Identifying Changes in Punitive Transcriptional Factor Binding Sites Created by PPAR α / δ / γ SNPs Associated with Disease

Single nucleotide polymorphisms (SNPs) located in the PPARα/δ/γ genes that have been previously found to be significantly associated with human disease or a condition were also found to alter the genes punitive transcriptional factor binding sites (TFBS). Two alleles (C/G) of the PPARα SNP (rs1800206) were found to generate 7 common and 8 unique punitive TFBS. One of the unique TFBS created by the minor G (0.02) allele is for the T-Box 4 (TBX4) transcription factor which is associated with heritable pulmonary arterial hypertension. Two alleles (A/G) of the PPARδ SNP (rs2016520) were found to generate 20 unique punitive TFBS while the two alleles (C/G) of the PPARδ SNP (rs9794) were found to generate 11 common and 11unique punitive TFBS. The alleles of the PPARγ SNPs (rs10865710, rs12629751, rs709158, rs1805192 and rs3856806) were found to generate 15, 12, 16, 2 and 21 common and 9, 4, 12, 4 and 7 unique punitive TFBS, respectively. These changes in TFBS are discussed with relation to alterations in gene expression that may result in disease or change in human condition.


Introduction
The peroxisome proliferator-activated receptors (PPARs) are ligand-activated transcriptional factors (TFs) that regulate many genes in cell differentiation and various metabolic processes including lipid and glucose homeostasis.They are nuclear hormone receptors belonging to a steroid receptor superfamily that include estrogen, thyroid hormone, vitamin D3 and glucocorticoid receptors [1] [2] [3].The PPAR isotypes, PPARα, PPARβ/δ and PPARγ are derived from three different genes found on chromosomes 22, 6 and 3, respectively.These isotypes modulate the expression of several genes which play a central role in regulating glucose, lipid and cholesterol metabolism [4].PPARα is expressed in the liver, skeletal muscles, heart, intestinal mucosa, and brown adipose tissue while PPARβ/δ is expressed in liver, skeletal and cardiac muscle, adipose tissue and macrophages.PPARγ occurs as three isoforms PPARγ 1 , PPARγ 3 , which are expressed in the liver, intestine and spleen, and PPARγ 2 , which is expressed in brown and white adipose tissue [5].There has been much published concerning the PPARs significant involvement in the progression of human disease [1] [3] [6] [7] [8].
There have been several PPARα/δ/γ single nucleotide polymorphisms (SNPs) significantly associated with various human diseases or conditions [9]- [17].A SNP can alter a transcriptional factor motif sequence or a transcriptional factor binding site (TFBS) which in turn can affect the process of gene regulation [18] [19] [20].A nucleotide change in a binding motif of a gene may increase or decrease the corresponding transcription factor's (TF) ability to bind the DNA and thereby affect gene expression [21] resulting in a disease or change in a human condition.In this study, eight PPARα/δ/γ SNPs that have been previously associated with a disease or condition were analyzed for producing alterations in punitive TFBS (Table 1 & Table 2).

PPARα/δ/γ Genes and SNPs
The PPARα/δ/γ SNPs that have been shown to be significantly associated with disease or sickness [9]- [17] are listed in Table 1 as well as the SNP alleles, frequencies and mutations.SNP information was collected using dbSNP, National Center for Biotechnology Information (NCBI), U.S. National Library of Medicine.The gene symbols of conserved (black) and unique (red)punitive TFBS between the two SNP alleles are found in the Table 2.The names of the punitive TFBS can be found in the Supplement.

Identifying TFBS
The JASPAR CORE database [22] [23] and Con Site [24] were used to identify the TFBS in previous studies [25]- [36].JASPAR is a collection of transcription factor DNA-binding preferences used for scanning genomic sequences where ConSite is a web-based tool for finding cis-regulatory elements in genomic sequences.The Vector NTI Advance 11 computer program (Invitrogen, Life Technologies) was used to locate SNPs and TFBS within all genes listed in Table 2.

Results
The PPARα gene is mainly expressed in tissues with extensive fatty acid catabolism and its activation results in alterations in the transcription of several genes that regulate lipid and lipoprotein metabolism [6] [37].One of its SNPs (rs18-Table 1. PPARα/δ/γ genes whose SNPs have been shown to be associated with disease or sickness.Listed are the genes and NCBI reference sequence; their chromosome location as well as the SNP genome position and gene location; SNPs, their alleles and mutations; disease or condition associated with the SNP as well as the ethnic group.See references for information related to the disease/condition.MAF is minor allele frequency.

