Posttranscriptional regulation in the circadian system:
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| Format: | Abschlussarbeit Buch |
| Sprache: | English |
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Bielefeld
[2018]
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| Beschreibung: | viii, 214 Seiten Illustrationen 21 cm |
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| 100 | 1 | |a Nolte, Christine |e Verfasser |0 (DE-588)1171385897 |4 aut | |
| 245 | 1 | 0 | |a Posttranscriptional regulation in the circadian system |c vorgelegt von Christine Nolte |
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Datensatz im Suchindex
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| adam_text | CONTENTS
ACRONYMS VI
1
INTRODUCTION 1
1.1 POSTTRANSCRIPTIONAL REGULATION IN A. THALIANA I
1.1.1 MECHANISMS OF POSTTRANSCRIPTIONAL REGULATION 4
1.2 THE CIRCADIAN CLOCK 11
1.3 ATGRPJ AND AFGRP8 ACT AS SLAVE OSCILLATORS OF THE CIRCADIAN CLOCK 13
1.3.1 NEGATIVE AUTOREGULATION OF ATGBPJ AND ATGRP8 13
1.3.2 PHYSIOLOGICAL FUNCTIONS OF ATGRPJ 14
1.3.3 PHYSIOLOGICAL FUNCTIONS OF ATGRP8 15
1.4 POSTTRANSLATIONAL REGULATION 16
1.4.1 PHOSPHORYLATION 16
1.4.2 ARGININE METHYLATION 16
1.5 ABIOTIC STRESS 17
1.5.1 COLD STRESS 18
1.5.2 DROUGHT STRESS 21
1.6 OBJECTIVE OF THIS WORK 27
2 MATERIAL AND METHODS
29
2.1 PLANT MATERIAL 29
2.2 PLANT GROWTH 30
2.2.1 PLANT GROWTH ON MS MEDIUM 30
2.2.2 PLANT GROWTH ON SOIL 30
2.2.3 HARVEST OF PLANT MATERIAL 31
2.3 MOLECULAR METHODS 31
2.3.1 ISOLATION OF GENOMIC DNA (GDNA) 31
2.3.2 PLASMID PREPARATION 31
2.3.3 SEMIQUANTITATIVE POLYMERASE CHAIN REACTION (PCR) 32
2.3.4 AGAROSE GELS FOR DNA VISUALISATION 33
2.3.5 RESTRICTIONAL DIGEST 34
2.3.6 ISOLATION OF TOTAL RNA FROM PLANT MATERIAL 34
2.3.7 DNASE DIGEST AND REVERSE TRANSCRIPTION (RT) OF TOTAL RNA 35
2.3.8 REALTIME PCR (QPCR) 36
2.4 SAMPLE PREPARATION FOR THE RNA-SEQ 37
2.5 BIOCHEMICAL METHODS 37
2.5.1 PROTEIN ISOLATION FROM PLANTS 37
2.5.2 . SDS-PAGE 37
2.5.3 COOMASSIE BLUE STAINING OF THE SDS-PAGE 38
2.5.4 WESTERN BLOT 38
2.6 CLONING AND CROSSES 38
2.6.1 EXCHANGE OFR141 A IN
ATGRPJ BY RESTRICTIONAL DIGEST 38
2.6.2 GENERATION OF PRMT^/ATGRPY-I AND PRMTS/ATGRPY-I 8I LINES
BY CROSSING 41
2.7 DETERMINATION OF THE ANTHOCYANIN CONTENT 41
2.8 FLOWERING TIME AND BRANCHING ANALYSIS 42
2.9 DROUGHT ANALYSIS 42
2.9.1 SURVIVAL RATE 42
2.9.2 RELATIVE LEAF WATER CONTENT (RWC) 42
2.9.3 RELATIVE SOIL WATER CONTENT (SWC) 43
2.10 BIOINFORMATIC ANALYSIS 43
3
RESULTS
45
3.1 BIOINFORMATIC RNA-SEQ ANALYSIS 45
3.2 DIFFERENTIAL GENE EXPRESSION 47
3.2.1 TIMEPOINT SPECIFIC UP- AND DOWNREGULATION OF DEGS 50
3.2.2 COMPARISON OF DIFFERENTIALLY EXPRESSED GENES TO THE ATHI
MICROARRAY RESULTS 51
3.2.3 EXPERIMENTAL VALIDATION OF DEGS 52
3.2.4 DIRECT AND INDIRECT REGULATION THROUGH ATGRPY AND
ATGKP8 54
3.2.5 ENRICHMENT ANALYSIS REVEALS REGULATION OF TRANSCRIPTIONAL
NETWORKS 55
3.3 RHYTHMIC EXPRESSION PATTERNS 57
3.3.1 GENERAL CONSIDERATIONS OF THE ANALYSIS BY RSIN, DYNAMIC
TIME WARPING AND JTK CYCLE 57
3.3.2 CHANGES IN RHYTHMIC TRANSCRIPT EXPRESSION 59
3.3.3 PEAK SHIFTS IN AFGRP7~OX AND ATGRPY-I 8I 60
3.3.4 SHIFTS IN THE PEAK IN AFGRP8 PLANTS AND DAMPENING OF THE
PEAK EXPRESSION 61
3.4 ATGRP7 AND ATGRP8 ARE INVOLVED IN THE DROUGHT STRESS RESPONSE 64
3.4.1 SURVIVAL RATE 68
3.4.2 RELATIVE LEAF WATER POTENTIAL 68
3.4.3 GENE EXPRESSION DIFFERENCES DURING DROUGHT 69
3.4.4 TIMECOURSE DROUGHT STRESS EXPERIMENT 72
3.5 ALTERNATIVE SPLICING ANALYSIS OF RNA-SEQ DATA 79
3.5.1 SPLICING ANALYSIS BY CALCULATING THE DIFFERENTIAL TRANSCRIPT
USAGE 80
3.5.2 SPLICING ANALYSIS USING THE NEWLY DEVELOPED ASPLI SOFT
WARE 81
3.5.3 SPLICING ANALYSIS WITH SUPPA 82
3.5.4 COMPARISON OF THE SPLICING ANALYSIS TOOLS 83
