Basic Study
Copyright ©The Author(s) 2016. Published by Baishideng Publishing Group Inc. All rights reserved.
World J Hematol. Nov 6, 2016; 5(4): 75-87
Published online Nov 6, 2016. doi: 10.5315/wjh.v5.i4.75
Identifying changes in punitive transcriptional factor binding sites from regulatory single nucleotide polymorphisms that are significantly associated with disease or sickness
Norman E Buroker
Norman E Buroker, Department of Pediatrics, University of Washington, Seattle, WA 98195, United States
Author contributions: Buroker NE analyzed all the data and wrote the manuscript.
Institutional review board statement: The manuscript did not use human or animal subjects.
Informed consent statement: The manuscript did not use human or animal subjects.
Conflict-of-interest statement: To the best of my knowledge, no conflict of interest exists.
Open-Access: This article is an open-access article which was selected by an in-house editor and fully peer-reviewed by external reviewers. It is distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited and the use is non-commercial. See: http://creativecommons.org/licenses/by-nc/4.0/
Correspondence to: Norman E Buroker, PhD, Department of Pediatrics, University of Washington, 1959 NE Pacific Street, Seattle, WA 98195, United States. nburoker@u.washington.edu
Telephone: +1-206-6160472 Fax: +1-206-6160471
Received: May 8, 2016
Peer-review started: May 9, 2016
First decision: June 13, 2016
Revised: June 24, 2016
Accepted: August 11, 2016
Article in press: August 13, 2016
Published online: November 6, 2016

Abstract
AIM

To identify punitive transcriptional factor binding sites (TFBS) from regulatory single nucleotide polymorphisms (rSNPs) that are significantly associated with disease.

METHODS

The genome-wide association studies have provided us with nearly 6500 disease or trait-predisposing SNPs where 93% are located within non-coding regions such as gene regulatory or intergenic areas of the genome. In the regulatory region of a gene, a SNP can change the DNA sequence of a transcriptional factor (TF) motif and in turn may affect the process of gene regulation. SNP changes that affect gene expression and impact gene regulatory sequences such as promoters, enhancers, and silencers are known as rSNPs. Computational tools can be used to identify unique punitive TFBS created by rSNPs that are associated with disease or sickness. Computational analysis was used to identify punitive TFBS generated by the alleles of these rSNPs.

RESULTS

rSNPs within nine genes that have been significantly associated with disease or sickness were used to illustrate the tremendous diversity of punitive unique TFBS that can be generated by their alleles. The genes studied are the adrenergic, beta, receptor kinase 1, the v-akt murine thymoma viral oncogene homolog 3, the activating transcription factor 3, the type 2 demodkinase gene, the endothetal Per-Arnt-Sim domain protein 1, the lysosomal acid lipase A, the signal Transducer and Activator of Transcription 4, the thromboxane A2 receptor and the vascular endothelial growth factor A. From this sampling of SNPs among the nine genes, there are 73 potential unique TFBS generated by the common alleles compared to 124 generated by the minor alleles indicating the tremendous diversity of potential TFs that are capable of regulating these genes.

CONCLUSION

From the diversity of unique punitive binding sites for TFs, it was found that some TFs play a role in the disease or sickness being studied.

Key Words: Regulatory single nucleotide polymorphisms, Alleles, Transcriptional factors, Transcriptional factor binding sites, Linkage disequilibrium, Disease or sickness

Core tip: Disease or trait-predisposing single nucleotide polymorphisms (SNPs) in or near genes can alter the transcriptional factor binding sites (TFBS) for the TFs regulating the gene; thereby affecting the health of an individual. In this report, the disease or sickness associated regulatory SNPs (rSNPs) within a sampling of nine human genes were studied with respect to the alterations in TFBS. From this sampling there were 73 punitive unique TFBS generated by the common rSNP alleles compared to 124 generated by the minor alleles indicating the tremendous diversity of potential TFs that are capable of affecting the health of person.



INTRODUCTION

The genome-wide association studies (GWAS) have over the past decade provided us with nearly 6500 disease or trait-predisposing single nucleotide polymorphisms (SNPs). Only seven percent of these SNPs are located in protein-coding regions of the genome[1,2] while the remaining 93% are located within non-coding regions[3,4] such as gene regulatory or intergenic areas of the genome. Much attention has been drawn to SNPs that occur in the putative regulatory region of a gene where a single nucleotide change in the DNA sequence of a potential transcriptional factor (TF) motif may affect the process of gene regulation[5-7]. A nucleotide change in a transcriptional factor binding site (TFBS) can have multiple consequences. Since a TF can usually recognize a number of different binding motifs in a gene, the SNP may not change the TFBS interaction with the TF and consequently not alter the process of gene expression. In other cases the nucleotide change may increase or decrease the TF’s ability to bind DNA which would result in allele-specific gene expression. In some cases a nucleotide change may eliminate the natural binding motif or generate a new binding site (BS) as a result the gene is no longer regulated by the original TF[8,9]. Single nucleotide changes that affect gene expression by impacting gene regulatory sequences such as promoters, enhancers, and silencers are known as regulatory SNPs (rSNPs)[5,6,10,11]. Therefore, functional rSNPs in TFBS may result in differences in gene expression, phenotypes and susceptibility to environmental exposure[7]. Examples of rSNPs associated with disease susceptibility are numerous and several reviews have been published[7,12-16]. Advances in understanding the functional relevance of SNPs in non-coding regions of the human genome using epi-genomics and genome engineering have been recently reviewed[17]. Computational tools can be used to identify punitive TFBS created by rSNPs which are associated with disease or sickness[18]. To this end, computational analysis has been used to identify punitive or potentially unique TFBS generated by the alleles of rSNPs[19] where unique TFBS occur with only one of the two rSNP alleles.

