Nucleolar epigenomics by dynamic molecular combing and nucleolar matrix analysis:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
2013
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| Schlagworte: | |
| Online-Zugang: | Volltext https://nbn-resolving.org/urn:nbn:de:bvb:355-epub-282218 Inhaltsverzeichnis |
| Beschreibung: | IX, 153 S. Ill., graph. Darst. |
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| 264 | 1 | |c 2013 | |
| 300 | |a IX, 153 S. |b Ill., graph. Darst. | ||
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Datensatz im Suchindex
| _version_ | 1804150458587021312 |
|---|---|
| adam_text | IMAGE 1
CONTENTS
SUMMARY III
LIST OF FIGURES V
LIST O F ABBREVIATIONS VII
1 INTRODUCTION 1
1.1 DNA MODIFICATIONS 1
1.1.1 5-METHYLCYTOSINE 2
1.1.2 OXIDATIVE PRODUCTS OF 5-METHYLCYTOSINE 4
1.1.3 OVERVIEW OF DNA MODIFICATION ANALYSES 6
1.1.4 THE IMPORTANCE AND DIFFICULTY OF LOCUS-SPECIFIC MODIFICATION
ANALYSIS OF REPETITIVE DNA 7
1.2 NUCLEOLAR GENOME CONTENT 7
1.2.1 SATELLITE-2 REPEATS 8
1.2.1.1 GENOMIC ORGANIZATION OF SATELLITE-2 DNA 8
1.2.1.2 METHYLATION OF SATELLITE-2 REPEATS 8
1.2.2 RIBOSOMAL RNA GENES 9
1.2.2.1 GENOMIC ORGANIZATION OF RIBOSOMAL DNA 9
1.2.2.2 EPIGENETICS OF RIBOSOMAL DNA 15
1.2.2.3 TIP5 AS A KEY REGULATOR OF RDNA SILENCING 18
2 RESULTS 2 3
2.1 SINGLE MOLECULE EPIGENOMICS BY DYNAMIC MOLECULAR COMBING . . . . 23
2.1.1 SUITABLE CONDITIONS FOR IN VITRO COMBING OF A DNA 23
2.1.2 PSORALEN-COMBING 25
2.1.2.1 IN VITRO PSORALEN-COMBING ON A PHAGE DNA . . . . 25 2.1.2.2
PSORALEN-COMBING ON GENOMIC DNA 30
2.1.3 CHROMATIN-COMBING 34
2.1.4 EPI-COMBING 35
2.1.4.1 IN VITRO EPI-COMBING ON A PHAGE DNA 37
2.1.4.2 EPI-COMBING ON GENOMIC DNA 40
2.2 DNA METHYLATION ANALYSIS OF SATELLITE-2 DNA 43
2.2.1 SATELLITE-2 DNA METHYLATION ANALYSIS BY METAPHASE IMMUNOFISH ON
METAPHASE CHROMOSOME SPREADS 43
2.2.2 SATELLITE-2 DNA METHYLATION ANALYSIS BY EPI-COMBING . . . . 43 2.3
DNA METHYLATION ANALYSIS OF RIBOSOMAL RNA GENES 46
2.3.1 RDNA METHYLATION ANALYSIS BY METAPHASE-IMMUNOFISH ON METAPHASE
CHROMOSOME SPREADS 46
2.3.2 EPIGENETIC ANALYSIS OF RIBOSOMAL DNA REPEATS REVEAL EPIGENETIC
CLUSTERS AND TRANSITIONS 49
HTTP://D-NB.INFO/1037847733
IMAGE 2
2.3.3 COMPARISON OF RIBOSOMAL DNA METHYLATION IN WERNER SYN
DROME CELLS AND PRIMARY FIBROBLASTS 55
2.4 ASSOCIATION OF RIBOSOMAL DNA WITH THE NUCLEAR MATRIX 64
2.4.1 TIP5 TARGETS RDNA TO THE NUCLEOLAR MATRIX 64
2.4.2 AT-HOOKS OF TIP5 DISPLAY MAR BINDING WITH COMPARABLE AFFINITIES 05
2.4.2.1 DNA BINDING FEATURES OF POTENTIAL MAR BINDING DO MAINS OF TIP5
65
2.4.2.2 SEQUESTERING OF RDNA TO THE NUCLEOLAR MATRIX RE QUIRES A
FUNCTIONAL TIP5 MOLECULE 71
