List of intestinal epithelial differentiation genes

Table of genes implicated in development and differentiation of the intestinal epithelium[1]

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.

OfficialCommonFunction/phenotypePMID
APCConditional deletion promotes Paneth cell differentiation at the expense of enterocyte, goblet and enteroendocrine cell differentiation. Negative regulator of beta-catenin15716339 [2]
ATOH1Math1, HATH1Commitment to secretory lineage20691176[3] 17570220[4] 11739954 [5]
BLIMP1PRDM1Postnatal epithelial maturation; suckling/weaning transition21878906 [6] 21670299 [7]
BMPR1AInvolved in terminal differentiation of secretory cells17678919 [8]
CBFA2T2Mtgr1Required for maintenance of secretory lineage16227606 [9]
CDH1E-cadherinRequired for maturation/localization of Paneth and goblet cells21179475 [10]
CDX1Cdx1Induced expression promoted enterocyte differentiation in IEC6 cells19059241 [11] 10579974 [12]
CDX2Cdx2Involves 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 cells21081128[13] 19386267[14] 8552090 [15]
CTNNB1Catenin, betaPaneth cell differentiation. Essential for stem cell/crypt maintenance. Villus and crypt morphogenesis with Tcf3 via c-Myc18948094[16] 17785439[17] 17681174 [18]
DLL1Functions 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 progenitors20170633[19] 21238454 [20]
DLL4Notch ligand in intestine. Required for the maintenance of stem and progenitors21238454 [20]
ELF3ESE-1Terminal differentiation of absorptive enterocytes19801644 [21]
EPHB3Localization of Paneth cells to crypt base12408869 [22]
FGF7KGFRegulate epithelial growth and promote differentiation19326389 [23]
FGFR3Paneth 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 expansion19407216 [24]
FOXA1HNF3AInvolved in goblet cell differentiation and enteroendocrine differentiation19737569 [25]
FOXA2HNF3BInvolved in goblet cell differentiation and enteroendocrine differentiation19737569 [25]
FZD5Required for Paneth cell maturation. Loss of Paneth cell genes after conditional deletion15778706 [26]
GADD45GIP1Crif1Essential Elf3 coactivator in differentiation of absorptive enterocytes19801644 [21]
GATA6Regulates proximal-distal identity in the intestines21262227 [27]
GATA4Required for proximal intestinal identity16940177 [28] 18812176 [29]
GFI1Required for proper allocation of secretory lineage16230531 [30]
HES1Hes1Commitment to absorptive lineage10615124 [31]
HNF1AHNF1-αRegulates terminal differentiation of enterocytes and secretory cells potentially by direct regulation of Atoh120133952 [32] 20388655 [33]
HNF1BHNF1-βRegulates terminal differentiation of enterocytes and secretory cells potentially by direct regulation of Atoh120133952 [32] 20388655 [33]
IHHColonocytes differentiation14770182 [34]
KLF4GKLFPromotes goblet cell differentiation in colon21070761[35] 12015290 [36]
LGR4GPR48Promotes Paneth cell differentiation and crypt cell proliferation. Along with LGR5, acts as the receptor for R-Spondin, a WNT co-ligand that amplifies WNT signaling21508962 [37] 21909076 [38]
LGR5GPR49Premature 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 signaling19394326 [39] 21727895 [40]
MMP9Negatively regulates terminal differentiation of goblet cells in colon17484881 [41]
MSI1Suppress paneth cell differentiation independent of Notch and Wnt signaling pathways19214660 [42]
MYBL2Regulates commitment of colon stem cells to differentiate20857481;[43] 20133952 [44]
MYCCrypt loss upon conditional deletion in the adult16954380 [45]
NEUROD1BETA2Differentiation of Ngn3 enteroendocrine cells into CCK and secretin cells18022152;[46] 15044355 [47]
NEUROG3NGN3, ATOH5 Commitment to the enteroendocrine cell lineage17706959;[48] 12456641 [49]
NKX2-2Nkx2.2Required for a subset of enteroendocrine cells differentiation18022152 [46]
NOTCH1Regulates absorptive cells vs secretory cells15959516;[50] 18274550 [51]
NOTCH2Regulates absorptive cells vs secretory cells15959516;[50] 18274550 [51]
NOX1Regulate ROS to activate Notch signaling and indirectly promote absorptive cell lineage in the colon20351171 [52]
PAX6Differentiation of GIP in enteroendocrine lineage18022152;[46] 10478839 [53]
PDX1IPF1Overexpression causes differentiation of immature intestinal epithelia to enteroendocrine cells. Conditional deletion alters enterocyte and enteroendocrine gene expression11408276;[54] 19808654 [55]
PPARDPPAR-δ/βInvolves in Paneth cell maturation by modulating IHH expression16890607 [56]
PTK6BRKPromote cell cycle exit in Wnt independent pathway and promote enterocyte differentiation16782882 [57]
RB1pRBRequired for enterocyte terminal differentiation in small intestine18981186 [58]
RBPJCBF1Conversion of progenitors and differentiated cells into goblet cells by conditional deletion15959515 [59]
REG4 Marker for enteroendocrine cells
26287467 [60]
SOX9Required for paneth cell differentiation17698607;[61] 17681175 [62]
SPDEFPDEFRegulates terminal differentiation of goblet cells and Paneth cells19786015;[63] 19549527 [64]
STK11LKB1Required for normal differentiation of goblet and Paneth cells19165340[65]
TGFBR2Tgf-βRIIThe critical downstream target of Elf3 for enterocyte differentiation17408644 [66]
VAVRequired for enterocyte differentiation in mouse cecum and colon19139088 [67]

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