In this report, rSNPs within a sample of nine human genes (Table 1) which have been significantly associated with disease or sickness were selected to illustrate the tremendous diversity of unique punitive TFBS that can be generated by SNP alleles (Table 2)[8,9,20-27]. The SNP alleles from these reports were found to share common TFBS between alleles but each SNP allele can also create unique TFBS only for that allele (Table 2). As an example in Table 2, the rs948988 ADRBK1-G allele creates two potential unique TFBS for the Kruppel-like factors 1 and 4 (KLF1,4) TFs that do not occur with the alternate ADRBK1-A allele while the ADRBK1-A allele creates ten other punitive unique TFBS not found with ADRBK1-G allele. Many of the rSNPs have been reported to be in linkage disequilibrium (LD) (Table 1), where LD is considered to be the non-random association of SNP alleles within a gene. LD between SNPs in the regulatory region of a gene can indicate strong associations of certain haplotypes and TFBS with sickness or disease[28].

Table 1 Genes and their single nucleotide polymorphisms that have been found to be associated with disease or sickness.
Protein and gene symbolChromosomeSNPSNP locationMutationLDRef.
Adrenergic, beta, receptor kinase 111q13.1rs948988intron 2c.190 + 653G > AYes[9,19]
rs43709463'UTRc.*217C > TYes
v-akt murine thymoma viral oncogene homolog 31q44rs4590656intron 1c.46 + 3654C > TYes[8,19]
rs10157763intron 1c.46 + 11386C > TYes
rs2125230intron 1c.47-26830G > AYes
Activating transcription factor 31q32.3rs3125289promoterc.-5 + 9322T > CUnknown[19,20]
rs11119982promoterc.-4-23516C > TUnknown
Type 2 demodkinase gene14q24.3rs2250153'UTRc.*1453G > AYes[19,21]
rs225011intron 1c. 330 + 366C > TYes
rs128853005'UTRc.-451C > TYes
Endothetal Per-Arnt-Sim domain protein 12p21rs6756667intron 2c.218-3881A > GNo[22]
rs18680923'UTRc.*2403G > ANo
Lysosomal acid lipase A10q23.31rs1412444intron 2c.229 + 2506C > Tn/a[23]
Signal transducer and activator of transcription 42q32.3rs8179673intron 2c.274-28290T > CYes[24]
rs10181656intron 2c.274-28828C > GYes
Thromboxane A2 receptor19p13.3rs2238631intron 1c.-84 + 2229G > AYes[19,25]
rs2238632intron 1c.-84 + 2030C > TYes
rs2238634intron 1c.-84 + 1799G > TYes
Vascular endothelial growth factor A6p21.1rs34357231promoterc. -2550-2568D > IYes[19,26,28]
rs1570360promoterc.-614A > GYes
rs30250393'UTRc.*237C > TYes
Table 2 Genes whose single nucleotide polymorphisms are significantly associated with human disease or sickness.
Gene symbol
ADRBK1Ethnic groupBB
disease or sickness1212
SNPrs948988 (G/A)rs4370946 (C/T)
alleles (MAF)GA (0.29)CT (0.2)
potential unique TFBSKLF1, 4BATF:JUNE2F1,3,4,6ARNT:AHR
ESR2EGR1ATOH1
FOSINSM1ELF1
FOSL2KLF4ESR2
JUNDNFKB1NR3C1
JUN:FOSNRF1
MYBSP1, 2
NFE2L1:MAF
NR3C1
SOX17
AKT3Ethnic groupGCC
disease or sickness11414
SNPrs4590656 (C/T)rs10157763 (C/T)rs2125230 (G/A)
alleles (MAF)CT (0.41)CT (0.33)GA (0.2)
potential unique TFBSARNT:AHRGFIELF5CTCFARNT:AHRGATA1
HIF1a:ARNTHNF4AELK1NFATC2FEVHNF4a
PAX2MYCNSOX17HIF1a:ARNTHOXA5
SPIBSPIBZNF354CSPI1IRF1
SPI1NR2F1
TFAP2ASOX17
ATF3Ethnic groupCC
disease or sickness1515
SNPrs3125289 (C/T)rs11119982 (C/T)
alleles (MAF)CT (0.10)CT (0.36)
potential unique TFBSARNTFOXA1, 2HLTFARID3A
ARNT:AHRFOXL1MAX
GABPaFOXO3MYB
MYCHLTFUSF1
MYCNSOX10ZEB1
MZF1SOX17
SPIBSRY
USF1
DIO2Ethnic groupFFC
disease or sickness2217
SNPrs225015 (G/A)rs225011 (C/T)rs12885300 (C/T)
alleles (MAF)GA (0.4)CT (0.42)CT (0.23)
potential unique TFBSEBF1ELF1CRXFOXL1ARID3A
ESRRAELK1RXRaMEF2ABATF:JUN
PPARg:RXRaERGPDX1IRF1
RFX5ETS1JUN:FOS
THAP1FLI1PAX2
RUNX1SOX6
SOX9
SPI1
TCF7L2
EPAS1Ethnic groupGG
disease or sickness11
SNPrs6756667 (A/G)rs1868093 (A/G)
alleles (MAF)AG (0.20)AG (0.25)
potential unique TFBSCEBPaATF7NR2C2HIC2
NFIAGMEB2NFIAKLF5
NRLJDP2YY1MGA
TEAD1
USF1
LIPAEthnic groupC, D, E
disease or sickness20, 21
SNPrs1412444 (C/T)
alleles (MAF)CT (0.32)
potential unique TFBSELF1FOXA1
ETS1FOXL1
GABPaFOXO3
HOXA5HNF1B
SPI1MEF2A
NFKB1
NFIC
PAX2
SOX6
SOX9
SRY
THAP1
STAT4Ethnic groupA, CA, C
disease or sickness2,6,102,10
SNPrs8179673 (T/C)rs10181656 (C/G)
alleles (MAF)TC (0.26)CG (0.26)
potential unique TFBSEN1FOXA2ARHNF4g
NFIL3FOXH1E2F6STAT3
FOXO1NR1H3:RXRa
FOXP1ZNF263
FOXQ1
HNF1a
HNF4g
TBXA2REthnic groupAAA
disease or sickness222222
SNPrs2238631 (G/A)rs2238632 (C/T)rs2238634 (G/T)
alleles (MAF)GA (0.2)CT (0.21)GT (0.22)
potential unique TFBSFOXC1ELK1ARNTHLTF
TFAP2aELK4CREB1HNF4a
ETS1HIF1a:ARNTNR2F1
GATA2MAXNR2E3
HAND1:TCFE2aUSF1NR4A2
SPZ1
VEGFAEthnic groupGGG
disease or sickness111
SNPrs34357231 (I/D)rs1570360 (G/A)rs3025039 (C/T)
alleles (MAF)DI (0.28)GA (0.13)CT (0.09)
potential unique TFBSHNF4aAREGR1EGR2BRCA1NFE2::MAF
HNF4gEGR1,2MZF1EHFESR2RFX5
JUNKLF5SP2FOXH1HIF1A:ARNTYY1
MYBMZF1_1-4MAFKNFE2L1:MAFG
NFICNFYBSPIB
NR2C2NFATC2THAP1
NR4A2NKX2-5
PAX2NKX3-2
RFX5SP1, 2
STAT5A:STAT5B
Ethnic GroupDiseaseDiseaseDisease
A. Asian1. Chronic mountain sickness8. Juvenile idiopathic arthritis15. Hypospadias
B. Black2. Diabetes9. Primary biliary cirrhosis and Crohn's disease16. Mental retardation
C. Caucasian3. Hepatitis B virus- related hepatocellular10. Lupus17. Osteoarthritis
D. Chinese4. Hepatitis B virus infection11. Ulcerative colitis18. Insulin resistance
E. Hispanic5. HBV viral clearance12. Cardiovascular disease19. Hepatic glucose output
F. Pima Indians6. Hepatocellular carcinoma13. Renal cell carcinoma risk20. Coronary artery disease
G. Tibetan7. Inflammatory bowel disease14. Aggressive prostate cancer21. Myocardial infarction
22. Asthma
MATERIALS AND METHODS
Identifying TFBS