2.5 EXTENDED AT-HOOKS AS A NOVEL DNA BINDING MOTIF 73
3 DISCUSSION 7 5
3.1 SINGLE MOLECULE EPIGENOMICS BY DYNAMIC MOLECULAR COMBING . . . . 75
3.1.1 PSOI ALEN-COMBING FOR SEQUENCE-SPECIFIC SINGLE MOLECULE CHRO
MATIN ANALYSIS 75
3.1.2 EPI-COMBING 77
3.2 DNA METHYLATION PATTERNS OF TANDEM REPEAT ARRAYS 80
3.2.1 DNA METHYLATION ANALYSIS OF SATELLITE-2 REPEATS 80
3.2.2 DNA METHYLATION ANALYSIS OF RIBOSOMAL DNA 81
3.2.2.1 DNA METHYLATION CLUSTERING AND TRANSITION OF RIBO SOMAL DNA
REPEATS 81
3.2.2.2 EPIGENETIC STATUS OF NON-CANONICAL RDNA REPEATS . 83 3.3
LARGE-SCALE ORGANIZATION OF RIBOSOMAL DNA CHROMATIN IS REGULATED BY TIP5
85
3.3.1 TARGETING OF RDNA TO THE NUCLEAR MATRIX 85
3.3.2 DNA BINDING FEATURES OF TIP5 AND ITS FUNCTIONAL CONSEQUENCES 86
3.3.3 A BIOLOGICAL ROLE FOR NORC BINDING TO DNA 88
4 MATERIALS AND METHODS 90
4.1 MATERIALS 90
4.1.1 TECHNICAL DEVICES 90
4.1.2 CHEMICALS AND REAGENTS 91
4.1.3 CONSUMABLES 93
4.1.4 SOFTWARE AND ONLINE TOOLS 94
4.1.5 BUFFERS, SOLUTIONS AND MEDIA 94
4.1.6 ENZYMES 96
4.1.7 KITS 97
4.1.8 STANDARD DNA AND PROTEIN WEIGHT MARKERS 98
4.1.9 ANTIBODIES 98
4.1.9.1 PRIMARY ANTIBODIES 98
4.1.9.2 SECONDARY AND TERTIARY ANTIBODIES 99
4.1.10 BACTERIAL STRAINS AND MAMMALIAN CELL TYPES 100
4.1.11 PLASMIDS 101
4.1.12 OLIGONUCLEOTIDES 102
4.2 METHODS 103
4.2.1 WORKING WITH NUCLEIC ACIDS 103
4.2.1.1 ISOLATION OF NUCLEIC ACIDS 103
4.2.1.2 DNA PURIFICATION 103
IMAGE 3
4.2.1.3 CHECKING THE QUALITY OF NUCLEIC ACIDS 104
4.2.1.4 POLYMERASE CHAIN REACTION 104
4.2.1.5 RESTRICTION DIGEST OF DNA 107
4.2.1.6 LIGATION OF DNA FRAGMENTS 108
4.2.1.7 DNA SEQUENCING 108
4.2.2 PROTEIN METHODS 108
4.2.2.1 DENATURING POLYACRYLAMIDE GEL ELECTROPHORESIS . . . 108 4.2.2.2
PROTEIN QUANTIFICATION 109
4.2.2.3 SEMI-DRY WESTERN BLOT AND PROTEIN DETECTION . . . 110 4.2.2.4
PURIFICATION OF GST-TAGGED PROTEINS I L L
4.2.3 MAMMALIAN CELL CULTURE 112
4.2.3.1 MAINTENANCE 112
4.2.3.2 TRANSFECTION OF MAMMALIAN CELLS 113
4.2.3.3 DETECTION OF SENESCENT CELLS 113
4.2.4 NUCLEOLUS ISOLATION 113
4.2.5 MICROSCOPY METHODS 115
4.2.5.1 FIXATION OF ADHERENTLY GROWING CELLS 115
4.2.5.2 IMMUNOFLUORESCENCE 116
4.2.5.3 FLUORESCENCE IN SITU HYBRIDIZATION - FISH 116
4.2.6 DYNAMIC MOLECULAR COMBING VARIANTS 119
4.2.6.1 DNA PLUG PREPARATION OF ADHERENT CELLS 119
4.2.6.2 DNA ISOLATION FOR COMBING 119
4.2.6.3 THE COMBING PROCESS 120
4.2.6.4 IN VITRO PSORALEN-COMBING 120
4.2.6.5 CHROMATIN-COMBING 122
4.2.6.6 EPI-COMBING 122
4.2.6.7 FLUORESCENCE IN SITU HYBRIDIZATION FOR ALL COMBING VARIANTS 123
4.2.7 NUCLEAR MATRIX PREPARATION 124
4.2.8 MICROSCALE THERMOPHORESIS 125
4.2.8.1 MICROSCALE THERMOPHORESIS TO QUANTIFY DNA:PROTEIN BINDING
