NANOG (Nanog homeobox)

2012-05-01   Hubert Schorle , Daniel Nettersheim 

University of Bonn Medical School, Institute of Pathology, Department of Developmental Pathology, Sigmund-Freud-Str. 25, 53127 Bonn, Germany




Atlas Image
Figure 1. (A) Genomic sequence of the human NANOG promoter region. Important regulatory elements, binding sites and CpG-dinucleotides are indicated in different colors. (B) Graphical illustration of the four different human NANOG transcripts.


The NANOG gene encompasses 8265 bp of DNA in humans and is located on the short arm of chromosome 12 (12p13.31) from 7940390 - 7948655. A 299 bp large NANOG promoter region (-264 to +35) upstream of exon 1 (Fig. 1A) contains five CpG-dinucleotides, which are subjected to DNA-methylation (Nettersheim et al., 2011a). Furthermore, this NANOG promoter region contains an OCT3/4-SOX2 binding motif, a TATA-box and binding sites for the transcription factors AP-2,SP1 and TFIID (Rodda et al., 2005; Nettersheim et al., 2011a) (PromoterScan 1.7). Functionality of this NANOG promoter element has been demonstrated by Luciferase-reporter experiments (Nettersheim et al., 2011a). A similar region (-229 to +193) has also been analysed by Wu et al. in mice (Wu da and Yao, 2005). There, binding sites for AP-1, SP1 and Oct3/4 could be found and functionality of this region in regulation of Nanog expression was demonstrated in F9 EC cells by Luciferase-assays.


The mRNA encoded by NANOG has four transcript variants (Fig. 1B). Transcript variants NANOG-001 (2101 bp mRNA) and -002 (870 bp mRNA) are known protein coding, while variant -004 (561 bp mRNA) is putatively protein coding and variant -003 is known as nonsense mediated decay. NANOG transcription can be regulated by binding of OCT3/4 and SOX2 to their binding motifs in the NANOG promoter (see Fig. 1A) (Nettersheim et al., 2011a; Kuroda et al., 2005; Rodda et al., 2005).


Ten NANOG-related nucleotide sequences (NANOGP2 - NANOGP11) plus one non-functional duplication (NANOGP1) have been discovered in the human genome (Booth and Holland, 2004). NANOGP2 - NANOGP11 are processed but are lacking introns, except NANOGP8 which is a retrogene.


Atlas Image
Figure 2: Graphical illustration of the NANOG protein sequence (A) and secondary structure motifs of the NANOG protein (B).


NANOG mRNA variants NANOG-001 and -002 encode for a protein with a length of 305 amino acid (aa) and 289 aa, respectively. NANOG-004 is putatively protein coding; translation would result in a 186 aa long protein.
NANOG-001, the 305 aa long protein with a molecular weight of 34.6 kDa is usually analyzed to study the role of NANOG (Fig. 2A). It consists of a Serine-, Threonine- and Proline-rich N-terminal region as well as eight W-repeats at its C-terminus (aa 104-151). The DNA-binding facilitating homeodomain spans from aa 95-155. Formation of secondary structures (helix, strand and turn) occurs mainly within the homeobox-coding region (Fig. 2B).
The NANOG protein is unstable with a half-life of 120 min in human ESCs (Ramakrishna et al., 2011).


NANOG is expressed in undifferentiated embryonic stem cells (ESCs) (Ezeh et al., 2005), glioma stem cells (Zbinden et al., 2010), fetal gonocytes (Hart et al., 2005; Hoei-Hansen et al., 2005), carcinoma-in-situ (CIS) of the testis (Hart et al., 2005; Hoei-Hansen et al., 2005), seminoma (Ezeh et al., 2005; Hoei-Hansen et al., 2005), embryonal carcinoma (Hoei-Hansen et al., 2005) and mammary carcinoma / breast cancer (Ezeh et al., 2005). Ezeh et al. found NANOG expression in adult germ cells throughout germ cell differentiation (spermatogonia to spermatids) (Ezeh et al., 2005). In contrast to the data of Ezeh et al., Hoei-Hansen et al. were unable to detect NANOG protein in adult testis tissue (Hoei-Hansen et al., 2005). NANOG is also expressed in the seminoma cell line TCam-2 and the embryonal carcinoma cell lines 2102EP, NCCIT, Tera-1, Tera-2, NT2/D1 and 833Ke (Nettersheim et al., 2011a; Nettersheim et al., 2011b; Eckert et al., 2008; You et al., 2009; Deb-Rinker et al., 2005; Freberg et al., 2007).
In germ cell tumors (GCTs), NANOG expression is regulated by binding of OCT3/4 and SOX2 (SOX17 putatively in seminomas) to the NANOG promoter (Nettersheim et al., 2011a). Furthermore, in GCTs NANOG expression can be epigenetically suppressed by DNA-methylation of CpG-dinucleotides in the promoter (Nettersheim et al., 2011a). NANOG expression correlates to the differentiation status of GCTs, i.e. the more differentiated the GCT, the lower the NANOG expression (Nettersheim et al., 2011a).
Expression of the NANOG pseudogene NANOGP8 has been detected in uterine cervix tumor tissue, breast tumor tissue, urinary bladder tissue and smooth muscle cells as well as in the cell lines OS732, HepG3 and MCF-7 (Zhang et al., 2006; Ambady et al., 2010). Expression of pseudogenes NANOGP4 and NANOGP5 has been demonstrated in the cell lines OS732, HepG3 and MCF-7, too (Zhang et al., 2006).