00206) has been associated with variation in lipid serum levels in Caucasian and
Indian populations [38] [39], hypertriglyceridemia risk, dyslipidemia risk and low-density lipoprotein-cholesterol risk in Han Chinese [10] [11] [16].The two alleles (C/G) of the SNP generates seven conserved punitive TFBS between the alleles while the common C allele generates an additional six unique TFBS and the minor G allele generates two unique TFBS (Table 2).Of the minor G allele TFBS, the TBX4 transcription factor is associated with the disease heritable pulmonary arterial hypertension [40] , which may in part be responsible for the variation in lipid serum levels and disease risks found to be significantly associated with the this SNP.
The PPARδ gene is expressed in high levels in liver, kidneys, cardiac and skeletal muscle, adipose tissue, brain, colon and vasculature [41].One of its SNPs   (rs2016520) has been associated with obesity risk and intracerebral hemorrhages while a second SNP (rs9794) has been found to be associated with hypertriglyceridemia and obesity in Han Chinese [9] [14] [17].The two alleles (A/G) of the rs2016520 SNP does not generate any conserved punitive TFBS between the alleles while the common A allele generates twelve punitive unique TFBS and the minor G alleles generates eight punitive unique TFBS (Table 2).Of the common A allele TFBS, the NEUROD2 transcriptional regulator is implicated in neuronal determination and the OLIG3 TF which promotes formation and maturation of oligodendrocytes, especially within the brain could in part be associated with obesity risk and intracerebral hemorrhages (Supplement).The second SNPs (rs9794) has been associated with hypertriglyceridemia and obesity risk in Han Chinese [10] [11] [17].The two alleles (C/G) of the rs9794 SNP generates eleven conserved punitive TFBS between the alleles while the common C allele generates eleven unique punitive TFBS and the minor G allele generates no unique TFBS (Table 2).Of the common C allele TFBS, the GCM1 and 2 TFs bind to the trophoblast specific element 2 (TSE2) of the aromatase gene enhancer and act as a master regulator of parathyroid development, respectively (Supplement).
The deletion of these TFBS caused by the minor G allele for these two TFs could in part be associated with hypertriglyceridemia and obesity risk in Han Chinese [10] [17].
The PPARγ gene is expressed at high levels in adipose tissue, lipid storage, glucose metabolism as well as the transcriptional regulation of genes involved in these metabolic processes [42].One of its SNPs (rs10865710) has been associated with obesity risk, systemic sclerosis and low-density lipoprotein-cholesterol in Han Chinese [9] [13] [16].The two alleles (C/G) of this SNP generates sixteen conserved punitive TFBS between the alleles while the common C allele generates nine unique punitive TFBS and the minor G allele generates six unique TFBS (Table 2).Of the common C allele unique punitive TFBS, the POU2F2 TFBS is found in immunoglobulin gene promoters and its absence from the minor G allele TFBS may in part be responsible for the association of this SNP with systemic sclerosis (Supplement).The presence of the MNX1 and RXF3 TFBS with the common C allele and the NKX6-1 TFBS with the minor G allele which are involve with pancreas development and function as well as insulin gene regulation, respectively, may in part be responsible for association of this SNP with obesity risk and low-density lipoprotein-cholesterol (Supplement).
A second PPARγ gene SNP (rs12629751) has been associated with osteoarthritis in southeast Chinese [12].The two alleles (C/T) of this SNP generates twenty-one common punitive TFBS between the alleles while the common C allele generates twelve unique punitive TFBS and the minor T allele generates four unique TFBS (Table 2).Of the common C allele unique TFBS, the NKX3-2 TFBS occurs whose TF is a repressor that acts as a negative regulator of chondrocyte maturation which may in part be responsible for the association of this SNP with osteoarthritis (Supplement).
A third PPARγ gene SNP (rs709158) has been associated with low-density lipoprotein-cholesterol in Han Chinese [16].The two alleles (A/G) of this SNP generates sixteen common punitive TFBS between the alleles while the common A allele generates twelve unique punitive TFBS and the minor A allele generates one unique TFBS (Table 2).Of the common A allele unique TFBS, the HOXC11 TFBS whose TF also binds to a promoter element of the lactase-phlorizin hydrolase gene which may in part be associated with low-density lipoprotein-cholesterol in Han Chinese [43] (Supplement).
A fourth PPARγ gene SNP (rs1805192) has been associated with hypertriglyceridemia, dyslipidemia and low-density lipoprotein-cholesterol in Han Chinese [10] [11] [16].The two alleles (C/G) of this SNP generates two common punitive TFBS between the alleles while the common C allele generates six unique punitive TFBS and the minor G allele generates four unique TFBS (Table 2).Of the common C allele unique TFBS, the ERS2 TFBS whose TF is expressed in many tissues including pulmonary epithelial cells and the MEF2C TFBS generated by the minor G allele whose transcriptional activator controls cardiac morphogenesis and myogenesis, and is also involved in vascular development are in part responsible for hypertriglyceridemia, dyslipidemia, low-density lipoprotein-cholesterol in Han Chinese (Supplement).
A fifth PPARγ gene SNP (rs3856806) has also been associated with hypertriglyceridemia, dyslipidemia and low-density lipoprotein-cholesterol in Han Chinese [10] [11] [16].The two alleles (C/T) of this SNP generates twenty common punitive TFBS between the alleles while the common C allele generates eight unique punitive TFBS and the minor T allele generates eight unique TFBS (Table 2).An examination of Table 2 would indicate that there are no apparent unique TFBS by either allele that would contribute to this SNPs' association with hypertriglyceridemia, dyslipidemia and low-density lipoprotein-cholesterol in Han Chinese (Table 1).However, the TF database used in this study (Materials and Methods) represent a small portion of the nuclear TFs that interact in nucleus.