3.6 TIMEPOINT SPECIFIC SPLICING ANALYSIS WITH SUPPA 84
3.6.1 DIRECTION OF REGULATION 86
3.6.2 REGIONAL DISTRIBUTION OF THE AS EVENTS 88
3.6.3 OVERLAP BETWEEN AS AND DEG 89
3.6.4 COMPARISON OF THE RNA-SEQ DATA WITH THE AS PANEL 90
3.6.5 EXPERIMENTAL VALIDATION OF THE SPLICING EVENTS REGULATED
BY ATGBPY 92
3.6.6 EXPERIMENTAL VALIDATION OF THE SPLICING EVENTS REGULATED
BY AFGRP8 97
3.6.7 DIRECT AND INDIRECT TARGETS OF ATGRP7 AND ATGRP8 98
3.6.8 GO TERM ANALYSIS 100
3.7 FUNCTIONAL ANALYSIS OF ABERRANTLY SPLICED EVENTS 101
3.7.1 ABERRANT SPLICING DURING COLD STRESS 101
3.7.2 ALTERNATIVE POLYADENYLATION 103
3.7.3 UPSTREAM OPEN READING FRAMES (UORFS) 105
3.8 INFLUENCE OF METHYLATION OF ATGKPY BY PRMT5 107
3.8.1 PHENOTYPIC ANALYSIS OF PRMTS/ATGRPY-I AND
PRMTS/ATGRPY-I
8I 107
3.8.2 BRANCHING IN AFGRP7-R141 A 112
4
D ISC U SS IO N
115
4.1 OPTIMIZATION OF THE RNA-SEQ ANALYSIS 115
4.1.1 OPTIMIZATION OF THE SPLICING ANALYSIS 116
4.1.2 TESTING FOR RHYTHMIC EXPRESSION PATTERNS 117
4.2 IDENTIFICATION AND VALIDATION OF NOVEL TARGETS 118
4.2.1 RNA-SEQ IDENTIFIES NOVEL TARGETS OF ATGRP7 AND AFGRP8
WITH ALTERED EXPRESSION LEVELS 118
4.2.2 RNA-SEQ IDENTIFIES RHYTHMIC EXPRESSION PATTERNS 120
4.2.3 ALTERED DROUGHT STRESS RESPONSE IN PLANTS MISEXPRESSING
ATGRPY 122
4.2.4 RNA-SEQ IDENTIFIES ABERRANT SPLICING IN ATGRP7- AND AFGRP8-
MISEXPRESSING PLANTS 124
4.3 FUNCTIONAL ROLE OF METHYLATION OF ATGRPY 129
4.3.1 METHYLATION OF R141 IS NOT NECESSARY FOR FLOWERING TIME
CONTROL BY ATGRPY 129
4.3.2 PRMT5 AND ATGRPY ARE INVOLVED IN BRANCHING 129
4.4 CONCLUSIONS AND FUTURE PERSPECTIVES 130
A
A P P E N D IX
133
BIBLIOGRAPHY
187
PUBLICATIONS 210
ERKLAERUNG 212
ACKNOWLEDGEMENTS
214
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| author_facet | Nolte, Christine |
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| building | Verbundindex |
| bvnumber | BV045544797 |
| ctrlnum | (OCoLC)1099925210 (DE-599)DNB1174707720 |
| discipline | Biologie |
| format | Thesis Book |
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| physical | viii, 214 Seiten Illustrationen 21 cm |
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| spelling | Nolte, Christine Verfasser (DE-588)1171385897 aut Posttranscriptional regulation in the circadian system vorgelegt von Christine Nolte Bielefeld [2018] viii, 214 Seiten Illustrationen 21 cm txt rdacontent n rdamedia nc rdacarrier Dissertation Universität Bielefeld 2018 (DE-588)4113937-9 Hochschulschrift gnd-content B:DE-101 application/pdf http://d-nb.info/1174707720/04 Inhaltsverzeichnis DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030928863&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Nolte, Christine Posttranscriptional regulation in the circadian system |
| subject_GND | (DE-588)4113937-9 |
| title | Posttranscriptional regulation in the circadian system |
| title_auth | Posttranscriptional regulation in the circadian system |
| title_exact_search | Posttranscriptional regulation in the circadian system |
| title_full | Posttranscriptional regulation in the circadian system vorgelegt von Christine Nolte |
| title_fullStr | Posttranscriptional regulation in the circadian system vorgelegt von Christine Nolte |
| title_full_unstemmed | Posttranscriptional regulation in the circadian system vorgelegt von Christine Nolte |
| title_short | Posttranscriptional regulation in the circadian system |
| title_sort | posttranscriptional regulation in the circadian system |
| topic_facet | Hochschulschrift |
| url | http://d-nb.info/1174707720/04 http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=030928863&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
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