NANOG promotes self-renewal and maintains pluripotency in undifferentiated cells, like ESCs (Boyer et al., 2005; Wang et al., 2006). Thereby, NANOG acts in concert with the transcription factors SOX2, OCT3/4 (POU5F1) and FOXD3 (Pan and Thomson, 2007) (Wang et al., 2006). NANOG activates expression of SOX2 and OCT3/4 (Pan and Thomson, 2007).
A NANOG knock-down leads to differentiation of ESCs into the extraembryonic endoderm and trophectoderm lineages (Hyslop et al., 2005), demonstrating NANOGs important role in repression of differentiation. However, siRNA/shRNA-mediated reduction of the NANOG protein in the seminoma cell line TCam-2 is tolerated without induction of differentiation (Nettersheim et al., 2011b). It is assumed that the observed upregulation of OCT3/4 and SOX17 compensates for reduced NANOG levels in TCam-2 cells (Nettersheim et al., 2011b). NANOG-shRNA transduced cancer cells exhibit decreased long-term clonal and clonogenic growth, reduced proliferation and altered differentiation (Jeter et al., 2009). Overexpression of NANOG in ESC enables their feeder-cell-free propagation for multiple passages during which the cells remain pluripotent (Darr et al., 2006).
NANOG is able to modulate gliomasphere clonogenicity and CD133+ stem cell behaviour (Zbinden et al., 2010). There, NANOG is regulated by the Hedgehog-GLI signalling pathway. GLI1 requires NANOG activity to form a positive loop, which is negatively controlled by p53 and vice versa (Zbinden et al., 2010).
Besides SOX2 and OCT3/4, protein interaction databases predict interaction of NANOG with SALL4, KLF4, ZFP42, ISYNA1, LIN28, FAM48A, SMAD1, GATA6, RIF1, TRIM28, SMARCA4 and SMARCA2 (by similarity) (String 9.0, UniProt, I2D).


NANOG and its pseudogenes (except NANOGP8) are present at their expected orthologous chromosomal positions in the chimpanzee genome when compared to the human genome (Fairbanks and Maughan, 2006). NANOGP8 is not found in the genome of the chimpanzee (Fairbanks and Maughan, 2006). The homeodomain of the human NANOG protein shares 87% identity to the murine NANOG homeodomain (Hart et al., 2004). A sequence comparison of murine, cow, chimp and human Nanog/NANOG promoters revealed that the CpG-dinucleotides are completely conserved in chimp and human (Nettersheim et al., 2011a).



NANOG is localized on the short arm of chromosome 12, which is often gained in type II germ cell tumors, mostly due to isochromosome formation (i(12p)) (Looijenga et al., 2003).

Implicated in

Entity name
Testicular germ cell tumors
A consistent structural chromosomal abnormality in invasive testicular germ cell tumors are gains of the short arm of chromosome 12 (12p), due to isochromosome formation (Looijenga et al., 2003). This gain results in an increase in copy numbers of genes on 12p, which is speculated to lead to suppression of apoptosis and Sertoli-cell independency of CIS cells (Looijenga et al., 2003). NANOG is located in 12p and therefore amplified in invasive germ cell tumors. Increased NANOG copy numbers, resulting in overexpression of NANOG in seminomas and non-seminomas might lead to maintenance of self-renewal and mediates a pluripotency-like status. During differentiation of embryonal carcinomas into teratoma, choriocarcinoma and yolk-sac tumors the 12p gain is maintained, but NANOG expression is downregulated.


