Studies of the role of nucleosome-remodelling complexes & activity on cell-type specific gene regulation by RelB:
Gespeichert in:
| 1. Verfasser: | |
|---|---|
| Format: | Abschlussarbeit Buch |
| Sprache: | English |
| Veröffentlicht: |
2013
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| Schlagworte: | |
| Online-Zugang: | Inhaltsverzeichnis |
| Beschreibung: | 172 Bl. Ill., graph. Darst. |
Internformat
MARC
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| 100 | 1 | |a Oruba, Agata |e Verfasser |4 aut | |
| 245 | 1 | 0 | |a Studies of the role of nucleosome-remodelling complexes & activity on cell-type specific gene regulation by RelB |c Agata Oruba |
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Datensatz im Suchindex
| _version_ | 1804150753521041408 |
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| adam_text | IMAGE 1
TABLE OF CONTENTS
ABBREVIATIONS 4
SUMMARY 6
1. INTRODUCTION 8
1.1 NF-KB AS A MODEL SYSTEM TO STUDY TRANSCRIPTIONAL SPECIFICITY 8
1.1.1 NF-KB FAMILY OF TRANSCRIPTION FACTORS 8
1.1.2 THE COMPLEXITY AND SPECIFICITY OF THE INFLAMMATORY RESPONSE 10
1.1.3 CELL-TYPE SPECIFICITY OF INFLAMMATION: MYELOID DCS AND FIBROBLASTS
11
1.1.4 RELB HAS A CELL-TYPE SPECIFIC PHENOTYPE 13
1.2 THE ROLE OF CHROMATIN IN NF-ICB-DEPENDENT TRANSCRIPTIONAL RESPONSES
14
1.2.1 TWO CLASSES OF NF-KB REGULATED GENES 14
1.2.2 CHROMATIN REMODELLING AT NF-KB DEPENDENT GENES 15
1.2.3 KB SITES AND NUCLEOSOMES 17
1.3 DETERMINANTS OF NUCLEOSOME POSITIONING 19
1.3.1 CHROMATIN STRUCTURE AND NUCLEOSOME POSITIONING AT PROMOTERS 19
1.3.2 THE ROLE OF DNA SEQUENCE IN NUCLEOSOME POSITIONING 22
1.3.3 THE EFFECT OF TRANSCRIPTION AND ELONGATING POL-LL ON NUCLEOSOME
POSITIONING 24
1.3.4 THE ROLE OF NUCLEOSOME REMODELERS IN POSITIONING OF THE
NUCLEOSOMES 25
1.3.5 THE ROLE OF NUCLEOSOME ORGANIZATION IN TRANSCRIPTION 27
1.4 SWI/SNF CHROMATIN-REMODELLING COMPLEXES 28
1.4.1 SWI/SNF SUBUNITS AND THEIR COMBINATORIAL ASSEMBLY 28
1.4.2 SWI/SNF MECHANISM OF ACTION AND TARGETING TO CHROMATIN 31
1.5 MECHANISMS OF TRANSCRIPTIONAL ACTIVATION AND REPRESSION 32
1.5.1 GENE ACTIVATION 32
1.5.2 GENE REPRESSION 35
1.5.3 CONCLUDING PERSPECTIVE 37
2. AIMS OF THE STUDY 38
3. MATERIALS AND METHODS 39
3.1 MATERIALS 39
1
HTTP://D-NB.INFO/1042398240
IMAGE 2
3.1.1 REAL-TIME PCR OLIGONUCLEOTIDES 39
3.1.2 CHIP OLIGONUCLEOTIDES 40
3.1.3 ANTIBODIES 41
3.1.4 BUFFERS 41
3.2 METHODS 43
3.2.1 PLASMIDS 43
3.2.2 CELL CULTURE 44
3.2.3 CO-IMMUNOPRECIPITATION (CO-IP) AND WESTERN BLOT 45
3.2.4 BI-MOLECULAR FLUORESCENCE COMPLEMENTATION (BIFC) 46
3.2.5 MRNA EXPRESSION ANALYSIS BY REAL-TIME PCR 46
3.2.6 CHROMATIN IMMUNOPRECIPITATION (CHIP) 47
3.2.7 QUANTIFICATION OF ABSOLUTE MRNA LEVELS OF SWI/SNF PROTEINS 48
3.2.8 CHLP-MNASE-SEQ: A NOVEL METHOD FOR MAPPING NUCLEOSOMES
AT TRANSCRIPTIONAL REGULATORY REGIONS 49
3.2.9 BIOINFORMATICS ANALYSIS OF CHLP-MNASE-SEQ DATA 53
4. RESULTS 60
4.1 CAN CELL-TYPE SPECIFICITY OF RELB BE EXPLAINED BY ITS ASSOCIATION
WITH CELL-TYPE SPECIFIC COFACTORS? 60
4.1.1 RELB HAS A CELL-TYPE SPECIFIC PHENOTYPE 60
4.1.2 IN FIBROBLASTS RELB PRE-BINDS PROMOTERS OF ITS TARGET GENES BEFORE
STIMULATION 62
4.1.3 META-ANALYSIS OF PUBLISHED PROTEOMIC DATA-SETS REVEALS THAT RELB
INTERACTS
WITH SWI/SNF CHROMATIN REMODELLING COMPLEX 64
4.1.4 RELB INTERACTS WITH SWI/SNF COMPLEX VIA ITS DIMERIZATION DOMAIN 69
4.1.5 SWI/SNF COMPLEX HAS CELL-TYPE SPECIFIC COMPOSITION 78
4.1.6 SWI/SNF COMPLEX HAS CELL-TYPE SPECIFIC BEHAVIOUR 83