Discussion
The PPARα/δ/γ genes have several SNPs that have been associated with human disease or conditions [9]- [17] (Table 1).SNPs in TFBS that alter the binding ability of the respective TF and cause changes in gene expression levels are considered regulatory (r) SNPs [44].There have been many reports on the possible outcome of such alterations by identifying punitive TFBS based on the two alleles of the SNP associated with a disease or sickness [25]- [36].The eight SNPs among the three genes studied in this report again provide several punitive TFBS changes per SNP allele (Table 1 & Table 2).
As an example, the PPARα gene has an exon five SNP (rs1800206) that has been associated with hypertriglyceridemia risk, dyslipidemia risk and low-density lipoprotein-cholesterol risk in Han Chinese (Table 1).The minor G allele of the SNP generates a punitive TBX4 (T-Box 4) TFBS not present with the common C allele (Table 2, Supplement).The TBX4 TF has been associated with the disease heritable pulmonary arterial hypertension [40] which may in part be responsible Another example is the PPARδ gene which has a 5'UTR SNP (rs2016520) that has been associated with obesity risk and intracerebral hemorrhages in Han Chinese (Table 1).The major A allele of the SNP generates a punitiveNEU-ROD2 TFBS not present with the minor G allele (Table 2, Supplement).The NEU-ROD2 TF is a regulator implicated in neuronal determination and is a critical factor essential for the repression of the genetic program for neuronal differentiation.The presence of this TFBS created by one SNP allele and not the other may in part be the reason for its association with intracerebral hemorrhages in Han Chinese [14].PPARδ promotes inflammation and tumor growth [47] and an increase in HDL-c concentration in cardiovascular disease [48].The SNPs major A allele generates a punitive ERG TFBS not present with the minor G allele whose TF is associated with inflammation (Table 2, Supplement) while the minor G allele generates the punitive NFKB1 & 2 and REL TFBS not found with the common A allele whose TFs are associated with inflammation and tumorigenesis (Table 2, Supplement).
A third example is the PPARγ gene which has an intron one SNP (rs1269751) that has been associated with osteoarthritis (OA) in southeast Chinese (Table 1).
The major C allele of the SNP generates a punitive NKX3-2 TFBS not present with the minor T allele (Table 2, Supplement).The NKX3-2 TF is a repressor that acts as a negative regulator of chondrocyte maturation.The presence of the NKX3-2 TFBS created by one SNP allele and not the other may in part be the reason for its association with osteoarthritis in southeast Chinese.Nkx3-2 has been found to induce chondrocyte precursor cells, maintained early-stage chondrocytes and down-regulated terminal-stage chondrocytes [49].One of the strongest environmental risk factors for knee OA is obesity [50] and is also considered to be a moderate risk factor for hip OA [51].The PPARγ gene has a SNP (rs10865710) in its promotor that is associated with obesity risk [9].The minor G allele of this SNP generates a punitive NKX6-1 TFBS not found with the major C allele (Table 2).The NKX6-1 TF is involved in transcriptional regulation of islet beta cells.This TF binds to the insulin promoter and is involved in the regulation of the insulin gene (Supplement).The lack of this BS with the major C allele could have a profound effect on obesity in humans.Other examples involving the presence or absence of unique SNP allele TFBS can be found in Table 2 and potential human health issues can be made.
The PPARα/δ/γ SNPs that provide changes in punitive TFBS are not only found in the promoter but in the introns, exons and the UTRs of these genes (Table 2).The nucleus of the cell is where epigenetic alterations and TFs operate to convert chromosomes into single stranded DNA for mRNA transcription while it is the cytoplasm where mRNA is processed by separating exons and introns for protein translation.Consequently, it doesn't matter where TFs bind the DNA in the nucleus because it is only there that TFs function.There are three SNPs in the coding regions (exons) of two genes which are PPARα (rs1800206), PPARγ (rs-1805192 and rs3856806).These SNPs result in missense mutations in which p.L162V and p.P12A are non synonymous changes and p.H449H is a synonymous change in the amino acids of the proteins (Table 1).In this study, the same SNPs result in multiple punitive TFBS changes in the DNA.This raises the question: are the significant associations of these SNPs with disease or change in condition the result of nucleotide or amino acid substitutions?(Table 1).All three amino acid substitutions are considered to be clinical benign changes to human health [52] while there are reports indicating these substitution are significant associations to disease or condition [10] [11] [15] [16].This might suggest that the nucleotide and not the amino acid substitutions are responsible for the significant associations that have been reported.
In conclusion, the alterations in punitive TFBS created by SNPs as identified in this study provides a nuclear solution as to why significant associations have been found between some SNPs and human disease or sickness.Alterations in TFBS would affect the TFs ability to regulate a gene which could result in human disease or sickness.

