Mechanisms of eukaryotic gene expression on a single molecule level: From transcription initiation to nucleosome remodeling:
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| Format: | Thesis Book |
| Language: | English |
| Published: |
München
Verl. Dr. Hut
2012
|
| Edition: | 1. Aufl. |
| Subjects: | |
| Online Access: | Inhaltstext Volltext https://nbn-resolving.org/urn:nbn:de:bvb:19-154993 Inhaltsverzeichnis |
| Physical Description: | XI, 188, XXVI S. Ill., graph. Darst. 240 mm x 170 mm, 468 g |
| ISBN: | 9783843905916 3843905916 |
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MARC
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| 245 | 1 | 0 | |a Mechanisms of eukaryotic gene expression on a single molecule level: From transcription initiation to nucleosome remodeling |c Barbara Treutlein |
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Record in the Search Index
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CONTENTS
CONTENTS XI
INTRODUCTION 1
1. TRANSCRIPTION AND CHROMATIN 7
1.1. STRUCTURE AND FUNCTION OF RNA POLYMERASE II 7
1.1.1. THE RNA POLYMERASE II TRANSCRIPTION CYCLE 7
1.1.2. STRUCTURE OF THE POL II ELONGATION COMPLEX 9
1.1.3. SPECIFIC FUNCTION OF INITIATION FACTORS 11
1.1.4. SINGLE MOLECULE STUDIES OF TRANSCRIPTION 11
1.2. CHROMATIN STRUCTURE AND DYNAMICS 15
1.2.1. CHROMATIN ORGANIZATION IN EUKARYOTES 15
1.2.2. NUCLEOSOME STABILITY AND DYNAMICS 17
1.2.3. CHROMATIN REMODELING COMPLEXES 18
1.2.4. THE CHD FAMILY OF CHROMATION REMODELERS 19
1.2.5. CHROMODOMAIN-HELICASE-DNA-BINDING PROTEIN 1 - CHDL 20
1.2.6. MECHANISMS OF NUCLEOSOME REPOSITIONING AND SPACING 23
1.2.7. SINGLE MOLECULE STUDIES OF NUCLEOSOME REMODELING 26
2. PHYSICAL BASICS 29
2.1. FLUORESCENCE 29
2.1.1. BASICS 29
2.1.2. FLUORESCENCE ANISOTROPY 32
2.1.3. FLUORESCENCE RESONANCE ENERGY TRANSFER (FRET) 32
2.1.4. FORSTER DISTANCE 34
2.1.5. SITE-SPECIFIC FLUORESCENT LABELING OF PROTEINS 36
2.1.6. SINGLE MOLECULE
FLUORESCENCE
37
2.2. TOTAL INTERNAL REFLECTION FLUORESCENCE MICROSCOPY (TIRFM) 38
2.2.1. EXPERIMENTAL SETUP 40
2.2.2. PREPARATION OF
FLOW
CHAMBER FOR SMFRET MEASUREMENTS 42
2.3. ACQUISITION, PROCESSING AND ANALYSIS OF SMFRET DATA 44
2.4. HIDDEN MARKOV MODELING (HMM) 48
IX
HTTP://D-NB.INFO/1026136237
CONTENTS
2.5. BAYESIAN DATA ANALYSIS AND THE NANO-POSITIONING SYSTEM 51