The JASPAR CORE database[29,30] and ConSite[31] were used to identify the TFBS in this study. 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 1.

RESULTS

The protein and gene symbol, chromosome position of the gene, SNP number and location within the gene and nucleotide (mutation) change are listed in Table 1. Also listed is whether or not linkage disequilibrium occurs between the SNPs within each gene (Table 1). Nine genes, ethnic groups, disease or sickness, SNPs and alleles as well as potential unique TFBS per allele that have been reported are found in Table 2. Not all of the SNPs for each gene are listed in the tables but can be found in the accompanying references (Table 1). From Table 2, it can be seen that there occur incidences when the SNP common allele does not have any unique punitive TFBS while the minor allele provide several (e.g., rs12885300 in DIO2; rs2238632 and rs2238634 in TBXA2R). There are other incidences where the SNP common allele provides one or two unique punitive TFBS while the minor alleles again provide several (e.g., rs948988 in ADRBK1; rs4590656 in AKT3; rs11119982 in ATF3; rs8179673 in STAT4 and rs2238631 in TBXA2R). A near balance between SNP alleles in unique punitive TFBS can also be found in the table (e.g., rs4370946 in ADRBK1; rs10157763 and rs2125230 in AKT3; rs3125289 in ATF3; rs6756667 in EPAS1; rs34357231 and rs3025039 in VEGFA). The minor allele of the SNP usually generates more punitive unique TFBS than the common allele (e.g., rs948988 in ADRBK1; rs1412444 in LIPA and rs8179673 in STAT4). In fact, from this sampling of SNPs among the nine genes, there are 73 potential unique TFBS generated by the common alleles compared to 124 by the minor alleles (Table 2).

DISCUSSION

The possible relationship of these punitive unique TFBS to disease and sickness has previously been discussed for each gene in the accompanying references (Table 1). The use of rSNPs that are in LD within a gene to identify punitive TFBS can be illustrated with a few SNPs from these nine genes. The ADRBK1 gene, which transcribes the GRK2 kinase, is an important regulator of beta-adrenergic signaling and plays a central role in heart failure (HF) pathology[32-34]. Two rSNPs in LD within the ADRBK1 gene are rs948988 and rs4370946 whose minor alleles create punitive unique TFBS for ESR2 that is a binding site for the beta estrogen receptor which is expressed in blood monocytes and pulmonary epithelial cells (Tables 1-3). The ESR2 TFBS is not found with the common (rs948988 and rs4370946) alleles of the gene and may be related to HF. The NR3C1 TFBS for the glucocorticoid receptor which regulates carbohydrate, protein and fat metabolism is also only found with the minor alleles of these rSNPs (Tables 2 and 3) and should have an impact on HF. Other TFBS generated by the rs948988 minor allele of interest in HF might be the MYB and NFE2L.1:MAF TFs which are involved with hematopoietic progenitor cells and cell differentiation of erythrocytes as well as the rs4370946 common allele for the NRF1 TF which is involved with heme biosynthesis and mitochondrial DNA transcription and replication (Tables 2 and 3).

