Exploring the role of structured DNA elements and their specific binders in genome regulation:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
2013
|
| Schlagworte: | |
| Online-Zugang: | kostenfrei https://nbn-resolving.org/urn:nbn:de:bvb:355-epub-286704 Inhaltsverzeichnis |
| Beschreibung: | XII, 155 S. Ill., graph. Darst. |
Internformat
MARC
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| 100 | 1 | |a Filarsky, Michael |d 1982- |e Verfasser |0 (DE-588)1041257961 |4 aut | |
| 245 | 1 | 0 | |a Exploring the role of structured DNA elements and their specific binders in genome regulation |c vorgelegt von Michael Filarsky |
| 264 | 1 | |c 2013 | |
| 300 | |a XII, 155 S. |b Ill., graph. Darst. | ||
| 336 | |b txt |2 rdacontent | ||
| 337 | |b n |2 rdamedia | ||
| 338 | |b nc |2 rdacarrier | ||
| 502 | |a Regensburg, Univ., Diss., 2013 | ||
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| 650 | 0 | 7 | |a Genregulation |0 (DE-588)4122166-7 |2 gnd |9 rswk-swf |
| 655 | 7 | |0 (DE-588)4113937-9 |a Hochschulschrift |2 gnd-content | |
| 689 | 0 | 0 | |a Genregulation |0 (DE-588)4122166-7 |D s |
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| 856 | 4 | 1 | |u http://epub.uni-regensburg.de/28670/ |x Verlag |z kostenfrei |3 Volltext |
| 856 | 4 | |u https://nbn-resolving.org/urn:nbn:de:bvb:355-epub-286704 |x Resolving-System | |
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Datensatz im Suchindex
| _version_ | 1804150706644451328 |
|---|---|
| adam_text | TABLE OF CONTENTS
LIST OF FIGURES V
LIST OF TABLES VII
LIST OF ABBREVIATIONS IX
1 SUMMARY 1
2 INTRODUCTION 3
2.1 STRUCTURED DNA ELEMENTS
- BEYOND THE DOUBLE HELIX 3
2.2 TRIPLEX DNA STRUCTURES 4
2.2.1 THE CONCEPT OF TRIPLEX DNA 4
2.2.2 ENCODING
THE TRIPLEX - FACTORS DETERMINING TRIPLEX FORMATION AND STABILITY. 6
2.2.3 THE CONCEPT OF THE TFO
ANTIGENE STRATEGY 8
2.2.4 EVIDENCE FOR THE EXISTENCE OF TRIPLEX STRUCTURES IN VIVO 9
2.2.5 UNRAVELING THE ABUNDANT TRIPLEX FORMING POTENTIAL OF MAMMALIAN
GENOMES 10
2.2.6 POSSIBLE FUNCTIONS
OF TRIPLEX STRUCTURES IN VIVO 12
2.3 THE NUCLEAR MATRIX 14
2.3.1 DEFINING
THE NUCLEAR MATRIX 15
2.3.2 NUCLEAR MATRIX FUNCTIONS 15
2.4 THE MAMMALIAN RIBOSOMAL RNA
GENES 17
2.4.1 ORGANIZATION OF THE MAMMALIAN RRNA GENES 17
2.4.2 EPIGENETIC REGULATION OF RRNA GENES 18
2.4.3 NORC IS A KEY PLAYER IN RRNA REPRESSION 19
2.4.4 TIP5 IS A MULTIFUNCTIONAL PROTEIN WITH A MODULAR STRUCTURE 22
2.4.5 LARGE-SCALE ORGANIZATION OF RDNA CHROMATIN 23
3 RESULTS 24
3.1 CHARACTERIZATION OF PUTATIVE TRIPLEX FORMING SITES LOCATED IN THE
RDNA
ENHANCER 24
3.1.1 THE MOUSE RRNA GENES CONTAIN CLUSTERS OF PUTATIVE TRIPLEX FORMING
SITES IN
THEIR REGULATORY ELEMENTS 24
I
HTTP://D-NB.INFO/1043119094
3.1.2 THE RDNA ENHANCER MOTIF FORMS A STABLE TRIPLEX COMPLEX IN VITRO 26
3.1.3 TRIPLEX FORMATION CAN BE MONITORED BY MICROSCALE
THERMOPHORESIS 28
3.1.4 THE THERMOPHORETIC BEHAVIOR OF TRIPLEX COMPLEXES CHANGES WITH
STABILITY...
33
3.1.5 TRIPLEX FORMATION IS DEPENDENT ON MULTIVALENT CATIONS AND PH 37
3.1.6 ENHANCER TRIPLEX FORMATION OCCURS IN NEAR PHYSIOLOGICAL BUFFER
CONDITIONS..