Supplement
Transcriptional factors (TF), protein name and their description or function.The protein encoded by this intronless gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions.It can also form heterodimers with the related protein CEBP-alpha.The encoded protein is important in the regulation of genes involved in immune and inflammatory responses, and may be involved in the regulation of genes associated with activation and/or differentiation of macrophages.

CEBPE CCAAT/enhancer binding protein (C/EBP), epsilon
The protein encoded by this gene is a bZIP transcription factor which can bind as a homodimer to certain DNA regulatory regions.It can also form heterodimers with the related protein CEBP-delta.

CEBPG CCAAT/enhancer binding protein (C/EBP), gamma
The C/EBP family of transcription factors regulates viral and cellular CCAAT/enhancer element-mediated transcription.C/EBP proteins contain the bZIP region, which is characterized by two motifs in the C-terminal half of the protein: a basic region involved in DNA binding and a leucine zipper motif involved in dimerization.

CLOCK Clock Circadian Regulator
Transcriptional activator which forms a core component of the circadian clock.circadianrhythms in gene expression, which are translated into rhythms in metabolism and behavior.The circadian clock, an internal time-keeping system, regulates various physiological processes through the generation of approximately 24 hour in gene expression, which are translated into rhythms in metabolism and behavior.The circadian clock, an internal time-keeping system.

DBP D-Box Binding PAR BZIP Transcription Factor
The protein encoded by this gene is a member of the PAR bZIP transcription factor family and binds to specific sequences in the promoters of several genes.The encoded protein can bind DNA as a homo-or heterodimer and is involved in the regulation of some circadian rhythm genes.

EGR1 Early growth response 1
The protein encoded by this gene belongs to the EGR family of C2H2-type zinc-finger proteins.It is a nuclear protein and functions as a transcriptional regulator.The products of target genes it activates are required for differentitation and mitogenesis.

ELF5 E74-like factor 5
A member of an epithelium-specific subclass of the Etstranscritpion factor family.

Continued EMX1 Empty Spiracles Homeobox 1
Transcription factor, which in cooperation with EMX2, acts to generate the boundary between the roof andarchipallium in the developing brain.

EMX2 Empty Spiracles Homeobox 2
Transcription factor, which in cooperation with EMX1, acts to generate the boundary between the roof andarchipallium in the developing brain.

EN2
Engrailed homeo box 2 The human engrailed homologs 1 and 2 encode homeodomain-containing proteins and have been implicated in the control of pattern formation during development of the central nervous system.

ERG v-ets avian erythroblastosis virus E26 oncogene homolog
This gene encodes a member of the erythroblast transformation-specific (ETS) family of transcriptions factors.All members of this family are key regulators of embryonic development, cell proliferation, differentiation, angiogenesis, inflammation, and apoptosis.

ESR2
Estrogen receptor beta Estrogen receptor β is a member of the family of estrogen receptors and the superfamily of nuclear receptor transcription factors and is expressed by many tissues including blood monocytes and tissue macrophages, colonic and pulmonary epithelial cells.GO annotations related to this gene include sequence-specific DNA binding.An important paralog of this gene is GBX2.

GBX2 Gastrulation Brain Homeobox 2
May act as a transcription factor for cell pluripotency and differentiation in the embryo GCM1 Glial Cells Missing Homolog 1 Transcription factor that is necessary for placental development.Binds to the trophoblast-specific element 2 (TSE2) of the aromatase gene enhancer.

GCM2 Glial Cells Missing Homolog 2
The protein is a transcription factor that acts as a master regulator of parathyroid development.

GLI2 GLI Family Zinc Finger 2
This gene encodes a protein which belongs to the C2H2-type zinc finger protein subclass of the Gli family.
Members of this subclass are characterized as transcription factors which bind DNA through zinc finger motifs.Gli family zinc finger proteins are mediators of Sonic hedgehog (Shh) signaling and they are implicated as potent oncogenes in the embryonal carcinoma cell.

HLF Hepatic leukemia factor
This gene encodes a member of the proline and acidic-rich (PAR) protein family, a subset of the bZIP transcription factors.The encoded protein forms homodimers or heterodimers with other PAR family members and binds sequence-specific promoter elements to activate transcription.

HLTF Helicase-like transcription factor
Member of the SWI/SNF (SWItch/Sucrose Non Fermen table) family which have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin.

HOXA1
Homeobox protein Hox-A1 The genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes.This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation.Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.Seems to act in the maintenance and/or generation of hindbrain segments.

HOXA2 Homeobox protein Hox-A2
Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

HOXA5
Homeobox protein Hox-A5 DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation.

HOXB2 Homeobox protein Hox-B2
This gene is a member of the Antphomeobox family and encodes a nuclear protein with a homeobox DNA-binding domain.The encoded protein functions as a sequence-specific transcription factor that is involved in development.

HOXB3 Homeobox protein Hox-B3
This gene is a member of the Antphomeobox family and encodes a nuclear protein with a homeobox DNA-binding domain.The encoded protein functions as a sequence-specific transcription factor that is involved in development.

HOXA11 Homeobox protein Hox-A11
Sequence-specific transcription factor which is part of a developmental regulatory system that provides cells with specific positional identities on the anterior-posterior axis.