Table 3 Transcriptional factors, protein name and their description or function.
TFProtein nameTF description/function
ARAndrogen receptorThe protein functions as a steroid-hormone activated transcription factor
Upon binding the hormone ligand, the receptor dissociates from accessory proteins, translocates into the nucleus, dimerizes, and then stimulates transcription of androgen responsive genes. They are expressed in bone marrow, mammary gland, prostate, testicular and muscle tissues where they exist as dimers coupled to Hsp90 and HMGB proteins
ARID3AAT rich interactive domain 3A (BRIGHT-like)This gene encodes a member of the ARID (AT-rich interaction domain) family of DNA binding proteins
ARNTAryl hydrocarbon receptor nuclear translocatorInvolved in the induction of several enzymes that participate in xenobiotic metabolism
ARNT:AHRHypoxia-inducible factor 1:Aryl hydrocarbonThe dimer alters transcription of target genes. Involved in the induction
receptor nuclear translocatorof several enzymes that participate in xenobiotic metabolism
ATF7Activating Transcription Factor 7Plays important functions in early cell signaling
Has no intrinsic transcriptional activity, but activates transcription on formation of JUN or FOS heterodimers
ATOH1Atonal homolog 1Transcriptional regulator. Activates E box-dependent transcription in collaboration with TCF3/E47
BATF::JUNBasic leucine zipper transcription factor, ATF-like Jun proto-oncogeneThe protein encoded by this gene is a nuclear basic leucine zipper protein that belongs to the AP-1/ATF superfamily of transcription factors. The leucine zipper of this protein mediates dimerization with members of the Jun family of proteins. This protein is thought to be a negative regulator of AP-1/ATF transcriptional events
BRCA1Breast cancer 1, early onsetThis gene encodes a nuclear phosphoprotein that plays a role in maintaining genomic stability, and it also acts as a tumor suppressor
CEBPACCAAT/enhancer binding protein, alphaCCAAT/enhancer binding protein is a DNA-binding protein that recognizes two different motifs: the CCAAT homology common to many promoters and the enhanced core homology common to many enhancers
CREB1cAMP responsive element binding protein 1Phosphorylation-dependent transcription factor that stimulates transcription upon binding to the DNA cAMP response element, a sequence present in many viral and cellular promoters
CRXCone-rod homeoboxThe protein encoded by this gene is a photoreceptor-specific transcription factor which plays a role in the differentiation of photoreceptor cells. This homeodomain protein is necessary for the maintenance of normal cone and rod function
CTCFCCCTC-binding factor (zinc finger protein)This gene is a member of the BORIS + CTCF gene family and encodes a transcriptional regulator protein with 11 highly conserved zinc finger domains. This nuclear protein is able to use different combinations of the zinc finger domains to bind different DNA target sequences and proteins
E2F1-6E2F transcription factors 1-6The protein encoded by this gene is a member of the E2F family of transcription factors. The E2F family plays a crucial role in the control of cell cycle and action of tumor suppressor proteins and is also a target of the transforming proteins of small DNA tumor viruses. The E2F proteins contain several evolutionally conserved domains found in most members of the family. These domains include a DNA binding domain, a dimerization domain which determines interaction with the differentiation regulated transcription factor proteins, a transactivation domain enriched in acidic amino acids, and a tumor suppressor protein association domain which is embedded within the transactivation domain
EBF1Transcription factor COE1EBF1 has been shown to interact with ZNF423 and CREB binding proteins
EGR1Early growth response 1The 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 differentiation and mitogenesis
EGR2Early growth response 2The protein encoded by this gene is a transcription factor with three tandem C2H2-type zinc fingers
Sequence-specific DNA-binding transcription factor
EHFEts homologous factorThis gene encodes a protein that belongs to an erythroblast transformation-specific transcription factor subfamily characterized by epithelial-specific expression. The encoded protein acts as a transcriptional repressor and may be involved in epithelial differentiation and carcinogenesis
ELF1E74-like factor 1 (ets domain transcription factor)The encoded protein is primarily expressed in lymphoid cells and acts as both an enhancer and a repressor to regulate transcription of various genes
ELF5E74-like factor 5A member of an epithelium-specific subclass of the Ets Transcription factor family
ELK1ELK1, member of ETS oncogene familyThis gene is a member of the Ets family of transcription factors and of the ternary complex factor subfamily. The protein encoded by this gene is a nuclear target for the ras-raf-MAPK signaling cascade
ELK4ELK4, ETS-domain protein (SRF accessory protein 1)This gene is a member of the Ets family of transcription factors and of the ternary complex factor subfamily. Proteins of the ternary complex factor subfamily form a ternary complex by binding to the serum response factor and the serum response element in the promoter of the c-fos proto-oncogene
EN1Engrailed homeobox 1Homeobox-containing genes are thought to have a role in controlling development
ERGv-ets avian erythroblastosis virus E26 oncogene homologThis gene encodes a member of the erythroblast transformation-specific family of transcriptions factors. All members of this family are key regulators of embryonic development, cell proliferation, differentiation, angiogenesis, inflammation, and apoptosis
ESR2Estrogen receptor betaEstrogen 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
ESRRAEstrogen-related receptor alphaThis nuclear receptor acts as a site-specific transcription regulator and has been also shown to interact with estrogen and the transcripton factor TFIIB by direct protein-protein contact. The binding and regulatory activities of this protein have been demonstrated in the regulation of a variety of genes including lactoferrin, osteopontin, medium-chain acyl coenzyme A dehydrogenase and thyroid hormone receptor genes
ETS1Protein C-ets-1The protein encoded by this gene belongs to the erythroblast transformation-specific family of transcription factors and has been shown to interact with TTRAP, UBE2I and Death associated protein
FEVETS oncogene familyIt functions as a transcriptional repressor
FLI1Fli-1 proto-oncogene, ETS transcription factorSequence-specific transcriptional activator
FOSFBJ murine osteosarcoma viral oncogene homologThe Fos gene family consists of 4 members: FOS, FOSB, FOSL1, and FOSL2. These genes encode leucine zipper proteins that can dimerize with proteins of the JUN family, thereby forming the transcription factor complex AP-1. As such, the FOS proteins have been implicated as regulators of cell proliferation, differentiation, and transformation. In some cases, expression of the FOS gene has also been associated with apoptotic cell death
FOSL1 and 2FOS-like antigen 1 and 2GO annotations related to this gene include RNA polymerase II regulatory region sequence-specific DNA binding and sequence-specific DNA binding transcription factor activity
FOXA1Forkhead box A1Transcription factor that is involved in embryonic development, establishment of tissue-specific gene expression and regulation of gene expression in differentiated tissues. Is thought to act as a "pioneer" factor opening the compacted chromatin for other proteins through interactions with nucleosomal core histones and thereby replacing linker histones at target enhancer and/or promoter sites
Involved in the development of multiple endoderm-derived organ systems such as liver, pancreas, lung and prostate. Modulates the transcriptional activity of nuclear hormone receptors
FOXA2Forkhead box A2Involved in embryonic development, establishment of tissue-specific gene expression and regulation of gene expression in differentiated tissues
FOXC1Forkhead box C1An important regulator of cell viability and resistance to oxidative stress in the eye
FOXL1Forkhead box L1Transcription factor required for proper proliferation and differentiation in the gastrointestinal epithelium. Target gene of the hedgehog signaling pathway
FOXO1Forkhead Box O1Transcription factor that is the main target of insulin signaling and regulates metabolic homeostasis in response to oxidative stress
FOXO3Forkhead Box O3This gene belongs to the forkhead family of transcription factors which are characterized by a distinct forkhead domain. This gene likely functions as a trigger for apoptosis through expression of genes necessary for cell death
FOXP1Forkhead box P1This gene belongs to subfamily P of the forkhead box transcription factor family. Forkhead box transcription factors play important roles in the regulation of tissue- and cell type-specific gene transcription during both development and adulthood. Transcriptional repressor. It plays an important role in the specification and differentiation of lung epithelium
FOXQ1Forkhead box Q1This gene belongs to the forkhead family of transcription factors which is characterized by a distinct DNA-binding forkhead domain. Plays a role in hair follicle differentiation
