Deposition, positioning and dynamics of H2A.Z in Saccharomyces cerevisiae:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
2012
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| Schlagworte: | |
| Online-Zugang: | Volltext https://nbn-resolving.org/urn:nbn:de:bvb:355-epub-254938 Inhaltsverzeichnis |
| Beschreibung: | IX, 138 S. Ill., graph. Darst. |
Internformat
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| 100 | 1 | |a Huber, Claudia |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Deposition, positioning and dynamics of H2A.Z in Saccharomyces cerevisiae |c vorgelegt von Claudia Huber |
| 264 | 1 | |c 2012 | |
| 300 | |a IX, 138 S. |b Ill., graph. Darst. | ||
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| 502 | |a Regensburg, Univ., Diss., 2012 | ||
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Datensatz im Suchindex
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| adam_text | IMAGE 1
TABLE OF CONTENTS
ABBREVIATIONS VII
1 SUMMARY 1
2 INTRODUCTION 3
2.1 NUCLEQSOME STRUCTURE 3
2.1.1 NUCLEOSOME POSITIONING 4
2.2 REGULATING FACTORS OF CHROMATIN 5
2.2.1 POSTTRANSLATIONAL MODIFICATIONS OFHISTONES 6
2.2.2 DAM METHYTATION 7
2.2.3 CHROMATIN REMODELING 7
2.2.4 HISTONE VARIANTS 9
2.3 CHROMATIN DYNAMICS 11
2.3.1 CHROMATIN DYNAMICS DURING REPLICATION 11
2.3.2 CHROMATIN DYNAMICS DURING TRANSCRIPTION 12
2.4 HISTONE VARIANT H2A.Z 13
2.4.1 UNIQUE PROPERTIES DISTINGUISH H2A.Z- FROM H2A-CONTAINING
NUCLEOSOMES 15
2.4.2 SPLICE ISOFORMS OFH2A.Z 18
2.4.3 SPECIALIZED FUNCTIONS 0FH2A.Z IB
2.4.4 H2A.Z SPECIFIC POSTTRANSLATIONAL MODIFICATION PATTERNS ASSOCIATED
WITH FUNCTION ....21
2.4.5 DEPOSITION OF H2A.Z INTO PRE-FORMED NUCLEOSOMES 22
3 OBJECTIVES 27
3.1 MECHANISMS OF H2A.Z DEPOSITION 27
3.2 IN VITRO AND IN VIVO POSITIONING DIFFERENCES OF HISTONE VARIANTS 27
3.3 NOVEL ROLES FOR THE H2A C-TERMINAL TAIL IN NUCLEOSOME STABILITY,
MOBILITY AND
BINDING OF LINKER HISTONE H1 28
4 RESULTS 29
4.1 DEPOSITION OF H2A.Z IN SACCHAROMYCES CEREVISIAE 29
4.1.1 PRELIMINARY ANALYSIS OF SELECTED GENOMIC REGIONS 29
4.1.2 KNOWN H2A.Z BINDING SITES CAN BE MAPPED USING CHROMATIN ENDOGENOUS
CLEAVAGE ANALYSIS (CHEC) 31
4.1.3 COTE HISTONES ARE ENRICHED AT PROMOTERS WHEN THEY ARE EXPRESSED
CONSTITUTIVELY. 33
4.1.4 H2A.Z IS DEPLETED WITHIN THE ORF REGION RATHER THAN ENRICHED AT
THE PROMOTER 38
4.1.5 H2A.Z DEPLETION FROM CODING REGIONS MIGHT CORRELATE WITH
TRANSCRIPTION LEVELS AT THE
RESPECTIVE GENES 40
4.1.6 THE H2A.Z DEPOSITION PATTERN IS ESTABLISHED INDEPENDENTLY OF THE
SWR COMPLEX. 44
HTTP://D-NB.INFO/1042071071
IMAGE 2
II
TABLE OF CONTENTS
4.1.7 CHIP ANALYSIS OF THE SWRC INFLUENCE 45
4.2 DYNAMICS AND POSITIONING OF VARIANT NUCLEOSOMES 49
4.2.1 VARIANT AND CANONICAL NUCLEOSOMES SHOW SIMILAR DYNAMICS DURING
THERMAL SLIDING49
4.2.2 POSITIONING DIFFERENCES OF VARIANT NUCLEOSOMES IN VITRO 50
4.2.3 CHEC SHOWS IN VIVO NUCLEOSOME POSITIONING DIFFERENCES 55
