Functional analysis of the role of GRF9 in leaf development and establishment of Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE) in Arabidopsis thaliana:
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| Format: | Thesis Book |
| Language: | English |
| Published: |
2014
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| Subjects: | |
| Online Access: | Inhaltsverzeichnis Inhaltsverzeichnis |
| Physical Description: | 10 Bl., 162 S. Ill., graph. Darst. |
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MARC
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| 100 | 1 | |a Omidbakhshfard, Mohammad Amin |e Verfasser |0 (DE-588)1073670279 |4 aut | |
| 245 | 1 | 0 | |a Functional analysis of the role of GRF9 in leaf development and establishment of Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE) in Arabidopsis thaliana |c von Mohammad Amin Omidbakhshfard |
| 264 | 1 | |c 2014 | |
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| _version_ | 1804174826161569792 |
|---|---|
| adam_text | CONTENTS
SUMMARY III
ZUSAMMENFASSUNG IX
ACKNOWLEDGMENTS XI
1 GENERAL INTRODUCTION 1
1.1 PLANT GROWTH AND DEVELOPMENT 1
1.1.1 LEAF INITIATION IS THE FIRST STEP OF LEAF DEVELOPMENT 2
1.1.2 PRIMARY MORPHOGENESIS OR CELL PROLIFERATION 3
1.1.3 TRANSITION FROM CELL PROLIFERATION TO CELL EXPANSION 6
1.1.4 CELL EXPANSION OR SECONDARY MORPHOGENESIS 7
1.1.5 COORDINATION OF CELL PROLIFERATION AND CELL EXPANSION 10
1.1.5.1 COMPENSATION IN LEAVES 11
1.1.5.2 HETEROBLASTY 11
1.1.6 GROWTH CONTROL BY PHYTOHORMONES 12
1.1.7 OTHER PARAMETERS AFFECTING LEAF GROWTH 13
1.2 REGULATION OF GENE EXPRESSION 14
1.2.1 CHROMATIN STRUCTURE AND NUCLEOSOME 15
1.2.2 DIFFERENT TECHNIQUES TO ISOLATE DNA REGULATORY ELEMENTS
GENOME-WIDE 15
1.3 THESIS STATEMENT 20
2 GROWTH-REGULATING FACTOR 9 NEGATIVELY REGULATES ARABIDOPSIS LEAF
GROWTH
BY RESTRICTING THE CELL PROLIFERATION AREA 23
2.1 ABSTRACT 24
2.2 INTRODUCTION 25
2.3 RESULTS 26
2.3.1 EXPRESSION ANALYSIS OF GRF9 26
2.3.2 GRF9 MUTANTS AND GRF9 OVEREXPRESSION PHENOTYPE 27
2.3.3 GRF9 AND GRF9OX PLANTS SHOW SIMILAR CELL PROLIFERATION KINETICS 29
2.3.4 GRF9 MUTANTS HAVE AN EXPANDED CELL PROLIFERATING AREA WITHIN LEAF
PRIMORDIA 31
2.3.5 GRF9 BINDING SITE IDENTIFICATION 33
HTTP://D-NB.INFO/1072248522
2.3.6 GENES AFFECTED BY ELEVATED GRF9 EXPRESSION 33
2.3.7 GRF9 BINDS IN VITRO TO THE ORG3 AND AT4GL2500 PROMOTERS 35
2.3.8 IN VIVO BINDING OF GRF9 TO THE ORG3 PROMOTER 36
2.3.9 TRANSACTIVATION OF THE ORG3 PROMOTER IN MESOPHYLL CELL PROTOPLASTS
37
2.3.10 ORG3 RESTRICTS ORGAN SIZE 37
2.4 DISCUSSION 38
2.4.1 GRF9 EXPRESSION IN LEAVES IS LIMITED TO THE PROLIFERATING ZONE AND
VASCULAR TISSUE 39
2.4.2 GRF9 RESTRICTS CELL PROLIFERATING AREA IN THE LEAF PRIMORDIUM 39
2.4.3 STRESS AND ABA RELATED GENES ARE AMONG THE GRF9 EARLY RESPONSIVE
GENES 41
2.4.4 GRF9 BINDING SITE CONTAINS A CONSERVED MOTIF IN MONO AND DICOTS 41
2.4.5 ORG3 IS A DIRECT TARGET OF GRF9 AND FUNCTIONS IN EARLY LEAF GROWTH
42
2.4.6 FUNCTIONAL CHARACTERIZATION OF ORG3/BHLH39 43
2.5 MATERIALS AND METHODS 44
2.5.1 GENERAL 44
2.5.2 PLANT MATERIAL AND GROWTH CONDITIONS 44
2.5.3 CONSTRUCTS 44
2.5.4 IN VITRO BINDING-SITE SELECTION 45
2.5.5 GRF9 BINDING ASSAY 45
2.5.6 GENE EXPRESSION ANALYSIS BY MICROARRAY HYBRIDISATION 46
2.5.7 QUANTITATIVE RT-PCR 46
2.5.8 MICROSCOPIC ANALYSES 46
2.5.9 VISUALIZATION OF CELL PROLIFERATING WITH 5-ETHYNYL-2 -DEOXYURIDINE