41
3.2 LARGE-SCALE ORGANIZATION
OF RIBOSOMAL DNA
CHROMATIN IS REGULATED BY TIP5.44
3.2.1 SERUM STARVATION INDUCES GLOBAL CHANGES IN NUCLEOLAR ARCHITECTURE
AND AN
ENRICHMENT OF RDNA IN THE NUCLEAR MATRIX 44
3.2.2 TIP5 IS ASSOCIATED WITH
THE NUCLEAR MATRIX 48
3.2.3 THE NUCLEAR MATRIX ASSOCIATION OF TIP5 SHOWS NO CHANGES UPON SERUM
STARVATION 50
3.2.4 TIP5 TARGETS RDNA
TO THE NUCLEAR MATRIX 51
3.2.5 THE POTENTIAL MAR BINDING DOMAINS OF TIP5 SHOW A PREFERENCE FOR
AT-RICH
DNA 52
3.2.6 THE DOUBLE AT-HOOK DOMAIN
IS A NUCLEOLAR TARGETING MODULE 54
3.2.7 THE DOUBLE AT-HOOK DOMAIN
IS NOT SUFFICIENT FOR NUCLEAR MATRIX TARGETING...
55
3.2.8 THE TAM DOMAIN MEDIATES NUCLEAR MATRIX ASSOCIATION AND NUCLEOLAR
TARGETING 56
3.3 THE EXTENDED AT-HOOK (EAT) IS A NOVEL NUCLEIC
ACID BINDING
DOMAIN 59
3.3.1 IDENTIFICATION OF A NEW NUCLEIC ACID BINDING DOMAIN IN HUMAN AND
MOUSE
PROTEOMES 59
3.3.2 THE EAT-HOOK DOMAINS OF PTOV1
AND GPBP1
SHOW DNA BINDING PROPERTIES
COMPARABLE TO CLASSIC AT-HOOK MOTIFS 59
3.3.3 THE EAT-HOOK DOMAINS SHOW A PREFERENCE FOR
RNA BINDING 66
3.3.4 LOSS OF THE EAT-HOOK DOMAIN IMPAIRS SHUTTLING OF PTOV1 FROM THE
NUCLEUS
TO THE CYTOPLASM 71
II
4 DISCUSSION 75
4.1 CHARACTERIZATION OF PUTATIVE TRIPLEX FORMING SITES PRESENT IN THE
RDNA
ENHANCER AND TERMINATOR REGIONS 75
4.1.1 THE MOUSE RRNA GENES CONTAIN CLUSTERS OF PUTATIVE TRIPLEX FORMING
SITES IN
THEIR REGULATORY REGIONS 75
4.1.2 THE RDNA ENHANCER
MOTIF FORMS A STABLE TRIPLEX COMPLEX IN VITRO 76
4.1.3 THE THERMOPHORETIC BEHAVIOR OF TRIPLEX COMPLEXES CHANGES WITH
STABILITY...
78
4.1.4 TRIPLEX FORMATION IS DEPENDENT ON CATION CONCENTRATION AND PH 79
4.1.5 ENHANCER TRIPLEX FORMATION OCCURS IN NEAR PHYSIOLOGICAL BUFFER
CONDITIONS
82
4.1.6 TRIPLEX FORMATION - SUMMARY, BIOLOGICAL IMPLICATIONS AND FURTHER
PERSPECTIVE 83
4.2 LARGE-SCALE ORGANIZATION
OF RIBOSOMAL DNA CHROMATIN IS REGULATED
BY TIP5.84
4.2.1 SERUM STARVATION INDUCES GLOBAL CHANGES IN NUCLEOLAR ARCHITECTURE
AND AN
ENRICHMENT OF RDNA IN THE NUCLEAR MATRIX 84
4.2.2 DEFINING THE NUCLEAR MATRIX 86
4.2.3 THE WHOLE RDNA
REPEAT IS RECRUITED TO THE NUCLEAR MATRIX 86
4.2.4 TIP5 IS A NUCLEAR MATRIX PROTEIN, MEDIATING THE ASSOCIATION OF THE
RDNA TO
THE NUCLEAR MATRIX 87
4.2.5 TAM AND AT-HOOK DOMAINS PLAY A ROLE IN NUCLEOLAR TARGETING AND
ASSOCIATION OF TIP5 TO THE NUCLEAR MATRIX 88
4.3 THE EXTENDED AT-HOOK (EAT-HOOK) IS A NOVEL
NUCLEIC ACID
BINDING DOMAIN...