2.5.1. PROBABILITY CALCULUS 52
2.5.2. BAYESIAN PARAMETER ESTIMATION 53
2.5.3. BAYESIAN PARAMETER ESTIMATION IN THE GLOBAL NPS 53
3. DYNAMIC ARCHITECTURE OF A MINIMAL POL II OPEN PROMOTER COMPLEX 59
3.1. ABSTRACT 59
3.2. INTRODUCTION 60
3.3. RESULTS 61
3.3.1. ASSEMBLY OF OCS WITH LABELED DNA AND FACTORS 61
3.3.2. DOWNSTREAM DNA OCCUPIES THE POL II CLEFT 64
3.3.3. DYNAMIC LOADING OF DOWNSTREAM DNA INTO THE CLEFT 64
3.3.4. TFIIF STABILIZES DOWNSTREAM DNA IN POL II CLEFT 67
3.3.5. TBP AND TATA DNA RESIDE ABOVE THE CLEFT 70
3.3.6. UPSTREAM DNA IS STABILIZED BY INITIATION FACTORS 70
3.3.7. MODEL OF THE OC 71
3.3.8. B-CORE IS DISPLACED FROM THE WALL . YY 72
3.4. DISCUSSION 76
3.5. SUMMARY AND OUTLOOK 79
3.6. EXPERIMENTAL PROCEDURES 82
3.6.1. PROTEIN EXPRESSION, PURIFICATION AND LABELING 82
3.6.2. NUCLEIC ACID SCAFFOLDS 83
3.6.3. OPEN AND ELONGATION COMPLEX ASSEMBLY 83
3.6.4. ELECTROPHORETIC MOBILITY SHIFT ASSAY 84
3.6.5. IN VITRO TRANSCRIPTION ASSAY 84
3.6.6. SMFRET MEASUREMENTS: EXPERIMENTAL SETUP AND DATA ANALYSIS . . 84
3.6.7. HIDDEN MARKOV MODEL (HMM) ANALYSIS OF DYNAMIC SMFRET TIME
TRACES 85
3.6.8. GLOBAL NANO-POSITIONING SYSTEM ANALYSIS 85
3.6.9. MODELING 88
4. SINGLE MOLECULE FRET STUDIES OF NUCLEOSOME REMODELING BY CHDL 89
4.1. ABSTRACT 89
4.2. INTRODUCTION 90
4.3. PROBING CHDL INDUCED NUCLEOSOME DYNAMICS BY SMFRET .
L
91
4.3.1. RESULTS .91
4.3.2. DISCUSSION. . 112
4.4. ARCHITECTURE OF A CHDL-NUCLEOSOME COMPLEX 119
4.4.1. RESULTS 119
4.4.2. DISCUSSION 135
4.5. SUMMARY AND OUTLOOK 139
X
CONTENTS
4.6. EXPERIMENTAL PROCEDURES 142
4.6.1. BUFFERS 142
4.6.2. NUCLEOSOMAL DNA 143
4.6.3. LCR PREPARATION OF LABELED NUCLEOSOMAL DNA 144
4.6.4. PCR PREPARATION OF LABELED NUCLEOSOMAL DNA 145
4.6.5. SEC PURIFICATION OF LABELED NUCLEOSOMAL DNA 146
4.6.6. UNLABELED NUCLEOSOMAL AND COMPETITOR DNA 147
4.6.7. PREPARATION OF HISTONE OCTAMERS 148
4.6.8. NUCLEOSOME ASSEMBLY VIA SALT GRADIENT DIALYSIS 148
4.6.9. EXPRESSION AND PURIFICATION OF CHDL 150
4.6.10. LABELING OF CHDL 152
4.6.11. CHDL BINDING ASSAY * 152
4.6.12. NUCLEOSOME REMODELING ASSAY 153
4.6.13. OXYGEN-SCAVENGING SYSTEM AND TROLOX 154
4.6.14. SMFRET ANALYSIS OF NUCLEOSOME DYNAMICS INDUCED BY CHDL .
.
.
. 155
4.6.15.
HIDDEN
MARKOV
MODELING
(HMM) ANALYSIS OF
NUCLEOSOME DYNAMICS
156
4.6.16.