4.1.7 CELL-TYPE SPECIFIC BEHAVIOUR OF SWI/SNF CAN BE AFFECTED BY
ALTERING ITS
SUBUNIT COMPOSITION 86
4.2 IS NF-KB TARGET GENE ACTIVITY CONTROLLED BY NUCLEOSOME POSITIONING?
91
4.2.1 CHLP-MNASE-SEQ: A NOVEL METHOD FOR MAPPING NUCLEOSOMES AT
TRANSCRIPTIONAL REGULATORY REGIONS 91
4.2.2 INITIAL ANALYSIS OF NUCLEOSOME POSITIONS AT TRANSCRIPTIONAL
REGULATORY REGIONS 102
5. DISCUSSION 129
2
IMAGE 3
5.1 MECHANISMS EXPLAINING THE DUAL FUNCTION OF RELB 129
5.1.1 RELB INTERACTS WITH SEVERAL PROTEINS BELONGING TO THE SWI/SNF
CHROMATINREMODELLING COMPLEX 130
5.1.1.1 RELB INTERACTS WITH THE SWI/SNF COMPLEX VIA ITS CONSERVED DIM
DOMAIN 132
5.1.2 GENERATION OF SWI/SNF INTERACTION-DEFICIENT MUTANT OF RELB 133
5.1.3 SWI/SNF COMPLEX HAS CELL-TYPE SPECIFIC COMPOSITION THAT DICTATES
ITS CELL-TYPE SPECIFIC FUNCTION 134
5.1.4 CELL-TYPE SPECIFICITY OF RELB: CONCLUDING REMARKS 136
5.2 MAPPING OF NUCLEOSOME POSITIONS TO UNDERSTAND THEIR ROLE IN
CELL-TYPE
SPECIFIC TRANSCRIPTION 137
5.2.1 DEVELOPMENT OF THE NEW METHOD FOR MAPPING NUCLEOSOME POSITIONS AT
REGULATORY REGIONS OF GENES 138
5.2.2 VALIDATION OF THE NEWLY ESTABLISHED METHOD FOR MAPPING OF
NUCLEOSOME
POSITIONS IN THE TRANSCRIPTIONAL REGULATORY REGIONS 142
5.2.3 FUTURE PERSPECTIVES 147
5.2.4 SUMMARY 149
6. REFERENCES 150
3
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| indexdate | 2024-07-10T00:43:56Z |
| institution | BVB |
| language | English |
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| physical | 172 Bl. Ill., graph. Darst. |
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| spelling | Oruba, Agata Verfasser aut Studies of the role of nucleosome-remodelling complexes & activity on cell-type specific gene regulation by RelB Agata Oruba 2013 172 Bl. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Freiburg (Breisgau), Univ., Diss., 2013 (DE-588)4113937-9 Hochschulschrift gnd-content DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=026255299&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Oruba, Agata Studies of the role of nucleosome-remodelling complexes & activity on cell-type specific gene regulation by RelB |
| subject_GND | (DE-588)4113937-9 |
| title | Studies of the role of nucleosome-remodelling complexes & activity on cell-type specific gene regulation by RelB |
| title_auth | Studies of the role of nucleosome-remodelling complexes & activity on cell-type specific gene regulation by RelB |
| title_exact_search | Studies of the role of nucleosome-remodelling complexes & activity on cell-type specific gene regulation by RelB |
| title_full | Studies of the role of nucleosome-remodelling complexes & activity on cell-type specific gene regulation by RelB Agata Oruba |
| title_fullStr | Studies of the role of nucleosome-remodelling complexes & activity on cell-type specific gene regulation by RelB Agata Oruba |
| title_full_unstemmed | Studies of the role of nucleosome-remodelling complexes & activity on cell-type specific gene regulation by RelB Agata Oruba |
| title_short | Studies of the role of nucleosome-remodelling complexes & activity on cell-type specific gene regulation by RelB |
| title_sort | studies of the role of nucleosome remodelling complexes activity on cell type specific gene regulation by relb |
| topic_facet | Hochschulschrift |
| url | http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=026255299&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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