GABPAGA-binding protein alpha chainOne of three GA-binding protein transcription factor subunits which functions as a DNA-binding subunit which shares identity with a subunit encoding the nuclear respiratory factor 2 gene and is likely involved in activation of cytochrome oxidase expression and nuclear control of mitochondrial function
GATA1GATA binding protein 1The protein plays an important role in erythroid development by regulating the switch of fetal hemoglobin to adult hemoglobin
GATA2GATA binding protein 2A member of the GATA family of zinc-finger transcription factors that are named for the consensus nucleotide sequence they bind in the promoter regions of target genes and play an essential role in regulating transcription of genes involved in the development and proliferation of hematopoietic and endocrine cell lineages
GATA3GATA binding protein 3Plays an important role in endothelial cell biology
GFIGrowth factor independent 1 transcription repressorThis gene encodes a nuclear zinc finger protein that functions as a transcriptional repressor. This protein plays a role in diverse developmental contexts, including hematopoiesis and oncogenesis. It functions as part of a complex along with other cofactors to control histone modifications that lead to silencing of the target gene promoters
GMEB2Glucocorticoid modulatory element binding protein 1This gene is a member of KDWK gene family. The product of this gene associates with GMEB1 protein, and the complex is essential for parvovirus DNA replication
HAND1:TCFE2αHeart- and neural-crest derivatives-expressed protein 1: Transcription factor E2AHand1 belongs to the basic helix-loop-helix family of transcription factors
The Tcfe2a gene encodes the transcription factor E2A, a member of the “class I” a family of basic helix-loop-helix transcription factors (also known simply as "E-proteins"). The transcription factor E2A controls the initiation of B lymphopoiesis
HIC1Hypermethylated in cancer 1This gene functions as a growth regulatory and tumor repressor gene
HIF1A:ARNT HLTFHypoxia-inducible factor 1: Aryl hydrocarbon receptor nuclear translocator Helicase-like transcription factorHIF1 is a homodimeric basic helix-loop-helix structure composed of HIF1a, the alpha subunit, and the aryl hydrocarbon receptor nuclear translocator (Arnt), the beta subunit. The protein encoded by HIF1 is a Per-Arnt-Sim transcription factor found in mammalian cells growing at low oxygen concentrations. It plays an essential role in cellular and systemic responses to hypoxia Member of the SWItch/Sucrose Non Fermentable family which have helicase and ATPase activities and are thought to regulate transcription of certain genes by altering the chromatin
HNF1AHepatocyte nuclear factor 1 homeobox ATranscriptional activator that regulates the tissue specific expression of multiple genes, especially in pancreatic islet cells and in liver
HNF1BHNF1 homeobox BThis gene encodes a member of the homeodomain-containing superfamily of transcription factors. The protein binds to DNA as either a homodimer, or a heterodimer with the related protein hepatocyte nuclear factor 1-alpha. The gene has been shown to function in nephron development, and regulates development of the embryonic pancreas
HNF4αHepatocyte nuclear factor 4, alphaThe protein encoded by this gene is a nuclear transcription factor which binds DNA as a homodimer. The encoded protein controls the expression of several genes, including hepatocyte nuclear factor 1 alpha, a transcription factor which regulates the expression of several hepatic genes. This gene may play a role in development of the liver, kidney, and intestines
HNF4γHepatocyte nuclear factor 4, gammaSteroid hormone receptor activity and sequence-specific DNA binding transcription factor activity. An important paralog of this gene is RXRA
HOXA5Homeobox protein Hox-A5DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation
ISNM1Insulinoma-associated 1Insulinoma-associated 1 gene is intronless and encodes a protein containing both a zinc finger DNA-binding domain and a putative prohormone domain. This gene is a sensitive marker for neuroendocrine differentiation of human lung tumors
IRF1,2Interferon regulatory factorMembers of the interferon regulatory transcription factor family that contain a conserved
N-terminal region of about 120 amino acids, which folds into a structure that binds specifically to the interferon consensus sequence
JDP2Jun dimerization protein 2Component of the AP-1 transcription factor that represses transactivation mediated by the Jun family of proteins. Involved in a variety of transcriptional responses associated with AP-1 such as UV-induced apoptosis, cell differentiation, tumorigenesis and antitumogeneris
JUNJun Proto-OncogeneThis gene is the putative transforming gene of avian sarcoma virus 17. It encodes a protein which is highly similar to the viral protein, and which interacts directly with specific target DNA sequences to regulate gene expression
JUNDJun D proto-oncogeneThe protein encoded by this intronless gene is a member of the JUN family, and a functional component of the AP1 transcription factor complex. This protein has been proposed to protect cells from p53-dependent senescence and apoptosis
JUN::FOSJun proto-oncogene FBJ murine osteosarcoma viral oncogene homologPromotes activity of NR5A1 when phosphorylated by HIPK3 leading to increased steroidogenic gene expression upon cAMP signaling pathway stimulation Has a critical function in regulating the development of cells destined to form and maintain the skeleton. It is thought to have an important role in signal transduction, cell proliferation and differentiation
KLF1Kruppel-like factor 1 (erythroid)Transcription regulator of erythrocyte development that probably serves as a general switch factor during erythropoiesis. Is a dual regulator of fetal-to-adult globin switching
KLF4Krueppel-like factor 4Transcription factor that can act both as activator and as repressor. Regulates the expression of key transcription factors during embryonic development
KLF5Krueppel-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-translational 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
MAXMYC associated factor XThe protein encoded by this gene is a member of the basic helix-loop-helix leucine zipper family of transcription factors
MAFKv-maf avian musculoaponeurotic fibrosarcoma oncogene homolog KSince they lack a putative transactivation domain, the small Mafs behave as transcriptional repressors when they dimerize among themselves. However, they seem to serve as transcriptional activators by dimerizing with other (usually larger) basic-zipper proteins and recruiting them to specific DNA-binding sites
MEF2AMyocyte enhancer factor 2AThe protein encoded by this gene is a DNA-binding transcription factor that activates many muscle-specific, growth factor-induced, and stress-induced genes. Mediates cellular functions not only in skeletal and cardiac muscle development, but also in neuronal differentiation and survival
MGAMGA, MAX Dimerization ProteinFunctions as a dual-specificity transcription factor, regulating the expression of both MAX-network and T-box family target genes. Functions as a repressor or an activator
MYBMyb proto-oncogene proteinThis gene encodes a transcription factor that is a member of the MYB family of transcription factor genes. Transcriptional activator and plays an important role in the control of proliferation and differentiation of hematopoietic progenitor cells
MYCv-myc myelocytomatosis viral oncogene homologThe protein encoded by this gene is a multifunctional, nuclear phosphoprotein that plays a role in cell cycle progression, apoptosis and cellular transformation
MYCNv-myc myelocytomatosis viral related oncogene, neuroblastoma derived (avian)This gene is a member of the MYC family and encodes a protein with a basic helix-loop-helix domain. Amplification of this gene is associated with a variety of tumors, most notably neuroblastomas
MZF1_1-4Myeloid zinc finger 1Binds to target promoter DNA and functions as transcription regulator. May be one regulator of transcriptional events during hemopoietic development. Isoforms of this protein have been shown to exist at protein level
NFATC2Nuclear factor of activated T-cells, cytoplasmic 2This protein is present in the cytosol and only translocates to the nucleus upon T cell receptor stimulation, where it becomes a member of the nuclear factors of activated T cells transcription complex
NFIANuclear Factor I/ARecognizes and binds the palindromic sequence 5-TTGGCNNNNNGCCAA-3 present in viral and cellular promoters transcription and replication and in the origin of replication of adenovirus type 2. These proteins are individually capable of activating transcription and replication
NFICNuclear factor 1 C-typeRecognizes 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
NFE2::MAFNuclear factor, erythroid 2 V-maf avian musculoaponeurotic fibrosarcoma oncogene homologRegulates erythroid and megakaryocytic maturation and differentiation. Plays a role in all aspects of hemoglobin production from globin and heme synthesis to procurement of iron. When overexpressed, represses anti-oxidant response element-mediated transcription
