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Homeobox C11 (HOXC11) is a member of the Abd-B homeobox family. The homeobox genes encode well conservedfamily of transcription factors that play a vital role in morphogenesis in all multicellular organisms. HOXC11is one of numerous homeobox HOXC genes placed in a cluster on chromosome 12. HOXC11 attaches to a promoterelement of the lactase-phlorizin hydrolase. HOXC11 also takes part in early intestinal development. An alternativelyspliced variant encoding a shorter isoform has been defined however, its full-length nature has not been determined.

DLX3 belongs to the Distal-less (Dlx) family of genes which includes at least 6 different members. DLX3 plays a regulatory role in the development of the ventral forebrain and also in craniofacial patterning and morphogenesis. Mutation in DLX3 is correlated with Trichodentoosseous syndrome which is an autosomal dominant condition. DLX3 is located in a tail-to-tail configuration with another member of the gene family on the long arm of chromosome 17.

Homeobox A9 (HOXA9) is a member of the Abd-B homeobox family. The HOXA9 protein is a transcription factor with a key role in both haemopoiesis and leukaemia. High levels of HOXA9 expression in haemopoietic cells is a distinctive feature of acute myeloid leukaemia (AML), and may be sufficient to cause this disease. HOXA9 overexpression noticeably expands hematopoietic stem cells. The HOXA9 gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which regulates gene expression, morphogenesis, and differentiation. HOXA9 is a sequence-specific transcription factor which is part of a developmental regulatory system, which provides cells with specific positional identities on the anterior-posterior axis. HOXA9 is essential for induction of E-selectin and VCAM-1, on the endothelial cells surface at sites of inflammation.

The homeobox protein family of transcription factors has many members that take part in developmental processes such as HHEX. HHEX is known to interact with Promyelocytic leukemia protein and expression in specific hematopoietic lines indicates that this protein is involved in hematopoietic differentiation.

HOXB13 is a transcription factor and a member of the homeobox gene family which are extremely conserved in vertebrates and vital for vertebrate embryonic development. HOXB13 is involved in fetal skin development and cutaneous regeneration. In mice, a similar gene displayed temporal and spatial colinearity in the main body axis of the embryo, however it was not expressed in the secondary axes, implying that it has a roles in body patterning along the axis.

Homeobox protein MOX-2 (MEOX2) is a part of a family of nonclustered, diverged homeobox genes which are expressed in overlapping patterns in the paraxial mesoderm and its derivatives. MEOX2 participates in the regulation of vertebrate limb myogenesis. MEOX2 also takes part in mesoderm induction and its earliest regional specification, somitogenesis, myogenic and sclerotomal differentiation. Mutations in the related mouse MEOX2 are related with craniofacial and/or skeletal abnormalities, in addition to neurovascular dysfunction observed in Alzheimer's disease.

Homeodomain-only protein (HOPX) functions via its interaction with SRF, thus modulating the expression of SRF-dependent cardiac-specific genes and cardiac development. HOPX inhibits SRF-dependent transcription either by hindering SRF binding to DNA or by engaging histone deacetylase (HDAC) proteins which prevent transcription by SRF. HOPX is a homeodomain protein which lacks certain conserved residues required for DNA binding. HOPX overexpression causes cardiac hypertrophy.

PRRX1 is part of the paired family of homeobox proteins. PRRX1 functions as a transcription co-activator, enhancing the DNA-binding activity of serum response factor, a protein required for the induction of genes by growth and differentiation factors. PRRX1 also regulates muscle creatine kinase, and therefore has a part in the establishment of diverse mesodermal muscle types. The protein binds to an A/T-rich element in the muscle creatine enhancer. Among the diseases associated with PRRX1 are agnathia-otocephaly complex, and pleomorphic liposarcoma.

NANOG is a multidomain homeobox transcription factor which functions to maintain the undifferentiated state of pluripotent stem cells. NANOG expression counteracts the differentiation-promoting signals induced by the extrinsic factors LIF, Stat3 and BMP. Once NANOG expression is downregulated, cell differentiation can proceed. Proteins which regulate NANOG expression include transcription factors Oct4, SOX2, FoxD3, and Tcf3 and tumor suppressor p53.

NANOGP8 belongs to the homeobox family of DNA binding transcription factors which is known to conserve pluripotency of embryonic stem cells. One change only separate NANOGP8 from NANOG – instead of 'Gln-253' in the inferred amino acid sequence in NANOG there is a ‘His-253’ in NANOGP8.

NK3 Homeobox1 (NKX3-1) is a homeobox-containing transcription factor, which binds preferentially the consensus sequence 5'-TAAGT[AG]-3' and may act as a transcriptional repressor. The NKX3-1 transcription factor functions as a negative regulator of epithelial cell growth in prostate tissue. NKX3-1 has an imperative role in normal prostate development, regulating proliferation of glandular epithelium and in the formation of ducts in prostate. In addition, NKX3-1 functions as a tumor suppressor controlling prostate carcinogenesis, as shown by its ability to inhibit proliferation and invasion activities of PC-3 prostate cancer cells. Abnormal expression of NKX3-1 is linked with prostate tumor progression.

SIX Homeobox 6 (SIX6) is a member of the SIX/Sine oculis homeobox family contains 1 homeobox DNA-binding domain. The SIX6 protein is essential in embryonic development by providing necessary instructions for the formation of the forebrain and eye development. SIX6 is expressed in the developing and adult retina, hypothalamic and the pituitary regions. SIX6 gene defects are the cause of microphthalmia isolated with cataract type 2.