Continued HOXC10 Homeobox protein Hox-C10
The protein level is controlled during cell differentiation and proliferation, which may indicate this protein has a role in origin activation

HOXC11 Homeobox protein Hox-C11
The product of this gene binds to a promoter element of the lactase-phlorizin hydrolase.It also may play a role in early intestinal development.

HOXC12 Homeobox protein Hox-C12
This gene is one of several homeobox HOXC genes located in a cluster on chromosome 12.

HOXC13 Homeobox protein Hox-C13
The product of this gene may play a role in the development of hair, nail, and filiform papilla.

HOXD11 Homeobox protein Hox-D11
Deletions that remove the entire HOXD gene cluster or the end of cluster have been associated with severe limb and genital abnormalities.The protein encoded by this gene is a multifunctional, nuclear phosphoprotein that plays a role in cell cycle progression, apoptosis and cellular transformation.It functions as a transcription factor that regulates transcription of specific target genes.The MYC:MAX complex is a transcriptional activator.

MEF2C Myocyte enhancer factor 2C
Transcription activator which binds specifically to the MEF2 element present in the regulatory regions of many muscle-specific genes.Controls cardiac morphogenesis and myogenesis, and is also involved in vascular development.Transcription regulator.Forms a sequence-specific DNA-binding protein complex with MAD1, MAD4, MNT, WBSCR14 and MLXIP which recognizes the core sequence 5-CACGTG-3.Plays a role in transcriptional activation of glycolytic target genes.Involved in glucose-responsive gene regulation.

MLXIPL MLX Interacting Protein Like
This protein forms a heterodimeric complex and binds and activates, in a glucose-dependent manner, carbohydrate response element (ChoRE) motifs in the promoters of triglyceride synthesis genes.

MAX Transcriptional Repressor
Binds DNA as a heterodimer with MAX and represses transcription.Binds to the canonical E box sequence 5-CACGTG-3 and, with higher affinity, to 5-CACGCG-3.

MNX1 Motor Neuron And Pancreas Homeobox 1
Putative transcription factor involved in pancreas development and function.

MZF1
Myeloid Zinc Finger 1 Binds to target promoter DNA and functions as transcription regulator.May be one regulator of transcriptional events during hemopoietic development.

NEUROD2 Neuronal Differentiation 2
Transcriptional regulator implicated in neuronal determination.Mediates calcium-dependent transcription activation by binding to E box-containing promoter.Critical factor essential for the repression of the genetic program for neuronal differentiation; prevents the formation of synaptic vesicle clustering at active zone to the presynaptic membrane in postmitotic neurons.

NFAT5
Nuclear Factor Of Activated T-Cells 5 The product of this gene is a member of the nuclear factors of activated T cells family of transcription factors.Proteins belonging to this family play a central role in inducible gene transcription during the immune response.This protein regulates gene expression induced by osmotic stress in mammalian cells.

NFATC1 Nuclear Factor Of Activated T-Cells 1
The product of this gene is a component of the nuclear factor of activated T cells DNA-binding transcription complex.This complex consists of at least two components: a preexisting cytosolic component that translocates to the nucleus upon T cell receptor (TCR) stimulation, and an inducible nuclear component.Proteins belonging to this family of transcription factors play a central role in inducible gene transcription during immune response.

NFATC3 Nuclear Factor Of Activated T-Cells 3
Acts as a regulator of transcriptional activation.Plays a role in the inducible expression of cytokine genes in T-cells, especially in the induction of the IL-2.

NFIC Nuclear factor 1 C-type
Recognizes and binds the palindromic sequence 5'-TTGGCNNNNNGCCAA-3' present in viral and cellular promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.

NFIX Nuclear Factor I X
Recognizes and binds the palindromic sequence 5-TTGGCNNNNNGCCAA-3 present in viral and cellular transcription and replication promoters and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication.

NFKB1
Nuclear factor of kappa light polypeptide oncogene homolog gene enhancer in B-cells 1 NF-kappa-B is a pleiotropic transcription factor present in almost all cell types and is the endpoint of a series of signal transduction events that are initiated by a vast array of stimuli related to many biological processes such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis.

NFKB2
Nuclear factor of kappa light polypeptide oncogene homolog gene enhancer in B-cells 2 This gene encodes a subunit of the transcription factor complex nuclear factor-kappa-B (NFkB).The NFkB complex is expressed in numerous cell types and functions as a central activator of genes involved in inflammation and immune function.The protein encoded by this gene can function as both a transcriptional activator or repressor depending on its dimerization partner.This gene encodes a protein that homodimerizes and functions as a transcription factor which activates the expression of some key metabolic genes regulating cellular growth and nuclear genes required for respiration, heme biosynthesis, and mitochondrial DNA transcription and replication.

OLIG1 Oligodendrocyte Transcription Factor 1
Promotes formation and maturation of oligodendrocytes, especially within the brain.Cooperates with OLIG2 to establish the pMN domain of the embryonic neural tube.