NFE2L1:MAFGNuclear factor erythroid 2-related factor 1 Transcription factor MafGNuclear factor erythroid 2-related factor coordinates the up-regulation of cytoprotective genes via the antioxidant response element. 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
NFIL3Nuclear factor, interleukin 3 regulatedExpression of interleukin-3 (MIM 147740) is restricted to activated T cells, natural killer cells, and mast cell lines
NFKB1Nuclear factor of kappa light polypeptide gene enhancer in B-cells 1natural killer-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
NFYBNuclear transcription factor Y, betaThe protein encoded by this gene is one subunit of a trimeric complex, forming a highly conserved transcription factor that binds with high specificity to CCAAT motifs in the promoter regions in a variety of genes. This gene product, subunit B, forms a tight dimer with the C subunit, a prerequisite for subunit A association. The resulting trimer binds to DNA with high specificity and affinity. Subunits B and C each contain a histone-like motif
NHLH1Nescient helix loop helix 1The helix-loop-helix proteins are a family of putative transcription factors, some of which have been shown to play an important role in growth and development of a wide variety of tissues and species
NKX2-5Natural killer 3 homeobox 2This gene encodes a member of the NK family of homeobox-containing proteins
Transcriptional repressor that acts as a negative regulator of chondrocyte maturation
NKX3-2Natural killer 3 homeobox 2This gene encodes a member of the NK family of homeobox-containing proteins Transcriptional repressor that acts as a negative regulator of chondrocyte maturation
NR1H3:RXRaNuclear Receptor Subfamily 1, Group H, Member 3 Retinoid X receptor, alphaThe protein encoded by this gene belongs to the NR1 subfamily of the nuclear receptor superfamily The NR1 family members are key regulators of macrophage function, controlling transcriptional programs involved in lipid homeostasis and inflammation. This protein is highly expressed in visceral organs, including liver, kidney and intestine. It forms a heterodimer with retinoid X receptor, and regulates expression of target genes containing retinoid response elements Studies in mice lacking this gene suggest that it may play an important role in the regulation of cholesterol homeostasis
NR2C2Nuclear receptor subfamily 2, group C, member 2Orphan nuclear receptor that can act as a repressor or activator of transcription. An important repressor of nuclear receptor signaling pathways such as retinoic acid receptor, retinoid X, vitamin D3 receptor, thyroid hormone receptor and estrogen receptor pathways
NR2E3Nuclear receptor subfamily 2, group E, member 3This protein is part of a large family of nuclear receptor transcription factors involved in signaling pathways
NR2F1 (COUP)Nuclear receptor subfamily 2, group F, member 1Binds to the ovalbumin promoter and, in conjunction with another protein (S300-II) stimulates initiation of transcription. Binds to both direct repeats and palindromes of the 5'-AGGTCA-3' motif. An important paralog of this gene is RXRA
NR3C1Nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor)Glucocorticoids regulate carbohydrate, protein and fat metabolism, modulate immune responses through suppression of chemokine and cytokine production and have critical roles in constitutive activity of the CNS, digestive, hematopoietic, renal and reproductive systems
NR4A2Nuclear receptor subfamily 4, group A, member 2Transcriptional regulator which is important for the differentiation and maintenance of meso-diencephalic dopaminergic neurons during development
NRF1Nuclear respiratory factor 1This 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
NRLNeural Retina Leucine ZipperThis gene encodes a basic motif-leucine zipper transcription factor of the Maf subfamily. The encoded protein is conserved among vertebrates and is a critical intrinsic regulator of photoceptor development and function
PAX2Paired box gene 2Probable transcription factor that may have a role in kidney cell differentiation
PDX1Pancreatic and duodenal homeobox 1Activates insulin, somatostatin, glucokinase, islet amyloid polypeptide and glucose transporter type 2 gene transcription. Particularly involved in glucose-dependent regulation of insulin gene transcription
PPARγ:RXRαPeroxisome proliferator-activated receptor gamma Retinoid X receptor, alphaPeroxisome proliferator-activated receptor gamma is a member of the nuclear receptor family of ligand-activated transcription factors that heterodimerize with the retinoic X receptor to regulate gene expression. Peroxisome proliferator-activated receptor gamma is located primarily in the adipose tissue, lymphoid tissue, colon, liver and heart and is thought to regulate adipocyte differentiation and glucose homeostasis
RXRaRetinoid X receptor, alphaRetinoid X receptors and retinoic acid receptors, are nuclear receptors that mediate the biological effects of retinoids by their involvement in retinoic acid-mediated gene activation
RFX5Regulatory factor X, 5Activates transcription from class II MHC promoters. Recognizes X-boxes. Mediates cooperative binding between RFX and natural killer-Y. Regulatory factor X binds the X1 box of MHC-II promoters
RUNX1Runt-related transcription factor 1Heterodimeric transcription factor that binds to the core element of many enhancers and promoters. The protein encoded by this gene represents the alpha subunit of core binding factor and is thought to be involved in the development of normal hematopoiesis
SOX6SRY (sex determining region Y)-box 6The encoded protein is a transcriptional activator that is required for normal development of the central nervous system, chondrogenesis and maintenance of cardiac and skeletal muscle cells
SOX9SRY (sex determining region Y)-box 9The protein encoded by this gene recognizes the sequence CCTTGAG along with other members of the involved in chondrogenesis by acting as a transcription factor for these genes
SOX10SRY (sex determining region Y)-box 10This gene encodes a member of the SRY-related HMG-box family of transcription factors involved in the regulation of embryonic development and in the determination of the cell fate
SOX17SRY (sex determining region Y)-box 17Acts as transcription regulator that binds target promoter DNA and bends the DNA
SP1Specificity Protein 1Can activate or repress transcription in response to physiological and pathological stimuli. Regulates the expression of a large number of genes involved in a variety of processes such as cell growth, apoptosis, differentiation and immune responses
SP2Specificity Protein 2This 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
SPIBTranscription factor Spi-BSPI1 and SPIB are members of a subfamily of erythroblast transformation-specific transcription factors; erythroblast transformation-specific proteins share a conserved erythroblast transformation-specific domain that mediates specific DNA binding SPIB and SPI1 bind to a purine-rich sequence, the PU box (5-prime-GAGGAA-3-)
SPI1Spleen focus forming virus proviral integration oncogene spi1This gene encodes an erythroblast transformation-specific-domain transcription factor that activates gene expression during myeloid and B-lymphoid cell development
SPZ1This gene encodes a basic helix-loop-helix-zip transcription factor which functions in the mitogen-activate protein kinase signaling pathway
SRYSex determining region YTranscriptional regulator that controls a genetic switch in male development
STAT3Signal transducer and activator of transcription 3 (acute-phase response factor)Signal transducer and transcription activator that mediates cellular responses to interleukins, KITLG/SCF and other growth factors
STAT5A:STAT5BSignal transducer and activator of transcription 5A and transcription 5BCarries out a dual function: signal transduction and activation of transcription Regulates the expression of milk proteins during lactation
TCF7L2Transcription factor 7-like 2 (T-cell specific, HMG-box)This gene encodes a high mobility group box-containing transcription factor that plays a key role in the Wnt signaling pathway. The protein has been implicated in blood glucose homeostasis
TEAD1TEA Domain Family Member 1This gene encodes a 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
TFAP2aActivator protein 2The AP2a protein acts as a sequence specific DNA-binding transcription factor recognizing and binding to the specific DNA sequence and recruiting transcription machinery
THAP1THAP domain containing, apoptosis associated protein 1DNA-binding transcription regulator that regulates endothelial cell proliferation and G1/S cell-cycle progression
USF1Upstream transcription factor 1This gene encodes 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
YY1YY1 transcription factorYY1 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 implicating histone modification in the function of YY1
ZEB1Zinc finger E-box-binding homeobox 1A member of the delta-EF1 (TCF8)/Zfh1 family of 2-handed zinc finger/homeodomain proteins and interacts SMADs with receptor-mediated, activated full-length activated full-length SMADs
ZNF263Zinc finger protein 263Might play an important role in basic cellular processes as a transcriptional repressor. An important paralog to ZNF496
ZNF354CZinc finger protein 354CMay function as a transcription repressor