Homeobox protein SIX1 (SIX1) belongs to the SIX gene family. SIX1 is characterized by a divergent DNA-binding homeodomain and an upstream SIX domain, which is involved both in determining DNA-binding specificity and in mediating protein-protein interactions. SIX1 has a role in vertebrate and insect development or in the maintenance of the differentiated state of tissues.

BP-1 gene, a member of the DLX homeobox gene family, is overexpressed in 80% of breast cancer patients, and thus represents a potential new target for diagnosis and treatment.
Members of the Dlx gene family contain a homeobox that is related to that of Distal-less (Dll), a gene expressed in the head and limbs of the developing fruit fly (Drosophila). The Distal-less (Dlx) family of genes comprises at least 6 different members, DLX1-DLX6. The DLX proteins are postulated to play a role in forebrain and craniofacial development. Three transcript variants have been described for this gene, however, the full length nature of one variant has not been described. Studies of the two splice variants revealed that one encoded isoform functions as a repressor of the beta-globin gene while the other isoform lacks that function.

POU6F1 is a member of the POU transcription factor family. POU6F1 is transcription factor that binds favorably to a variant of the octamer motif (5'-ATGATAAT-3'). POU6F1 is exclusively expressed in the embryo in the developing brain, however in the adult its expression is confined to the brain, heart, skeletal muscle and lung. In the brain, the highest expression levels are found in specific cell layers of the cortex, the olfactory bulb, the hippocampus and the cerebellum.

PDX1 activates insulin, somatostatin, glucokinase, islet amyloid polypeptide and glucose transporter type 2 gene transcription. IPF1 is particularly involved in glucose-dependent regulation of insulin gene transcription. Pancreas Duodenum Homeobox-1 binds preferentially the DNA motif 5'-[ct]taat[tg]-3'. During development, specifies the early pancreatic epithelium, permitting its proliferation, branching and subsequent differentiation. At adult stage, it is required for maintaining the hormone-producing phenotype of the beta-cell.

TGFB-Induced Factor Homeobox 2-Like, X-Linked (TGIF2LX) belongs to the TALE/TGIF homeobox family of transcription factors and takes part in spermatogenesis. A homolog of TGIF2LX is located in the male specific region of chromosome Y, in a block of sequence which is the outcome of a large X-to-Y transposition.

POU5F1 is a homeodomain transcription factor of the POU family, expressed in embryonic stem (ES) cells and embryonic carcinoma (EC) cells.POU5F1 is significantly involved in the signaling pathway for maintaining self-renewal and pluripotency of ES cells. POU5F1 has 2 distinct DNA binding domains which independently bind half-sites of the canonical octamer motif. This flexibility allows POU5F1 to bind with distinct DNA motifs by forming heterodimers with other transcription factors or by forming homodimers in several conformations. Human POU5F1 contains a 75aa POU specific (POUS) domain and a 60aa POU-Homeo-(POUH) domain connected by a linker region. The Human POU5F1 specifically interacts with Octamer motif ATGCAAAT. In addition, 2 proline-rich domains in the N-terminal and C-terminal regions are vital for POU5F1 transactivation. POU5F1 regulates a number of target genes and has been shown to work jointly with other transcription factors including Sox2 as well as Nanog to sustain stem cell potency and self-renewal.

NANOG is a multidomain homeobox transcription factor which functions to maintain the undifferentiated state of pluripotent stem cells. NANOG expression counteracts the differentiation-promoting signals induced by the extrinsic factors LIF, Stat3 and BMP. Once NANOG expression is downregulated, cell differentiation can proceed. Proteins which regulate NANOG expression include transcription factors Oct4, SOX2, FoxD3, and Tcf3 and tumor suppressor p53.

PBX/Knotted 1 Homeobox 1 (PKNOX1) is a DNA-binding factor which takes part in the regulation of the transcriptional activity of AP-1 containing promoters. PKNOX1, which is also known as UEF3, PRP-1 and p64, is a Hmeobox protein. PKNOX1 forms stable complexes containing PBX proteins which synergize with AP-1 binding factors.

NANOG is a multidomain homeobox transcription factor which functions to maintain the undifferentiated state of pluripotent stem cells. NANOG expression counteracts the differentiation-promoting signals induced by the extrinsic factors LIF, Stat3 and BMP. Once NANOG expression is downregulated, cell differentiation can proceed. Proteins which regulate NANOG expression include transcription factors Oct4, SOX2, FoxD3, and Tcf3 and tumor suppressor p53.

NANOG is a multidomain homeobox transcription factor which functions to maintain the undifferentiated state of pluripotent stem cells. NANOG expression counteracts the differentiation-promoting signals induced by the extrinsic factors LIF, Stat3 and BMP. Once NANOG expression is downregulated, cell differentiation can proceed. Proteins which regulate NANOG expression include transcription factors Oct4, SOX2, FoxD3, and Tcf3 and tumor suppressor p53.

LIM Homeobox Transcription Factor 1, Beta (LMX1B) is a part of LIM-homeodomain family of proteins which consists of 2 N-terminal zinc-binding LIM domains, 1 homeodomain, and a C-terminal glutamine-rich domain. LMX1B plays a role as a transcription factor and is necessary for the specification of dorsal limb fate at the zeugopodal and autopodal levels. Mutations in LMX1B are associated with nailpatella syndrome.

TGFB-Induced Factor Homeobox 2-Like Y-Linked (TGIF2LY) is a part of the TALE/TGIF homeobox family of transcription factors. TGIF2LY is located in the male specific region of chromosome Y, in a block of sequence which is the outcome of a large X-to-Y transposition. TGIF2LY act as a regulator of TGIF2LX due to the fact that the C-terminus of TGIF2LY is different from that of its chromosome X homolog (TGIF2LX). TGIF2LY has also a transcription role in testis.