OLIG2
Oligodendrocyte Transcription Factor 1 Required for oligodendrocyte and motor neuron specification the spinal cord, as well as for the development of somatic motor neurons in the hindbrain.Cooperates with OLIG1 to establish the pMN domain of the embryonic neural tube.

OLIG3
Oligodendrocyte Transcription Factor 1 May determine the distinct specification program of class A neurons in the dorsal part of the spinal cord and suppress specification of class B neurons.

OTX1
Orthodenticle Homeobox 1 This gene encodes a member of the bicoid sub-family of homeodomain-containing transcription factors.The encoded protein acts as a transcription factor and may play a role in brain and sensory organ development.

PITX3 Paired Like Homeodomain 3
Transcriptional regulator which is important for the differentiation and maintenance of meso-diencephalic dopaminergic (mdDA) neurons during development.

POU2F1
POU Class 2 Homeobox 1 Transcription factor that binds to the octamer motif (5-ATTTGCAT-3) and activates the promoters of the genes for some small nuclear RNAs (snRNA) and of genes such as those for histone H2B and immunoglobulins.

POU2F2 POU class 2 homeobox 2
The protein encoded by this gene is a homeobox-containing transcription factor of the POU domain family.The encoded protein binds the octamer sequence 5'-ATTTGCAT-3', a common transcription factor binding site in immunoglobulin gene promoters.

POU3F1 POU Class 3 Homeobox 1
Transcription factor that binds to the octamer motif (5-ATTTGCAT-3).Thought to be involved in early embryogenesis and neurogenesis.

POU3F2 POU Class 3 Homeobox 2
This gene encodes a member of the POU-III class of neural transcription factors.The encoded protein is involved in neuronal differentiation and enhances the activation of corticotropin-releasing hormone regulated genes.Overexpression of this protein is associated with an increase in the proliferation of melanoma cells.

POU5F1B POU Class 5 Homeobox 1B
has been shown to be a weak transcriptional activator and may play a role in carcinogenesis and eye development.

RAX Retina And Anterior Neural Fold Homeobox
This gene encodes a homeobox-containing transcription factor that functions in eye development.The gene is expressed early in the eye primordia, and is required for retinal cell fate determination and also regulates stem cell proliferation.

REL v-rel avian reticuloendotheliosis viral oncogene homolog
Proto-oncogene that may play a role in differentiation and lymphopoiesis.NF-kappa-B is a pleiotropic transcription factor which is present in almost all cell types and is involved in many biological processed such as inflammation, immunity, differentiation, cell growth, tumorigenesis and apoptosis.

RFX3 Regulatory factor X3
Transcription factor required for ciliogenesis and islet cell differentiation during endocrine pancreas development.Essential for the differentiation of nodal monocilia and left-right asymmetry specification during embryogenesis.Required for the biogenesis of motile cilia by governing growth and beating efficiency of motile cells.Also required for ciliated ependymal cell differentiation.

RFX4 Regulatory factor X4
This gene is a member of the regulatory factor X gene family, which encodes transcription factors that contain a highly-conserved winged helix DNA binding domain.The protein encoded by this gene is structurally related to regulatory factors X1, X2, X3, and X5.It has been shown to interact with itself as well as with regulatory factors X2 and X3, but it does not interact with regulatory factor X1.

RHOXF1 RhoxHomeobox Family Member 1
This gene is a member of the PEPP subfamily of paired-like homoebox genes.The gene may be regulated by androgens and epigenetic mechanisms.The encoded nuclear protein is likely a transcription factor that may play a role in human reproduction.

RUNX1
Runt-related transcription factor 1 Core binding factor (CBF) is a heterodimeric transcription factor that binds to the core element of many enhancers and promoters.The protein encoded by this gene represents the alpha subunit of CBF and is thought to be involved in the development of normal hematopoiesis.

STAT1
Signal transducer and activator of transcription 1 In response to cytokines and growth factors, STAT family members are phosphorylated by the receptor associated kinases, and then form homo-or heterodimers that translocate to the cell nucleus where they act as transcription activators.This protein can be activated by various ligands including interferon-alpha, interferon-gamma, EGF, PDGF and IL6.The protein mediates the expression of a variety of genes, which is thought to be important for cell viability in response to different cell stimuli and pathogens.