The type 2 demodkinase gene (DIO2) encodes a deiodinase that coverts the thyroid prohormone, thyroxine (T4), to the biologically active triiodothyronine (T3) where T3 plays an important role in the regulation of energy balance and glucose metabolism[35-38]. Two rSNPs in LD within the DIO2 gene are rs225015 and rs225011 whose major alleles create unique punitive TFBS for TFs that are involved with energy balance and glucose metabolism (Tables 1-3). The ESRRα an alpha estrogen-related receptor that is involved with regulating thyroid hormone receptor genes while PPARα:RXRα and RXRα are involved with the regulation of adipocyte differentiation and glucose homeostasis (Tables 2 and 3). The minor allele of the rs225015 rSNP creates a unique punitive TFBS for the TCF7L2 TF whose protein is implicated in blood glucose homeostasis (Tables 2 and 3). The minor allele of the rs225011 rSNP creates a unique punitive TFBS for the PDX1 TF whose protein activates insulin, somatostatin, glucokinase, islet amyloid polypeptide and glucose transporter type 2 gene transcription (Tables 2 and 3).

The thromboxane A2 receptor (TBXA2R) gene is a member of the seven-transmembrane G-protein-coupled receptor super family, which interacts with intracellular G proteins, regulates different downstream signaling cascades, and induces many cellular responses including the intracellular calcium influx, cell migration and proliferation as well as apoptosis[39]. Two rSNPs in LD within the TBXA2R gene are rs2238631 and rs2238634 whose minor alleles create unique punitive TFBS for TFs that are involved in signaling cascades and apoptosis (Tables 1-3). The ELK1 and SPZ1 TFs are involved with the ras-raf-MAPK signaling cascade while the ETS1 TF is involved with cell death (Tables 2 and 3). NR2E3 is part of a large family of nuclear receptor TFs involved in signaling pathways (Tables 2 and 3).