CHDL POSITIONING
EXPERIMENTS 157
4.6.17. GLOBAL NPS ANALYSIS OF A CHDL-NUCLEOSOME COMPLEX 157
5. OUTLOOK 163
A. SUPPLEMENTAL DATA 169
A.L. NPS ANALYSIS OF POL II OC 169
A.2. HMM ANALYSIS OF DYNAMIC FRET TRACES DURING CHDL REMODELING 175
A.3. NPS ANALYSIS OF CHDL-NUCLEOSOME COMPLEX 180
BIBLIOGRAPHY I
XI |
| any_adam_object | 1 |
| author | Treutlein, Barbara 1982- |
| author_GND | (DE-588)1032383224 |
| author_facet | Treutlein, Barbara 1982- |
| author_role | aut |
| author_sort | Treutlein, Barbara 1982- |
| author_variant | b t bt |
| building | Verbundindex |
| bvnumber | BV040889084 |
| collection | ebook |
| ctrlnum | (OCoLC)835563979 (DE-599)DNB1026136237 |
| dewey-full | 572.865 |
| dewey-hundreds | 500 - Natural sciences and mathematics |
| dewey-ones | 572 - Biochemistry |
| dewey-raw | 572.865 |
| dewey-search | 572.865 |
| dewey-sort | 3572.865 |
| dewey-tens | 570 - Biology |
| discipline | Biologie |
| edition | 1. Aufl. |
| format | Thesis Book |
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| spelling | Treutlein, Barbara 1982- Verfasser (DE-588)1032383224 aut Mechanisms of eukaryotic gene expression on a single molecule level: From transcription initiation to nucleosome remodeling Barbara Treutlein 1. Aufl. München Verl. Dr. Hut 2012 XI, 188, XXVI S. Ill., graph. Darst. 240 mm x 170 mm, 468 g txt rdacontent n rdamedia nc rdacarrier Zugl.: München, Univ., Diss., 2012 Einzelmolekülspektroskopie (DE-588)4396226-9 gnd rswk-swf Fluoreszenz-Resonanz-Energie-Transfer (DE-588)4773018-3 gnd rswk-swf Eukaryontische Zelle (DE-588)4153142-5 gnd rswk-swf Genexpression (DE-588)4020136-3 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Eukaryontische Zelle (DE-588)4153142-5 s Genexpression (DE-588)4020136-3 s Einzelmolekülspektroskopie (DE-588)4396226-9 s Fluoreszenz-Resonanz-Energie-Transfer (DE-588)4773018-3 s DE-604 Erscheint auch als Online-Ausgabe urn:nbn:de:bvb:19-154993 X:MVB text/html http://deposit.dnb.de/cgi-bin/dokserv?id=4125196&prov=M&dok_var=1&dok_ext=htm Verlag kostenfrei Inhaltstext http://edoc.ub.uni-muenchen.de/15499/ Verlag kostenfrei Volltext https://nbn-resolving.org/urn:nbn:de:bvb:19-154993 Resolving-System DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025868772&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Treutlein, Barbara 1982- Mechanisms of eukaryotic gene expression on a single molecule level: From transcription initiation to nucleosome remodeling Einzelmolekülspektroskopie (DE-588)4396226-9 gnd Fluoreszenz-Resonanz-Energie-Transfer (DE-588)4773018-3 gnd Eukaryontische Zelle (DE-588)4153142-5 gnd Genexpression (DE-588)4020136-3 gnd |
| subject_GND | (DE-588)4396226-9 (DE-588)4773018-3 (DE-588)4153142-5 (DE-588)4020136-3 (DE-588)4113937-9 |
| title | Mechanisms of eukaryotic gene expression on a single molecule level: From transcription initiation to nucleosome remodeling |
| title_auth | Mechanisms of eukaryotic gene expression on a single molecule level: From transcription initiation to nucleosome remodeling |
| title_exact_search | Mechanisms of eukaryotic gene expression on a single molecule level: From transcription initiation to nucleosome remodeling |
| title_full | Mechanisms of eukaryotic gene expression on a single molecule level: From transcription initiation to nucleosome remodeling Barbara Treutlein |
| title_fullStr | Mechanisms of eukaryotic gene expression on a single molecule level: From transcription initiation to nucleosome remodeling Barbara Treutlein |
| title_full_unstemmed | Mechanisms of eukaryotic gene expression on a single molecule level: From transcription initiation to nucleosome remodeling Barbara Treutlein |
| title_short | Mechanisms of eukaryotic gene expression on a single molecule level: From transcription initiation to nucleosome remodeling |
| title_sort | mechanisms of eukaryotic gene expression on a single molecule level from transcription initiation to nucleosome remodeling |
| topic | Einzelmolekülspektroskopie (DE-588)4396226-9 gnd Fluoreszenz-Resonanz-Energie-Transfer (DE-588)4773018-3 gnd Eukaryontische Zelle (DE-588)4153142-5 gnd Genexpression (DE-588)4020136-3 gnd |
| topic_facet | Einzelmolekülspektroskopie Fluoreszenz-Resonanz-Energie-Transfer Eukaryontische Zelle Genexpression Hochschulschrift |
| url | http://deposit.dnb.de/cgi-bin/dokserv?id=4125196&prov=M&dok_var=1&dok_ext=htm http://edoc.ub.uni-muenchen.de/15499/ https://nbn-resolving.org/urn:nbn:de:bvb:19-154993 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=025868772&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT treutleinbarbara mechanismsofeukaryoticgeneexpressiononasinglemoleculelevelfromtranscriptioninitiationtonucleosomeremodeling |