EVX1 Even-Skipped Homeobox 1 FLI1Fli- 1 FOSL1 & 2 FOS-like antigen 1 & 2 TheFOXH1
FIGLA This gene is one of several homeobox HOXD genes located in a cluster on chromosome 2ID4Inhibitor Of DNA Binding 4, HLH ProteinTranscriptional regulator (lacking a basic DNA binding domain) which negatively regulates the basic helix-loop-helix (bHLH) transcription factors by forming heterodimers and inhibiting their DNA binding and transcriptional activity.Implicated in regulating a variety of cellular processes, including cellular growth, senescence, differentiation, apoptosis, angiogenesis, and neoplastic transformation.ISL2 ISL LIM Homeobox 2Transcriptional factor that defines subclasses of motoneurons that segregate into columns in the spinal cord and select distinct axon pathways.KLF5 Krueppel-like factor 5This gene encodes a member of the Kruppel-like factor subfamily of zinc finger proteins.The encoded protein is a transcriptional activator that binds directly to a specific recognition motif in the promoters of target genes.This protein acts downstream of multiple different signaling pathways and is regulated by post-translationalm modification.It may participate in both promoting and suppressing cell proliferation.Expression of this gene may be changed in a variety of different cancers and in cardiovascular disease.Alternative splicing results in multiple transcript variants.KLF16 Krueppel-like factor 16Transcription factor that binds GC and GT boxes and displaces Sp1 and Sp3 from these sequences.Modulates dopaminergic transmission in the brain.LHX2 LIM Homeobox 2Acts as a transcriptional activator.Stimulates the promoter of the alpha-glycoprotein gene.Transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural factor erythroid 2-related factor (Nrf2) coordinates the up-regulation of cytoprotective genes via the antioxidant response element (ARE).MafG is a ubiquitously expressed small maf protein that is involved in cell differentiation of erythrocytes.It dimerizes with P45 NF-E2 protein and activates expression of a and b-globin.MAX MYC Associated Factor X Transcription regulator.Forms a sequence-specific DNA-binding protein complex with MYC or MAD which recognizes the core sequence 5-CAC[GA]TG-

MEIS1 MeisHomeobox 1
Homeobox genes, of which the most well-characterized category is represented by the HOX genes, play a crucial role in normal development.MEOX1Mesenchyme Homeobox 1Mesodermal transcription factor that plays a key role in somitogenesis and is specifically required for sclerotome development.Required for maintenance of the sclerotome polarity and formation of the cranio-cervical joints.Binds specifically to the promoter of target genes and regulates their expression.Activates expression of NKX3-2 in the sclerotome.Activates expression of CDKN1A and CDKN2A in endothelial cells, acting as a regulator of vascular cell proliferation.Continued MIXL1 Mix Paired-Like Homeobox Homeodomain proteins, such as MIXL1, are transcription factors that regulate cell fate during development MLX MLX, MAX Dimerization Protein a homeodomain-containing transcription factor.The encoded protein is a member of the NKX family of homeodomain transcription factors.a member of the NK family of homeobox-containing proteins.Transcriptional repressor that acts as a negative regulator of chondrocyte maturation.NKX6-1 NK6 Homeobox 1 Transcription factor which binds to specific A/T-rich DNA sequences in the promoter regions of a number of genes.Involved in transcriptional regulation in islet beta cells.Binds to the insulin promoter and is involved in regulation of the insulin gene.NKX6-2 NK6 Homeobox 2 An important paralog of this gene is NKX6-1.Continued NOTO Notochord Homeobox Transcription regulator acting downstream of both FOXA2 and T during notochord development.Required for node morphogenesis NRF1 Nuclear respiratory factor 1 transcription activator that mediates cellular responses to interleukins, KITLG/SCF and other growth factors TBX4 T-Box 4 This gene is a member of a phylogenetically conserved family of genes that share a common DNA-binding domain, the T-box.T-box genes encode transcription factors involved in the regulation of developmental processes.Associated with the human disease of Heritable Pulmonary Arterial Hypertension.TBX5 T-Box 5 DNA-binding protein that regulates the transcription of several genes and is involved in heart development and limb pattern formation.Involved in the initiation of neuronal differentiation.Heterodimers between TCF3 and tissue-specific basic helix-loop-helix (bHLH) proteins play major roles in determining tissue-specific cell during embryogenesis, like muscle or early B-cell differentiation.binds to the immunoglobulin enchancer Mu-E5/KE5-motif.Involved in the initiation of neuronal differentiation.Activates transcription by binding to the E box (5-CANNTGa ubiquitous transcriptional enhancer factor that is a member of the TEA/ATTS domain family.This protein directs the transactivation of a wide variety of genes and, in placental cells, also acts as a transcriptional repressor.TEAD3 TEA Domain Family Member 3 This gene product is a member of the transcriptional enhancer factor (TEF) family of transcription factors, which contain the TEA/ATTS DNA-binding domain.It is predominantly expressed in the placenta and is involved in the transactivation of the chorionic somatomammotropin-B gene enhancer.TEAD4 TEA Domain Family Member 4 Transcription factor which plays a key role in the Hippo signaling pathway, a pathway involved in organ size control and tumor suppression by restricting proliferation and promoting apoptosis.Continued TEF TEF, PAR BZIP Transcription FactorThis gene encodes a member of the PAR (proline and acidic amino acid-rich) subfamily of basic region/leucine zipper (bZIP) transcription factors.It is expressed in a broad range of cells and tissues in adult animals, however, during embryonic development, TEF expression appears to be restricted to the developing anterior pituitary gland, coincident with the appearance of thyroid-stimulating hormone, beta a basic helix-loop-helix domain-containing transcription factor that binds MUE3-type E-box sequences in the promoter of genes.The encoded protein promotes the expression of genes downstream of transforming growth factor beta (TGF-beta) signaling.TFEB Transcription Factor EB Transcription factor specifically recognizes and binds E-box sequences (5-CANNTG-3).Efficient DNA-binding requires dimerization with itself or with another MiT/TFE family member such as TFE3 or MITF.In association with TFE3, activates the expression of CD40L in T-cells, thereby playing a role in T-cell-dependent antibody responses in activated CD4(+) T-cells and thymus-dependent humoral immunity.TFEC Transcription Factor EC Transcriptional regulator that acts as a repressor or an activator.play roles in multiple cellular processes including survival, growth and differentiation.TFCP2 Transcription Factor CP2 This gene encodes a transcription factor that binds the alpha-globin promoter and activates transcription of the alpha-globin gene.The encoded protein regulates erythroid gene expression, plays a role in the transcriptional switch of globin gene promoters, and it activates many other cellular and viral gene promoters.TFAP2a Transcription Factor AP-2 Alpha The AP2a protein acts as a sequence specific DNA-binding transcription factor recognizing and binding to the specific DNA sequence and recruiting transcription machinery.TFAP2b Transcription Factor AP-2 Beta This gene encodes a member of the AP-2 family of transcription factors.AP-2 proteins form homo-or hetero-dimers with other AP-2 family members and bind specific DNA sequences.transcription regulator that regulates endothelial cell proliferation and G1/S cell-cycle progression.a member of the basic helix-loop-helix leucine zipper family, and can function as a cellular transcription factor.The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs.USF2 Upstream transcription factor 2, C-Fos Interacting This gene encodes a member of the basic helix-loop-helix leucine zipper family of transcription factors.The encoded protein can activate transcription through pyrimidine-rich initiator (Inr) elements and E-box motifs and is involved in regulating multiple cellular processes.VAX2 Ventral Anterior Homeobox 2 Transcription factor that may function in dorsoventral specification of the forebrain.Plays a crucial role in eye development and, in particular, in the specification of the ventral optic vesicle.YY1 YY1 transcription factor YY1 is a ubiquitously distributed transcription factor belonging to the GLI-Kruppel class of zinc finger proteins.The protein is involved in repressing and activating a diverse number of promoters.YY1 may direct histone deacetylases and histone acetyltransferases to a promoter in order to activate or repress the promoter, thus mplicating histone modification in the function of YY1.ZBTB7A Zinc Finger And BTB Domain Containing 7A Plays a key role in the instruction of early lymphoid progenitors to develop into B lineage by repressing T-cell instructive Notch signals.ZBTB7B Zinc Finger And BTB Domain Containing 7B This gene encodes a zinc finger-containing transcription factor that acts as a key regulator of lineage commitment of immature T-cell precursors.plays a role in various developmental processes such as myogenesis and brain development.Plays a key role in myogenesis by directly repressing the expression of ID2 and ID3, 2 inhibitors of skeletal myogenesis.ZEB1 Zinc Finger E-Box Binding Homeobox 1 This gene encodes a zinc finger transcription factor.The encoded protein likely plays a role in transcriptional repression of interleukin 2. ZNF354C Zinc Finger Protein 354C May function as a transcription repressor.Suppresses osteogenic effects of RUNX2.Binds to 5-CCACA-3 core sequence.May be involved in osteoblastic differentiation.ZNF740 Zinc Finger Protein 740 May be involved in transcriptional regulation