The other six genes can be analyzed in the same manner to identify punitive TFBS created by the rSNP alleles of these genes (Tables 2 and 3). What a change in the rSNP alleles can do, is to alter the DNA landscape around the SNP for potential TFs to attach and regulate a gene. This change in the DNA landscape can alter gene regulation which in turn can result in a change of a biological process or signaling pathway resulting in disease or illness. The process laid out in this report is a convenient way of identifying potential TFBS created by rSNP alleles that have been found to be significantly associated with disease or sickness. Any potential alterations in TFBS obtained by computational analyses need to be verified by protein/DNA electrophoretic mobility gel shift assays and gene expression studies[40]. CHIP-seq[41] experiments have become the standard method of validating TFBS and studying gene regulation[42-44].

In conclusion, SNPs in the regulatory region of a gene can alter the DNA landscape for TFs resulting in TFBS changes. Consequently, alterations in TF binding can affect gene regulation. Examples of this for nine genes are presented in this report where SNP alleles will either have no effect on TF binding or each allele will create unique punitive TFBS and alter a TFs ability to bind the DNA and regulate the gene.

COMMENTS
Background

Transcriptional factors (TFs) bind the DNA near a gene at transcriptional factor binding sites (TFBS) in order to regulate the gene. Single nucleotide polymorphisms (SNPs) that occur in the TFBS can alter the TFs ability to bind the DNA and thereby affect gene regulation. Such regulatory (r)SNPs have been associated with human disease and sickness. In this report, the alteration of TFBS created by rSNP alleles associated with disease has been documented for nine human genes. Sometimes the rSNP alleles will have no effect on the TFBS and not change the TF ability to bind the DNA. Other times each allele will create unique punitive TFBS that alter the TFs ability to regulate the gene.

Research frontiers

This article addresses an emerging concept in understanding how rSNPs which are significantly associated with disease can alter the TFBS for TFs that regulate a gene.

Innovations and breakthroughs

TFBS alteration by rSNPs is a newly emerging field of research and provides a different direction in examining changes in gene regulation resulting in human disease and sickness.

Applications

Given the great diversity of punitive unique TFBS generated by each allele of a rSNP, the author suspects that alterations in TFBS affect how well a gene is expressed. The outcome may result in disease or sickness. The methods outlined in the article should be applied to all rSNPs that are associated with disease or sickness of a regulatory nature.

Terminology

rSNP: A regulatory single nucleotide polymorphism that affects gene expression; TF: Transcriptional factor that is involved with regulating a gene; TFBS: Transcription factor DNA binding site in the regulatory region of a gene; Unique TFBS: A TFBS created by one rSNP allele and not the alternate allele.

Peer-review

This study is technically well performed and a very interesting result. The interpretation was also sound. The report applied a computational approach to predict functional rSNPs in TFBS, focusing on several genes published earlier. Computational modeling and analysis for functional prediction is one of the approaches recently developed, particularly to address GWAS findings.

Footnotes

Manuscript source: Invited manuscript

Specialty type: Hematology

Country of origin: United States

Peer-review report classification

Grade A (Excellent): 0

Grade B (Very good): 0

Grade C (Good): C, C

Grade D (Fair): 0

Grade E (Poor): 0

P- Reviewer: Jeong BH, Xuei XL S- Editor: Qiu S L- Editor: A E- Editor: Lu YJ

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