(EDU) 46
2.5.10 GUS ASSAYS 47
2.5.11 ELECTROPHORETIC MOBILITY SHIFT ASSAY (EMSA) 47
2.5.12 TRANSACTIVATION ASSAY 47
2.5.13 CHLP-QPCR 47
B GROWTH-REGULATING FACTORS (GRFS): A SMALL TRANSCRIPTION FACTOR FAMILY
WITH IMPORTANT FUNCTIONS IN PLANT BIOLOGY 49
3.1 ABSTRACT 50
3.2 INTRODUCTION 51
3.3 STRUCTURAL FEATURES OF GRF TRANSCRIPTION FACTORS 51
3.4 FUNCTIONS OF GRFS IN ARABIDOPSIS 52
3.5 A MIR396/GRF REGULATORY MODULE 54
3.6 GRFS IN RICE 55
3.7 FLORAL ORGAN DEVELOPMENT 57
3.8 GRFS AND ROOTS 58
3.9
GRFS AND LONGEVITY
58
3.10 GRFS ARE UPSTREAM REPRESSORS OF KNOX GENES 59
3.11 A GRF AFFECTING SEED WEIGHT AND OIL CONTENT 60
3.12 GRFS COORDINATE PLANT GROWTH WITH STRESS RESPONSES 61
3.13 GRFS IN OTHER SPECIES 62
3.14 GRF-LNTERACTING FACTORS (GIFS) 64
3.15 GRFS EXPANDED THROUGH LARGE-SCALE GENOME DUPLICATION AND GENE
RETENTION 67
3.16 CONCLUSIONS AND PERSPECTIVES 68
4 A STEP-BY-STEP PROTOCOL FOR FORMALDEHYDE-ASSISTED ISOLATION OF
REGULATORY
ELEMENTS FROM ARABIDOPSIS THALIANA 69
4.1 ABSTRACT 70
4.2 INTRODUCTION 71
4.3 RESULTS 73
4.3.1 A FAIRE PROTOCOL FOR ARABIDOPSIS 73
4.3.2 IDENTIFICATION OF FAIRE-PEAKS 75
4.4 DISCUSSION 77
4.5 MATERIALS AND METHODS 79
4.5.1 PLANTS 79
4.5.2 REAGENTS 79
4.5.3 SOLUTIONS 80
4.5.4 STEP-BY-STEP PROTOCOL FOR NDR ISOLATION BY FAIRE 80
4.5.4.1 SAMPLING OF PLANT MATERIAL 80
4.5.4.2 FORMALDEHYDE CROSSLINKING (FIXATION) 82
4.5.4.3 ISOLATION AND SONICATION OF CHROMATIN 83
4.5.4.4 ISOLATION OF NDRS 85
5 COMPUTATIONAL ANALYSIS PIPELINE FOR IDENTIFICATION AND ANNOTATION OF
TRANSCRIPTIONAL REGULATORY REGIONS FROM FAIRE-SEQ DATASETS: A CASE STUDY
ON
GENOME-WIDE ISOLATION OF REGULATORY ELEMENTS UNDER OXIDATIVE STRESS IN
ARABIDOPSIS THALIANA
87
5.1 ABSTRACT 88
5.2 INTRODUCTION 89
5.3 MATERIALS AND METHODS 91
5.3.1 PLANT GROWTH CONDITIONS AND 3-AT TREATMENT 91
5.3.2 QUANTITATIVE PCR 91
5.3.3 RNA EXTRACTION AND GENE EXPRESSION ANALYSIS BY MICROARRAY 92
5.3.4 DEEP SEQUENCING 92
5.3.5 IMPLEMENTATION OF THE PIPELINE 92
5.3.5.1 OVERVIEW 92
5.3.5.2 PRE-PROCESSING OF READS: QUALITY CONTROL AND CLEANING/FILTERING
94
5.3.5.3 SHORT-READ MAPPING 94
5.3.5.4 PEAK CALLING 94
5.3.5.5 FINDING NEIGHBOURING GENOMIC FEATURES: EXPLOITING GENOME
ANNOTATION 96
5.3.5.6 INTERSECTION ANALYSIS 97
5.3.5.7 GENE ONTOLOGY (GO) TERM ENRICHMENT ANALYSIS 97
5.3.5.8 IDENTIFICATION OF DNA SEQUENCE MOTIFS 98
5.4 RESULTS AND DISCUSSION 98
5.4.1 GLOBAL EXPRESSION PROFILES OF H
2
0
2
-INDUCED GENES 102
5.4.2 NDRS IN PROMOTER REGIONS OF GENES HIGHLY INDUCED AFTER 3-AT
TREATMENT 103
5.5 CONCLUSIONS 105
5.5.1 AVAILABILITY AND REQUIREMENTS 106
6 GENERAL DISCUSSION AND FUTURE DIRECTIONS 107
6.1 GROWTH-REGULATING FACTORS (GRFS) 107
6.2 GRF9 AND ITS FUNCTIONS IN LEAF DEVELOPMENT 107
6.2.1 GRF9 RESTRICTS THE CELL PROLIFERATING AREA IN THE LEAF PRIMORDIUM
109
6.3 FURTHER CHARACTERIZATION OF THE GRF9 REGULATORY NETWORK 113
6.4 ISOLATION OF NUCLEOSOME-DEPLETED REGIONS USING FAIRE 115
6.5 FUTURE WORKS FOR FAIRE 118
BIBLIOGRAPHY 119
SUPPLEMENTARY FILES 139
AUTHOR CONTRIBUTIONS 163
DECLARATION
165
|
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| author | Omidbakhshfard, Mohammad Amin |
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| indexdate | 2024-07-10T07:06:33Z |
| institution | BVB |
| language | English |
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| physical | 10 Bl., 162 S. Ill., graph. Darst. |
