Title Page

Contents

Abbreviations 13

Abstract 14

Introduction 16

1.0. Introduction 16

1.1. Biological background 16

1.2. Regulation of Gene expression and Promoter 16

1.3.1. GFRα1 20

1.3.2. Ref-1 Induced GFRα1 Promoter Activity in Human Fibroblast cell line GM00637. 21

1.4.1. JAGGED1 24

1.4.2. Ref-1 Induced JAG1 Promoter Activity in Human fibroblast cell line GM00637 25

1.5. APE(ref-1) 28

Aims of the study 33

Materials and methods 34

(1) Reagents 34

(2) Maintenance of cell Lines 34

(3) Genomic DNA Extraction 34

(4) Cloning and DNA sequence Analysis 35

(5) Site-Directed Mutagenesis 36

(6) Transfection 36

(7) Luciferase Activity Measurement 36

(8) Total RNA Isolation 37

(9) Transient Transfection of APE 37

(10) Reverse Transcription (RT)-PCR 38

(11) Western Blotting 38

(12) Primer Extension 39

(13) Nuclear Protein Extraction 39

(14) EMSA-Binding Reaction 40

(15) Detection 40

(16) Chromatin immunoprecipitation assays 41

(17) Statistical analysis 41

Results 51

I. Ref-1 Induced GFRα1 Promoter Activity in Human fibroblast cell line GM00637. 51

I-1) GFRα1 transcript levels were increased in ref-l expressed GM00637 cells. 51

I-2) Isolation of the 5' flanking region of the human GFRα1 gene. 52

I-3) The transcription start sites of the GFRα1 gene. 56

I-4) Deletion analysis of the GFRα1 promoter. 57

I-5) Roles of the Putative NF-κB DNA Binding sites in the GFRα1 promoter activation. 58

I-6) Identification of NF-κB BS #I binding to the sub-region -575/-66 of the GFRα1 promoter. 61

I-7) Evaluations of transcriptional activities of all putative NF-κB binding sites in the GFRα1 promoter region -575/-66. 64

I-8) Determination of functional NF-KB-BS #I-binding sites in the GFRα1 promoter region -575/-66. 65

I-9) Cellular NF-κB binding to the cognate cis-element in the GFRα1 promoter. 67

I-10) Precise mechanism of the ref-1 regulation to the functionalities of the GFRα1 promoter. 68

II. Ref-1 Induced JAGl Promoter Activity in Human fibroblast cell line GM00637. 70

II-1) Ref-1 Induced JAGl Expression in human fibroblast GM00637 Cells. 70

II-2) Isolation of the 5' flanking region of the human JAGl gene. 71

II-3) The transcription start sites of the JAG1 gene. 74

II-4) Deletion analysis of the JAGl promoter. 75

II-5) Roles of the putative EGR-1 in the JAGl promoter activation. 77

II-6) Identification of EGR-1 binding to the sub-region -850/-383 of the JAG1 promoter. 78

II-7) Evaluations of transcriptional activities of putative EGR-1 BS #II in JAG1 promoter region -850/382. 80

II-8) Determination of functional EGR-1 BS #II in the JAG1 promoter region. 81

II-9) Cellular EGR-1 binding to the cognate cis-element in the JAG1 promoter. 83

II-10) Precise mechanism of the ref-1 regulation to the functionalities of the JAG1 promoter. 84

Discussion 86

I. Ref-1 Induced GFRα1 Promoter Activity in Human fibroblast cell line GM00637. 86

II. Ref-1 Induced JAC1 Promoter Activity in Human fibroblast cell line GM00637. 89

References 91

국문초록 103

Acknowledgements 105

Table 1. APE-1/ref-1 enhances DNA binding of transcription factors. 30

Table I-1. GFRα1 Primer sets for Cloning 42

Table I-2. Oligos for EMSA 43

Table I-3. Oligos for Site Directed Mutagenesis 44

Table I-4. GFRα1 Primer sets for Chromatin Immunoprecipitation 45

Table II-1. JAG1 Primer sets for Cloning 46

Table II-2. JAG1 Oligos for EMSA 47

Table II-3. Oligos for Site Directed Mutagenesis 48

Table II-4. JAG1 Primer sets for Chromatin Immunoprecipitation 49

Introduction 9

Fig. 1.1. Stages of gene expression in cell. 17

Fig. 1.2. A typical promoter structure showing modular organization of TFBSs. Taken from Werner 2003. 19

Fig. 1.3. Detail diagrammatic structure of the genomic configuration of exon-intron of the GFRα1 gene. 20