4.2.4 THE INOBO COMPLEX CONTRIBUTES TO NUCLEOSOME POSITIONING IN VIVO 56
4.3 HLSTONE H2A C-TERMINUS REGULATES CHROMATIN DYNAMICS, REMODELING AND
HISTONE
H1 BINDING 58
4.3.1 INFLUENCE OF THE H2A C-TERMINAL TAIL ON NUCLEOSOME ASSEMBLY AND
MOBILITY 58
4.3.2 TRUNCATIONS OF THE H2A C-TERMINUS AFFECT NUCLEOSOME REMODELING 59
4.3.3 THE C-TERMINUS OF H2A INTERACTS WITH LINKER HISTONE H1 61
5 DISCUSSION 63
5.1 MECHANISMS OF H2A.Z DEPOSITION 63
5.1.1 TRANSCRIPTION IS CRUCIAL FOR THE ESTABLISHMENT OF H2A.Z ENRICHMENT
PATTERNS 63
5.1.2 THE H2A.Z ENRICHMENT PATTERN IS ESTABLISHED INDEPENDENTLY OF THE
SWR COMPLEX 66
5.1.3 EXPLAINING CHEC AND CHIP DISCREPANCIES 67
5.2 DYNAMICS AND POSITIONING OF VARIANT NUCLEOSOMES 69
5.2.1 IN VIVO NUCLEOSOME STABILITY MIGHT DEPEND ON MORE THAN PURE
HISTONE CONTENT 69
5.2.2 H2A.Z INFLUENCES NUCLEOSOME POSITIONING IN VITRO AND IN VIVO 70
5.2.3 THE IN080 COMPLEX INFLUENCES NUCLEOSOME POSITIONS 73
5.3 HISTONE H2A C-TERMINUS REGULATES CHROMATIN DYNAMICS, REMODELING AND
HISTONE
H1 BINDING 74
5.3.1 DYNAMICS AND NUCLEOSOME POSITIONING ARE INFLUENCED BY THE H2A
C-TERMINAL TAIL. 74
5.3.2 THE H2A C-TERMINAL TAIL IS NECESSARY FOR EFFICIENT CHROMATIN
REMODELING 74
5.3.3 THE H2A C-TERMINUS AS A NEW TARGETING DOMAIN FORH1? 75
6 OUTLOOK TF
6.1 FURTHER EXPERIMENTS ON THE ROLE OF H2A.Z IN TRANSCRIPTION COMPETENT
CHROMATIN
STATES 77
6.2 IN VIVO POSITIONING OF H2A.Z 77
6.3 THE C-TERMINAL H2A TAIL AS A NEW FACTOR IN CHROMATIN REGULATION 78
7 MATERIAL 79
7.1 CHEMICALS : 79
7.2 BUFFERS AND MEDIA 79
7.3 NUCLEIC ACIDS 83
7.3.1 OLIGONUCLEOTIDES 83
7.3.2 PLASMIDS 92
7.3.3 DNA PROBES FOR SOUTHERN BLOT DETECTION 94
7.4 ENZYMES AND POLYPEPTIDES 95
7.5 ORGANISMS 95
IMAGE 3
TABLE OF CONTENTS
III
7.5.1 BACTERIA 95
7.5.2 YEAST STRAINS 95
7.6 SOFTWARE AND ONUNE TOOLS 97
7.6.1 SOFTWARE 97
7.6.2 ONLINE TOOLS 97
7.7 CONSUMABLES 98
7.8 APPARATUS 99
I METHODS 101
8.1 DNA 101
8.1.1 ENZYMATIC MANIPULATION OF DNA 101
8.1.2 PURIFICATION OF NUCLEIC ACIDS 102
8.1.3 QUANTITATIVE AND QUALITATIVE ANALYSIS OF NUCLEIC ACIDS 103
8.1.4 FORMALDEHYDE CROSSLINK 104
8.1.5 PREPARATION OF NUCLEI 104
8.1.0 CHROMATIN ENDOGENOUS CLEAVAGE (CHEC) 105
8.1.7 LLNSPECIFIC ENDONUDEASE DIGESTION (UNASE) 106
8.1.8 SOUTHERN BLOT, HYBRIDIZATION AND DETECTION OF RADIOACTIVE PROBES
106
8.1.9 CHROMATIN IMMUNO PRECIPITATION (CHIP) 108
8.1.10 QUANTITATIVE REAL-TIME PCR (QPCR) 109
8.2 MANIPULATION OF ESCHERICHIA COU 110
8.2.1 LIQUID CULTURE 110
8.2.2 GLYCEROL STOCK HO
8.2.3 PREPARATION OF CHEMICALLY COMPETENT BACTERIA 110
8.2.4 TRANSFORMATION OF COMPETENT BACTERIA HO
8.3 MANIPULATION OF SACCHAROMYCES CEREVISIAE 111
8.3.1 LIQUID CULTURE M
8.3.2 GLYCEROL STOCK M
8.3.3 PREPARATION OF COMPETENT YEAST CELLS 111
8.3.4 TRANSFORMATION OF COMPETENT YEAST CELLS 111
8.3.5 ESTABLISHMENT OF KNOCK OUT STRAINS 112
8.3.6 ESTABLISHMENT OF MNASE FUSION STRAINS FOR HISTONES EXPRESSED UNDER
THE CONTROL OF