89
4.3.1 THE EAT-HOOK DOMAINS OF PTOV1
AND GPBP1
SHOW DNA BINDING PROPERTIES
COMPARABLE TO CLASSIC AT-HOOK MOTIFS 90
4.3.2 THE EAT-HOOK DOMAINS SHOW A PREFERENCE FOR RNA BINDING 91
4.3.3 LOSS OF THE EAT-HOOK DOMAIN IMPAIRS SHUTTLING OF PTOV1 FROM THE
NUCLEUS
INTO THE CYTOPLASM 93
4.3.4 EAT-HOOK - SUMMARY, BIOLOGICAL
IMPLICATIONS AND FURTHER PERSPECTIVE 94
III
5 MATERIAL AND METHODS 96
5.1 MATERIALS 96
5.1.1 TECHNICAL DEVICES 96
5.1.2 SOFTWARE TOOLS 97
5.1.3 CHEMICALS AND
CONSUMABLES 98
5.1.4 STANDARD SOLUTIONS 101
5.1.5 ENZYMES 105
5.1.6 KITS 106
5.1.7 STANDARD DNA AND
PROTEIN MARKER 106
5.1.8 PROTEASE INHIBITORS, RNASE INHIBITORS
AND ANTIBIOTICS 107
5.1.9 BACTERIAL CELL
LINES AND
MEDIA 107
5.1.10 EUKARYOTIC CELL LINES AND
MEDIA 108
5.1.11 ANTIBODIES 109
5.1.12 OLIGONUCLEOTIDES 110
5.1.13 PLASMIDS 112
5.2 METHODS 114
5.2.1 WORKING WITH DNA 114
5.2.2 PROTEIN BIOCHEMICAL METHODS 119
5.2.3 E. COLI CULTURE
AND METHODS 121
5.2.4 EXPRESSION AND
PURIFICATION OF RECOMBINANT PROTEINS FROM E. COLI 122
5.2.5 MAMMALIAN CELL CULTURE AND METHODS 124
5.2.6 MICROSCOPY METHODS 126
5.2.7 NUCLEAR MATRIX PREPARATION 127
5.2.8 MICROSCALE THERMOPHORESIS 128
6 APPENDIX 135
6.1 CURRICULUM VITAE 136
6.2 LIST OF PUBLICATIONS 137
7 ACKNOWLEDGEMENTS 139
8 BIBLIOGRAPHY 140
IV
|
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| spelling | Filarsky, Michael 1982- Verfasser (DE-588)1041257961 aut Exploring the role of structured DNA elements and their specific binders in genome regulation vorgelegt von Michael Filarsky 2013 XII, 155 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Regensburg, Univ., Diss., 2013 Antisense-Oligonucleotide (DE-588)4371006-2 gnd rswk-swf Genregulation (DE-588)4122166-7 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Genregulation (DE-588)4122166-7 s Antisense-Oligonucleotide (DE-588)4371006-2 s b DE-604 Erscheint auch als Online-Ausgabe urn:nbn:de:bvb:355-epub-286704 http://epub.uni-regensburg.de/28670/ Verlag kostenfrei Volltext https://nbn-resolving.org/urn:nbn:de:bvb:355-epub-286704 Resolving-System DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=026225636&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Filarsky, Michael 1982- Exploring the role of structured DNA elements and their specific binders in genome regulation Antisense-Oligonucleotide (DE-588)4371006-2 gnd Genregulation (DE-588)4122166-7 gnd |
| subject_GND | (DE-588)4371006-2 (DE-588)4122166-7 (DE-588)4113937-9 |
| title | Exploring the role of structured DNA elements and their specific binders in genome regulation |
| title_auth | Exploring the role of structured DNA elements and their specific binders in genome regulation |
| title_exact_search | Exploring the role of structured DNA elements and their specific binders in genome regulation |
| title_full | Exploring the role of structured DNA elements and their specific binders in genome regulation vorgelegt von Michael Filarsky |
| title_fullStr | Exploring the role of structured DNA elements and their specific binders in genome regulation vorgelegt von Michael Filarsky |
| title_full_unstemmed | Exploring the role of structured DNA elements and their specific binders in genome regulation vorgelegt von Michael Filarsky |
| title_short | Exploring the role of structured DNA elements and their specific binders in genome regulation |
| title_sort | exploring the role of structured dna elements and their specific binders in genome regulation |
| topic | Antisense-Oligonucleotide (DE-588)4371006-2 gnd Genregulation (DE-588)4122166-7 gnd |
| topic_facet | Antisense-Oligonucleotide Genregulation Hochschulschrift |
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