| publishDate | 2014 |
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| spelling | Omidbakhshfard, Mohammad Amin Verfasser (DE-588)1073670279 aut Functional analysis of the role of GRF9 in leaf development and establishment of Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE) in Arabidopsis thaliana von Mohammad Amin Omidbakhshfard 2014 10 Bl., 162 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Potsdam, Univ., Diss., 2014 Ackerschmalwand (DE-588)4141299-0 gnd rswk-swf Genregulation (DE-588)4122166-7 gnd rswk-swf (DE-588)4113937-9 Hochschulschrift gnd-content Ackerschmalwand (DE-588)4141299-0 s Genregulation (DE-588)4122166-7 s DE-604 DE-601 pdf/application http://www.gbv.de/dms/tib-ub-hannover/827011431.pdf Inhaltsverzeichnis DNB Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028074130&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Omidbakhshfard, Mohammad Amin Functional analysis of the role of GRF9 in leaf development and establishment of Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE) in Arabidopsis thaliana Ackerschmalwand (DE-588)4141299-0 gnd Genregulation (DE-588)4122166-7 gnd |
| subject_GND | (DE-588)4141299-0 (DE-588)4122166-7 (DE-588)4113937-9 |
| title | Functional analysis of the role of GRF9 in leaf development and establishment of Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE) in Arabidopsis thaliana |
| title_auth | Functional analysis of the role of GRF9 in leaf development and establishment of Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE) in Arabidopsis thaliana |
| title_exact_search | Functional analysis of the role of GRF9 in leaf development and establishment of Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE) in Arabidopsis thaliana |
| title_full | Functional analysis of the role of GRF9 in leaf development and establishment of Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE) in Arabidopsis thaliana von Mohammad Amin Omidbakhshfard |
| title_fullStr | Functional analysis of the role of GRF9 in leaf development and establishment of Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE) in Arabidopsis thaliana von Mohammad Amin Omidbakhshfard |
| title_full_unstemmed | Functional analysis of the role of GRF9 in leaf development and establishment of Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE) in Arabidopsis thaliana von Mohammad Amin Omidbakhshfard |
| title_short | Functional analysis of the role of GRF9 in leaf development and establishment of Formaldehyde Assisted Isolation of Regulatory Elements (FAIRE) in Arabidopsis thaliana |
| title_sort | functional analysis of the role of grf9 in leaf development and establishment of formaldehyde assisted isolation of regulatory elements faire in arabidopsis thaliana |
| topic | Ackerschmalwand (DE-588)4141299-0 gnd Genregulation (DE-588)4122166-7 gnd |
| topic_facet | Ackerschmalwand Genregulation Hochschulschrift |
| url | http://www.gbv.de/dms/tib-ub-hannover/827011431.pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=028074130&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA |
| work_keys_str_mv | AT omidbakhshfardmohammadamin functionalanalysisoftheroleofgrf9inleafdevelopmentandestablishmentofformaldehydeassistedisolationofregulatoryelementsfaireinarabidopsisthaliana |
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