INTERACTIONS 125
4.2.8.2 PREPARATION OF DNA TEMPLATE 127
4.2.8.3 PREPARATION OF THE TITRATION SERIES 128
4.2.8.4 MEASUREMENT AND ANALYSIS OF THE BINDING AFFINITY . 129
5 APPENDIX 131
5.1 CURRICULUM VITAE 131
5.2 SCIENTIFIC CONTRIBUTIONS 133
5.3 GRANTS, AWARDS AND FELLOWSHIPS 135
6 ACKNOWLEDGEMENTS 138
BIBLIOGRAPHY 139
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| spelling | Zillner, Karina 1984- Verfasser (DE-588)1035777673 aut Nucleolar epigenomics by dynamic molecular combing and nucleolar matrix analysis vorgelegt von Karina Zillner 2013 IX, 153 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Regensburg, Univ., Diss., 2013 Epigenetik (DE-588)7566079-9 gnd rswk-swf DNS (DE-588)4070512-2 gnd rswk-swf Methylierung (DE-588)4123751-1 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content DNS (DE-588)4070512-2 s Methylierung (DE-588)4123751-1 s Epigenetik (DE-588)7566079-9 s b DE-604 Erscheint auch als Online-Ausgabe urn:nbn:de:bvb:355-epub-282218 http://epub.uni-regensburg.de/28221/ Verlag kostenfrei Volltext https://nbn-resolving.org/urn:nbn:de:bvb:355-epub-282218 Resolving-System DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=026061930&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Zillner, Karina 1984- Nucleolar epigenomics by dynamic molecular combing and nucleolar matrix analysis Epigenetik (DE-588)7566079-9 gnd DNS (DE-588)4070512-2 gnd Methylierung (DE-588)4123751-1 gnd |
| subject_GND | (DE-588)7566079-9 (DE-588)4070512-2 (DE-588)4123751-1 (DE-588)4113937-9 |
| title | Nucleolar epigenomics by dynamic molecular combing and nucleolar matrix analysis |
| title_auth | Nucleolar epigenomics by dynamic molecular combing and nucleolar matrix analysis |
| title_exact_search | Nucleolar epigenomics by dynamic molecular combing and nucleolar matrix analysis |
| title_full | Nucleolar epigenomics by dynamic molecular combing and nucleolar matrix analysis vorgelegt von Karina Zillner |
| title_fullStr | Nucleolar epigenomics by dynamic molecular combing and nucleolar matrix analysis vorgelegt von Karina Zillner |
| title_full_unstemmed | Nucleolar epigenomics by dynamic molecular combing and nucleolar matrix analysis vorgelegt von Karina Zillner |
| title_short | Nucleolar epigenomics by dynamic molecular combing and nucleolar matrix analysis |
| title_sort | nucleolar epigenomics by dynamic molecular combing and nucleolar matrix analysis |
| topic | Epigenetik (DE-588)7566079-9 gnd DNS (DE-588)4070512-2 gnd Methylierung (DE-588)4123751-1 gnd |
| topic_facet | Epigenetik DNS Methylierung Hochschulschrift |
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