THE H2A.Z PROMOTER. 112
8.4 PROTEIN-BIOCHEMICAL METHODS 112
8.4.1 DENATURING PROTEIN EXTRACTION FROM YEAST CELLS 112
8.4.2 SDS-POLYACRYLAMIDE GEL ELECTROPHORESIS 113
8.4.3 COOMASSIE STAINING OF SDS POLYACRYLAMIDE GELS 113
8.4.4 WESTERN BLOT, SEMI-DRY 11*
8.4.5 IMMUNODETECTION OF PMTEINS 11*
8.4.6 EXPRESSION AND PURIFICATION OF RECOMBINANT HISTONES 115
8.4.7 RECONSTITUTION OFHISTONE OCTAMERS 116
8.4.8 CHROMATIN RECONSTITUTION 117
IMAGE 4
IV TABLE OF CONTENTS
8:4.9 MOBILIZATION OF NUCLEOSOMES 118
9 BIBLIOGRAPHY 121
APPENDIX 135
LIST OF PUBLICATIONS 135
CONFERENCES 135
ACKNOWLEDGMENTS - DANKSAGUNG 137
|
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| spelling | Huber, Claudia Verfasser aut Deposition, positioning and dynamics of H2A.Z in Saccharomyces cerevisiae vorgelegt von Claudia Huber 2012 IX, 138 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Regensburg, Univ., Diss., 2012 Histon H2 (DE-588)4469522-6 gnd rswk-swf Chromatin (DE-588)4010152-6 gnd rswk-swf Saccharomyces cerevisiae (DE-588)4178812-6 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Saccharomyces cerevisiae (DE-588)4178812-6 s Chromatin (DE-588)4010152-6 s Histon H2 (DE-588)4469522-6 s b DE-604 Erscheint auch als Online-Ausgabe urn:nbn:de:bvb:355-epub-254938 http://epub.uni-regensburg.de/25493/ Verlag kostenfrei Volltext https://nbn-resolving.org/urn:nbn:de:bvb:355-epub-254938 Resolving-System DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=026158592&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Huber, Claudia Deposition, positioning and dynamics of H2A.Z in Saccharomyces cerevisiae Histon H2 (DE-588)4469522-6 gnd Chromatin (DE-588)4010152-6 gnd Saccharomyces cerevisiae (DE-588)4178812-6 gnd |
| subject_GND | (DE-588)4469522-6 (DE-588)4010152-6 (DE-588)4178812-6 (DE-588)4113937-9 |
| title | Deposition, positioning and dynamics of H2A.Z in Saccharomyces cerevisiae |
| title_auth | Deposition, positioning and dynamics of H2A.Z in Saccharomyces cerevisiae |
| title_exact_search | Deposition, positioning and dynamics of H2A.Z in Saccharomyces cerevisiae |
| title_full | Deposition, positioning and dynamics of H2A.Z in Saccharomyces cerevisiae vorgelegt von Claudia Huber |
| title_fullStr | Deposition, positioning and dynamics of H2A.Z in Saccharomyces cerevisiae vorgelegt von Claudia Huber |
| title_full_unstemmed | Deposition, positioning and dynamics of H2A.Z in Saccharomyces cerevisiae vorgelegt von Claudia Huber |
| title_short | Deposition, positioning and dynamics of H2A.Z in Saccharomyces cerevisiae |
| title_sort | deposition positioning and dynamics of h2a z in saccharomyces cerevisiae |
| topic | Histon H2 (DE-588)4469522-6 gnd Chromatin (DE-588)4010152-6 gnd Saccharomyces cerevisiae (DE-588)4178812-6 gnd |
| topic_facet | Histon H2 Chromatin Saccharomyces cerevisiae Hochschulschrift |
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