Fig. 1.4. Multifunctional activities of the human AP endonuclease. Ape1/ref-1 is a multifunctional protein involved in BER, transcription factor regulation, and oxidative signaling. In DNA BER, it functions as an AP endonuclease. It is also involved in the... 29

Fig. 1.5. Schematic diagram of important residues and putative phosphorylation sites in Ape1/ref-1. CKI, CKII, and PKC have been shown to phosphorylate Ape1/ref-1 in vitro, however, the other phosphorylation sites are putative. There were no phosphorylation sites... 30

I. Ref-1 Induced GFRα1 Promoter Activity in Human fibroblast cell line GM00637. 10

Fig. I-1. Relative transcript levels of the GFRα1 receptor in GM00637 cells. A. Messenger RNA levels were determined by a RT-PCR method and normalized to GAPDH transcripts. B. Relative GFRα1 protein content in ref-1 expressed cell lines were identified by western blot... 52

Fig. I-2. Nucleotide sequence of the 5'flanking region of the GFRα1 gene. Nucleotides are numbered corresponding to the translational initiation site at + 1 at the start. On the based of Ensemble data, first and second exon as shown highlighted, Binding sites for the transcription... 53

Fig. I-3. Primer extension analysis for GFRα1 transcription start sites. Reverse oligonucleotide as indicated above was end-labeled with [γ-32P] ATP and used in a primer extension experiment with 20 ㎍ of total cellular RNA isolated from ref-1 expressing... 56

Fig. I-4.A. Schematic representation of GFRα1 promoter-reporter chimeras with putative NF-κB binding sites. Scheme of the 5'-upstream region of the human GFRα1 promoter showing major luciferase constructs which were used to identify the promoter activity and... 57

Fig. I-4.B. Relative luciferase activities of GFRα1 promoter-deletion constructs. GFRα1 promoter-deletion constructs were transiently transfected into ref-1 expressing GM00637 cells. Forty eight hour after transfection, cells were harvested for assaying luciferase activities. The... 58

Fig. I-5.A. General overview of 5'deleted luciferase reporter constructs in human GRFα1 gene focusing to purposed NF-κB regulatory region. 59

Fig. I-5.B. Relative luciferase activities of NF-κB oriented GFRα1 promoter-reporter constructs. The GFRα1 promoter-reporter constructs each as shown in Fig.I-5.A and the PGL3 luciferase reporter vector, an internal control, were transiently co-transfected... 59

Fig. I-5.C. General overview of 3' deleted luciferase reporter constructs in human GRFα1 gene focusing to purposed NF-κB regulatory region. 60

Fig. I-5.D. Relative luciferase activities of 3' deleted NF-κB oriented GFRα1 promoter-reporter constructs. The GFRα1 promoter-reporter constructs each as shown in Fig.I-5.A and the PGL3 luciferase reporter vector, an internal control, were transiently co-transfected... 60

Fig. I-6. Identification of the NF-κB binding site in the sub-region -575/-66 of the GFRα1 promoter. A. NF-κB binding to the sub-region -348/-332 of the GFRα1 promoter determined by EMSA assays. 5'-Biotin labeled synthetic GFRα1 promoter... 62

Fig. I-7. Effects of NF-κB-BS-WT and its mutants on the SV40 promoter-directed reporter gene expression. The NF-κB-BS-WT and various mutants as shown in schematic drawing in the left were inserted upstream of the SV40 promoter in the pGL-3 basic reporter... 64

Fig. I-8. Determination of functional NF-κB-binding site in the GFRα1 promoter region-575/-66. [32P]-labeled synthetic GFRα1 promoter fragments containing putative NF-κB BS#I binding sites as shown in fig. I-8 and 5 ㎍ nuclear extracts (NE) prepared from ref-1 expressed... 66

Fig. I-9. Determination of cellular NF-κB binding to the GFRα1 gene promoter by the ChIP assay. GM00637,GM00637-pcDNA3.1 and GM00637-ref-1 cells were incubated from 1 x 106 cells for each group, and immunoprecipitated with an antibody all NF-κB-p50... 67

Fig. I-10. Ref-1 regulation to the functionalities of the GFRα1 promoter. Ref-1 regulated GFRα1 transcriptional activity was determined by using various ref-1 expression constructs with site directed mutations and NF-κB GFRα1 Promoter-reporter constructs (-575/-66) were... 69

II. Ref-1 Induced JAGl Promoter Activity in Human fibroblast cell line GM00637. 12

Fig. II-1. Relative transcript levels of the JAG1 receptor in GM00637 cells. A. Messenger RNA levels were determined by a RT-PCR method and normalized to GAPDH transcripts. B. Relative JAG1 protein content in ref-1 expressed cell lines were identified by western blot... 70

