19214660
MYBL2		Regulates commitment of colon stem cells to differentiate	20857481; 20133952
MYC		Crypt loss upon conditional deletion in the adult	16954380
NEUROD1	BETA2	Differentiation of Ngn3 enteroendocrine cells into CCK and secretin cells	last1 = Schonhoff	first1 = SE	last2 = Giel-Moloney	first2 = M	last3 = Minireview	first3 = Leiter AB.	date = Jun 2004	title = Development and differentiation of gut endocrine cells	journal = Endocrinology	volume = 145	issue = 6	pages = 2639–44	doi = 10.1210/en.2004-0051	pmid = 15044355	doi-access = free }}
NEUROG3	NGN3, ATOH5		Commitment to the enteroendocrine cell lineage	17706959; 12456641
NKX2-2	Nkx2.2	Required for a subset of enteroendocrine cells differentiation	18022152
NOTCH1		Regulates absorptive cells vs secretory cells	last1 = Riccio	first1 = O	last2 = van Gijn	first2 = ME	last3 = Bezdek	first3 = AC	last4 = Pellegrinet	first4 = L	last5 = van Es	first5 = JH	last6 = Zimber-Strobl	first6 = U	last7 = Strobl	first7 = LJ	last8 = Honjo	first8 = T	last9 = Clevers	first9 = H	last10 = Radtke	first10 = F	date = Apr 2008	title = Loss of intestinal crypt progenitor cells owing to inactivation of both Notch1 and Notch2 is accompanied by derepression of CDK inhibitors p27Kip1 and p57Kip2	journal = EMBO Rep	volume = 9	issue = 4	pages = 377–83	doi = 10.1038/embor.2008.7	pmid = 18274550	pmc = 2288761 }}
NOTCH2		Regulates absorptive cells vs secretory cells	15959516; 18274550
NOX1		Regulate ROS to activate Notch signaling and indirectly promote absorptive cell lineage in the colon	20351171
PAX6		Differentiation of GIP in enteroendocrine lineage	last1 = Hill	first1 = ME	last2 = Asa	first2 = SL	last3 = Drucker	first3 = DJ	date = Sep 1999	title = Essential requirement for Pax6 in control of enteroendocrine proglucagon gene transcription	journal = Mol Endocrinol	volume = 13	issue = 9	pages = 1474–86	doi = 10.1210/mend.13.9.0340	pmid = 10478839	doi-access = free }}
PDX1	IPF1	Overexpression causes differentiation of immature intestinal epithelia to enteroendocrine cells. Conditional deletion alters enterocyte and enteroendocrine gene expression	11408276; 19808654
PPARD	PPAR-δ/β	Involves in Paneth cell maturation by modulating IHH expression	16890607
PTK6	BRK	Promote cell cycle exit in Wnt independent pathway and promote enterocyte differentiation	16782882
RB1	pRB	Required for enterocyte terminal differentiation in small intestine	18981186
RBPJ	CBF1	Conversion of progenitors and differentiated cells into goblet cells by conditional deletion	15959515
REG4		Marker for enteroendocrine cells
SOX9		Required for paneth cell differentiation	17698607; 17681175
SPDEF	PDEF	Regulates terminal differentiation of goblet cells and Paneth cells	19786015; 19549527
STK11	LKB1	Required for normal differentiation of goblet and Paneth cells	19165340
TGFBR2	Tgf-βRII	The critical downstream target of Elf3 for enterocyte differentiation	17408644
VAV		Required for enterocyte differentiation in mouse cecum and colon	19139088