Table 2 .
Location of PPARα/δ/γ gene SNPs contained in potential TFBS.(−/+) is the DNA strand location of the TFBS.TFBS in red are only present for the given allele.
The protein encoded by this gene belongs to the ETS family of transcription factors and has been shown to interact with TTRAP, UBE2I and Death associated protein.This gene encodes a member of the ETS (E twenty-six) family of transcription factors.differentiation.The ETS proteins regulate many target genes that modulate biological processes like cell growth, angiogenesis, migration, proliferation and differentiation.
ETV4ETS Variant 4GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding is ETV1 and RNA polymerase II core promoter proximal region sequence-specific DNA binding.An important paralog of this gene ETV1.ETV5 ETS Variant 5GO annotations related to this gene include transcription factor activity, sequence-specific DNA binding is ETV1 and RNA polymerase II core promoter proximal region sequence-specific DNA binding.An important paralog of this gene ETV1.
This gene encodes a member of the Snail family of C2H2-type zinc finger transcription factors.The encoded protein acts as a transcriptional repressor that binds to E-box motifs and is also likely to repress E-cadherin transcription in breast carcinoma.This gene encodes a member of the Sp subfamily of Sp/XKLF transcription factors.Sp family proteins are sequence-specific DNA-binding proteins characterized by an amino-terminal trans-activation domain and three carboxy-terminal zinc finger motifs.This protein contains the least conserved DNA-binding domain within the Sp subfamily of proteins, and its DNA sequence specificity differs from the other Sp proteins.It localizes primarily within subnuclear foci associated with the nuclear matrix, and can activate or in some cases repress expression from different promoters.Transcriptional factor that can act as an activator or repressor depending on isoform and/or post-translational modifications.Binds to GT and GC boxes promoter elements.Competes with SP1 for the GC-box promoters.Weak activator of transcription but can activate a number of genes involved in different processes such as cell-cycle regulation, hormone-induction and house-keeping.