Pubmed IDLast YearTitleAuthors
211363802010Expression of NANOG and NANOGP8 in a variety of undifferentiated and differentiated human cells.Ambady S et al
152339882004Eleven daughters of NANOG.Booth HA et al
161537022005Core transcriptional regulatory circuitry in human embryonic stem cells.Boyer LA et al
165011722006Overexpression of NANOG in human ES cells enables feeder-free growth while inducing primitive ectoderm features.Darr H et al
156157062005Sequential DNA methylation of the Nanog and Oct-4 upstream regions in human NT2 cells during neuronal differentiation.Deb-Rinker P et al
180080882008TCam-2 but not JKT-1 cells resemble seminoma in cell culture.Eckert D et al
162289882005Human embryonic stem cell genes OCT4, NANOG, STELLAR, and GDF3 are expressed in both seminoma and breast carcinoma.Ezeh UI et al
164691012006Evolution of the NANOG pseudogene family in the human and chimpanzee genomes.Fairbanks DJ et al
173143942007Epigenetic reprogramming of OCT4 and NANOG regulatory regions by embryonal carcinoma cell extract.Freberg CT et al
162062932005The pluripotency homeobox gene NANOG is expressed in human germ cell tumors.Hart AH et al
159823232005Stem cell pluripotency factor NANOG is expressed in human fetal gonocytes, testicular carcinoma in situ and germ cell tumours.Hoei-Hansen CE et al
159833652005Downregulation of NANOG induces differentiation of human embryonic stem cells to extraembryonic lineages.Hyslop L et al
194157632009Functional evidence that the self-renewal gene NANOG regulates human tumor development.Jeter CR et al
157438392005Octamer and Sox elements are required for transcriptional cis regulation of Nanog gene expression.Kuroda T et al
127522582003Role of gain of 12p in germ cell tumour development.Looijenga LH et al
216496652011TGF-β1, EGF and FGF4 synergistically induce differentiation of the seminoma cell line TCam-2 into a cell type resembling mixed non-seminoma.Nettersheim D et al
172114512007Nanog and transcriptional networks in embryonic stem cell pluripotency.Pan G et al
212994132011PEST motif sequence regulating human NANOG for proteasomal degradation.Ramakrishna S et al
158604572005Transcriptional regulation of nanog by OCT4 and SOX2.Rodda DJ et al
224737732012Nanog regulates self-renewal of cancer stem cells through the insulin-like growth factor pathway in human hepatocellular carcinoma.Shan J et al
170934072006A protein interaction network for pluripotency of embryonic stem cells.Wang J et al
159167192005Isolation and characterization of the murine Nanog gene promoter.Wu DY et al
195676772009Depletion of embryonic stem cell signature by histone deacetylase inhibitor in NCCIT cells: involvement of Nanog suppression.You JS et al
205818022010NANOG regulates glioma stem cells and is essential in vivo acting in a cross-functional network with GLI1 and p53.Zbinden M et al
166237082006NANOGP8 is a retrogene expressed in cancers.Zhang J et al

Other Information

Locus ID:

NCBI: 79923
MIM: 607937
HGNC: 20857
Ensembl: ENSG00000111704


dbSNP: 79923
ClinVar: 79923
TCGA: ENSG00000111704


Gene IDTranscript IDUniprot

Expression (GTEx)



PathwaySourceExternal ID
Proteoglycans in cancerKEGGhsa05205
Proteoglycans in cancerKEGGko05205
Signaling pathways regulating pluripotency of stem cellsKEGGhsa04550
Signaling pathways regulating pluripotency of stem cellsKEGGko04550
Immune SystemREACTOMER-HSA-168256
Cytokine Signaling in Immune systemREACTOMER-HSA-1280215
Signaling by InterleukinsREACTOMER-HSA-449147
Developmental BiologyREACTOMER-HSA-1266738
Transcriptional regulation of pluripotent stem cellsREACTOMER-HSA-452723
POU5F1 (OCT4), SOX2, NANOG activate genes related to proliferationREACTOMER-HSA-2892247
POU5F1 (OCT4), SOX2, NANOG repress genes related to differentiationREACTOMER-HSA-2892245
Interleukin-4 and 13 signalingREACTOMER-HSA-6785807

Protein levels (Protein atlas)

Not detected


Pubmed IDYearTitleCitations
161537022005Core transcriptional regulatory circuitry in human embryonic stem cells.1612
235419212013Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal.266
254568342014m(6)A RNA modification controls cell fate transition in mammalian embryonic stem cells.252
185939852008Positive correlations of Oct-4 and Nanog in oral cancer stem-like cells and high-grade oral squamous cell carcinoma.233
217268332011CD24(+) liver tumor-initiating cells drive self-renewal and tumor initiation through STAT3-mediated NANOG regulation.205
270018472016Hypoxia induces the breast cancer stem cell phenotype by HIF-dependent and ALKBH5-mediated m⁶A-demethylation of NANOG mRNA.189
224825082012Distinct lineage specification roles for NANOG, OCT4, and SOX2 in human embryonic stem cells.178
186822412008NANOG is a direct target of TGFbeta/activin-mediated SMAD signaling in human ESCs.177
172114512007Nanog and transcriptional networks in embryonic stem cell pluripotency.169
184413252008Hyaluronan-CD44 interaction activates stem cell marker Nanog, Stat-3-mediated MDR1 gene expression, and ankyrin-regulated multidrug efflux in breast and ovarian tumor cells.154


Hubert Schorle ; Daniel Nettersheim

NANOG (Nanog homeobox)

Atlas Genet Cytogenet Oncol Haematol. 2012-05-01

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