References

(Jun 2011). "Lgr4 is required for Paneth cell differentiation and maintenance of intestinal stem cells ex vivo". EMBO Rep.
(2011). "LGR4 and LGR5 are R-spondin receptors mediating Wnt/β-catenin and Wnt/PCP signalling". EMBO Rep..
Garcia MI, Ghiani M, Lefort A, Libert F, Strollo S, Vassart G. LGR5 deficiency deregulates Wnt signaling and leads to precocious Paneth cell differentiation in the fetal intestine. Dev Biol. 2009 Jul 1;331(1):58-67.
de Lau W, Barker N, Low TY, Koo BK, Li VS, Teunissen H, Kujala P, Haegebarth A, Peters PJ, van de Wetering M, Stange DE, van Es JE, Guardavaccaro D, Schasfoort RB, Mohri Y, Nishimori K, Mohammed S, Heck AJ, Clevers H. Lgr5 homologues associate with Wnt receptors and mediate R-spondin signalling. Nature. 2011 Jul 4;476(7360):293-7.
(May 2007). "Matrix metalloproteinase-9 regulates MUC-2 expression through its effect on goblet cell differentiation". Gastroenterology.
(2009). "Musashi-1 suppresses expression of Paneth cell-specific genes in human intestinal epithelial cells". J Gastroenterol.
(Mar 2011). "MYBL2, a link between proliferation and differentiation in maturing colon epithelial cells". J Cell Physiol.
(2010). "Cooperation between HNF-1alpha, Cdx2, and GATA-4 in initiating an enterocytic differentiation program in a normal human intestinal epithelial progenitor cell line". Am J Physiol Gastrointest Liver Physiol.
(Nov 2006). "Rapid loss of intestinal crypts upon conditional deletion of the Wnt/Tcf-4 target gene c-Myc". Mol Cell Biol.
Desai S, Loomis Z, Pugh-Bernard A, Schrunk J, Doyle MJ, Minic A, McCoy E, Sussel L. Nkx2.2 regulates cell fate choice in the enteroendocrine cell lineages of the intestine. Dev Biol. 2008 Jan 1;313(1):58-66.
(Jun 2004). "Development and differentiation of gut endocrine cells". Endocrinology.
López-Díaz L, Jain RN, Keeley TM, VanDussen KL, Brunkan CS, Gumucio DL, Samuelson LC. Intestinal Neurogenin 3 directs differentiation of a bipotential secretory progenitor to endocrine cell rather than goblet cell fate. Dev Biol. 2007 Sep 15;309(2):298-305.
Jenny M, Uhl C, Roche C, Duluc I, Guillermin V, Guillemot F, Jensen J, Kedinger M, Gradwohl G. Neurogenin3 is differentially required for endocrine cell fate specification in the intestinal and gastric epithelium. EMBO J. 2002 Dec 2;21(23):6338-47.
Fre S, Huyghe M, Mourikis P, Robine S, Louvard D, Artavanis-Tsakonas S. Notch signals control the fate of immature progenitor cells in the intestine. Nature. 2005 Jun 16;435(7044):964-8.
(Apr 2008). "Loss of intestinal crypt progenitor cells owing to inactivation of both Notch1 and Notch2 is accompanied by derepression of CDK inhibitors p27Kip1 and p57Kip2". EMBO Rep.
(Jun 2010). "NADPH oxidase 1 modulates WNT and NOTCH1 signaling to control the fate of proliferative progenitor cells in the colon". Mol Cell Biol.
(Sep 1999). "Essential requirement for Pax6 in control of enteroendocrine proglucagon gene transcription". Mol Endocrinol.
(Jul 2001). "Differentiation of immature enterocytes into enteroendocrine cells by Pdx1 overexpression". Am J Physiol Gastrointest Liver Physiol.
(Dec 2009). "Pdx1 inactivation restricted to the intestinal epithelium in mice alters duodenal gene expression in enterocytes and enteroendocrine cells". Am J Physiol Gastrointest Liver Physiol.
(Aug 2006). "PPARbeta/delta regulates paneth cell differentiation via controlling the hedgehog signaling pathway". Gastroenterology.
(Jul 2006). "Protein tyrosine kinase 6 negatively regulates growth and promotes enterocyte differentiation in the small intestine". Mol Cell Biol.
Guo J, Longshore S, Nair R, Warner BW. Retinoblastoma protein (pRb), but not p107 or p130, is required for maintenance of enterocyte quiescence and differentiation in small intestine. J Biol Chem. 2009 Jan 2;284(1):134-40.
van Es JH, van Gijn ME, Riccio O, van den Born M, Vooijs M, Begthel H, Cozijnsen M, Robine S, Winton DJ, Radtke F, Clevers H. Notch/gamma-secretase inhibition turns proliferative cells in intestinal crypts and adenomas into goblet cells. Nature. 2005 Jun 16;435(7044):959-63.
(2015-09-10). "Single-cell messenger RNA sequencing reveals rare intestinal cell types". Nature.
Bastide P, Darido C, Pannequin J, Kist R, Robine S, Marty-Double C, Bibeau F, Scherer G, Joubert D, Hollande F, Blache P, Jay P. Sox9 regulates cell proliferation and is required for Paneth cell differentiation in the intestinal epithelium. J. Cell Biol. 2007 Aug 13;178(4):635-48.
Mori-Akiyama Y, van den Born M, van Es JH, Hamilton SR, Adams HP, Zhang J, Clevers H, de Crombrugghe B. SOX9 is required for the differentiation of paneth cells in the intestinal epithelium ''Gastroenterology'' 2007 Aug;133(2):539-46.
Noah TK, Kazanjian A, Whitsett J, Shroyer NF. SAM pointed domain ETS factor (SPDEF) regulates terminal differentiation and maturation of intestinal goblet cells. Exp Cell Res. 2010 Feb 1;316(3):452-65.
(Oct 2009). "The ets-domain transcription factor Spdef promotes maturation of goblet and paneth cells in the intestinal epithelium". Gastroenterology.
(2009). "Lkb1 deficiency alters goblet and paneth cell differentiation in the small intestine". PLOS ONE.
(Apr 2007). "TGF-betaRII rescues development of small intestinal epithelial cells in Elf3-deficient mice". Gastroenterology.
Liu JY, Seno H, Miletic AV, Mills JC, Swat W, Stappenbeck TS. Vav proteins are necessary for correct differentiation of mouse cecal and colonic enterocytes. J Cell Sci. 2009 Feb 1;122(3):324-34.

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