Fig. II-2. Nucleotide sequence of the 5'flanking region of the JAG1 gene. Nucleotides are numbered corresponding to the translational initiation site at + 1 at start. Binding sites for the transcription factors EGR-1 and others are boxed. Primers which were used for primer... 72

Fig. II-3. Primer extension analysis for JAG1 transcription start sites. 74

Fig. II-4.A. Schematic representation of JAG1 promoter-deletion constructs. 76

Fig. II-4.B. Luciferase activities in ref-1 expressing GM00637 cells transfected with JAG1 promoter-deletion constructs. JAG1 promoter-deletion constructs were transiently transfected into ref-1 expressed GM00637 cells. 48 h after transfection, cells were... 76

Fig. II-5.A. General overview of 5'deleted luciferase reporter constructs in human JAG1 gene focusing to purposed EGR-1 regulatory region. 77

Fig. II-5.B. Relative luciferase activities of EGR-1 oriented JAG1 promoter-reporter constructs. The JAG1 promoter-reporter constructs each as shown in Fig.I-5.A and the PGL3 luciferase reporter vector, an internal control, were transiently co-transfected... 78

Fig. II-6.A. Identification of the EGR-1 binding site in the sub-region -850/-382 of the JAG1 promoter. A. EGR-1 binding to the subregion -638/-622 of the JAG1 promoter determined by EMSA assays. 5'-Biotin labeled synthetic JAG1 promoter... 79

Fig. II-7. Effects of EGR-1-BS-WT and its mutants on the SV40 promoter-directed reporter gene expression. The EGR-1-BS-WT and EGR-1 BS #II mutant as shown in schematic drawing in the left were inserted upstream of the SV40 promoter in the pGL-3... 80

Fig. I-8. Determination of functional EGR-1-binding sites in the JAG1 promoter region -850/382. 5'-biotin labeled synthetic JAG1 promoter fragments containing putative EGR-1 binding sites as shown in Fig. II-8 and 5 ㎍ nuclear extracts (NE) prepared from ref-1... 82

Fig. II-9. Determination of cellular EGR-1 binding to the JAG1 promoter by the ChIP assay. GM00637, GM00637-pcDNA3.1 and GM00637-APE1 cells were incubated from 2 x 106 cells for each group, and immunoprecipitated with an antibody against all EGR-1 Anti... 83

Fig. II-10. Ref-1 regulation to the functionalities of the JAC1 promoter. Ref-1 regulated JAG1 transcriptional activity was determined by using various ref-1 expression constructs with site directed mutations and EGR-1 JAG1 Promoter-reporter constructs (-850/-382) were... 85

본 연구의 목적은 인간 섬유아세포 GM00637에서 GFRα1과 JAG1의 발현을 유도하는 APE1/Ref-1의 역할을 밝히는 것이다. GFRα1과 JAG1 promoter에 전사인자 NFk-B의 결합은 APE1을 발현하는 GM00637 세포에서 기능적인 GFRα1의 유도를 뚜렷하게 조절한다. 또한, DNA 복구 활성에서 APE1은 redox 기작에 의해서 많은 전사인자들의 DNA 결합 활성을 조절할 수 있다. 우리는 GFRα1 promoter와 JAG1 promoter에서 3개의 잘 보존되고 기능적인 NFk-B와 EGR-1 결합부분을 찾았다. EMSA super shift assay를 이용하여 NFk-B p50과 EGR-1 APE1 interacting 단백질로 확인되었고, nuclear translocation에 의해 GFRα1 promoter이 NFk-B와 JAG1 promoter이 EGR-1 결합부분에 결합하였다. 또한, in vivo ChIP를 이용하여 NFk-B와 EGR-1 결합 DNA 요소들이 GFRα1 promoter와 JAG1 promoter와 결합하는것을 밝혔다. 더 나아가, 이러한 부분의 돌연변이는 promoter 활성을 뚜렷하게 감소시켰다. 그러므로, APE1 유도된 GFRα1은 NFk-B와 JAG1은 EGR-1 결합 motifs에 의해 조절되고, 이러한 결과에 의해서 APE1이 GFRα1과 JAG1 promoter의 NFk-B와 EGR-1 결합부분의 전사인자들을 통해서 GFRα1과 JAG1 기능을 조절하는 새로운 기작을 뒷받침 한다. 결론적으로, 이 논문은 APE1과 관련된 GFRα1과 JAG1의 새로운 promoter 분석을 증명하였다. 또한, APE1이 GFRα1과 JAG1 promoter 분석과 GFRα1과 JAG1 유도를 매개하는 정확한 기작을 나타내었다.