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| DC Field | Value | Language |
|---|---|---|
| dc.contributor.advisor | 곽준명 | - |
| dc.contributor.author | Seonghwan Kim | - |
| dc.date.accessioned | 2025-01-20T20:50:49Z | - |
| dc.date.available | 2025-01-20T20:50:49Z | - |
| dc.date.issued | 2024 | - |
| dc.identifier.uri | http://hdl.handle.net/20.500.11750/57565 | - |
| dc.identifier.uri | http://dgist.dcollection.net/common/orgView/200000798093 | - |
| dc.description | Abscission, Transdifferentiation, Single cell transcriptome, MYB74, KNAT1/BP, Residuum cell (REC), iREC and oREC, Fate transition | - |
| dc.description.tableofcontents | I. Background Introduction 1 1.1. Abscission 1 1.2. Abscission zone formation 4 1.3. Abscission induction 7 1.4. Cell Separation 11 1.5. Abscission zone scar sealing 12 1.6. Role of KNAT1/BP in non-epidermis to epidermis fate conversion 15 1.7. Thesis hypothesis and specific aim 17 II. The molecular mechanism of de novo specification of epidermis in Arabidopsis abscission zone 18 2.1. Introduction 18 2.2. Results 20 2.2.1. The scRNA-seq demonstrates three distinct developmental trajectories in RECs after abscission. 20 2.2.2. The photosynthesis genes disappear right after abscission in the outermost layer of RECs. 20 2.2.3. Stress-related genes maintain their expression until transdifferentiation is completed, after which their expression diminishes 23 2.2.4. The cuticle and epidermis markers are expressed during transdifferentiation, providing strong evidence for non-pidermis to epidermis fate transition in the RECs. 25 2.2.5. MYB74 plays a key role in transcriptomic changes during REC transdifferentiation 28 2.2.6. Validation of MYB74 expression pattern in the abscission zone suggests MYB74 might be important for the transdifferentiation 30 2.2.7. Loss of function of MYB74 and higher-order mutants did not exhibit a significant abscission zone phenotype. 32 2.2.8. Bulk RNA-seq of β-estradiol-inducible MYB74 overexpression plants reveals MYB74 inhibits the photosynthesis GOs and upregulates cuticle synthesis genes. 34 2.2.9. Comparative analyses of iMYB74 bulk RNA-seq and scRNA-seq data with MYB74 DAP-seq data suggest that MYB74 is a potential key player of transdifferentiation after abscission. 40 2.2.10. Overexpression of MYB74 leads to growth retardation and cuticle-like wax accumulation. 41 2.2.11. MYB74-SRDX plants have delayed transdifferentiation phenotype and developmental retardation of receptacles and siliques 45 2.2.12. Overexpression by prMYB74:MYB74-eYFP influenced cell morphology and cuticle formation specifically in the abscission zone. 45 2.2.13. MYB74 might inhibit the lignin synthesis to ensure proper receptacle growth by synthesizing the cuticle. 47 2.2.14. The abscission induction signaling and MYB74-mediated transdifferentiation might have an independent mechanism 49 2.3. Discussion 51 III. KNAT1/BP regulates fate conversion of the abscission zone 55 3.1. Background 55 3.2. Results 56 3.2.1. RECs are comprised of multiple layers 56 3.2.2. RECs of outermost cells can be transdifferentiated into epidermis 61 3.2.3. The KNAT1/BP is specifically expressed in iRECs after abscission 61 3.2.4. The loss of function of KNAT1/BP results in a phenotype characterized by the transdifferentiation of iRECs into oRECs-like cell fate 63 3.2.5. The BP-GFP protein cannot rescue the bp-3 phenotype 71 3.2.6. Spatiotemporal regulation of KNAT1/BP proteins has revealed their significance in the conversion of iRECs to oRECs fate in the abscission zone after abscission 73 3.2.7. iRECs exhibit distinct characteristics compared to oRECs 78 3.2.8. Relationship between fate regulation of RECs and AZ formation genes 80 3.2.9. HAESA-IDA abscission induction signaling is independent of KNAT1/BP expression pattern in the abscission zone 84 3.2.10. NEVERSHED is independent of IDA-HAE abscission induction signaling and is intertwined with receptacle morphology and cell fate 87 3.2.11. The maintenance of iREC by KNAT1/BP is crucial for the fitness of plant. 89 3.2.12. Molecular mechanism of KNAT1/BP to regulate fate change of RECs 91 3.3 Discussion 93 IV. Appendix 99 4. Beyond from the floral abscission zone to the organ boundary region in Arabidopsis 99 4.1. Introduction 99 4.2. Background 102 4.3. Results 103 4.4. Discussion 110 V. Materials & Methods in this thesis 111 5.1. Plant materials and growth condition 111 5.2. Plasmid construction and plant transfection 111 5.3. Inducible system construction for MYB74 (iMYB74) or MYB74-SRDX (iMYBY74-SRDX) in Arabidopsis and induction methods 112 5.4. Gus staining for gene expression pattern 113 5.5. Tissue clearing and confocal microscopic observation 113 5.6. Light-sheet microscopy 114 5.7. Permeability test for transdifferentiation in AZ 114 5.8. Dual luciferase assay and transient expression in Nicotiana benthamiana 115 5.9. EdU labeling assay 115 5.10. RNA extraction and quantitative real-time (qRT)-PCR 116 5.11. Preparation of protoplasts and fluorescence-activated cell sorting (FACS) 116 5.12. Single-cell RNA sequencing (scRNA-seq) 117 5.13. scRNA-seq data preprocessing and quality control 117 5.14. Signature score 118 5.15. Gene ontology (GO) enrichment analysis of scRNA-seq data 118 5.16. Trajectory inference 119 5.17. RNA velocity 119 5.18. Cell-type label transfer 120 5.19. Bulk RNA-seq data processing and analysis 120 5.20. Differential gene expression (DEG) analysis 120 5.21. Chromatin immunoprecipitation (ChIP) 121 5.22. Scanning electron microscopy 123 VI. Reference 128 Summary (korean) 152 |
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| dc.format.extent | 152 | - |
| dc.language | eng | - |
| dc.publisher | DGIST | - |
| dc.title | Molecular mechanism of transdifferentiation of residuum cells in the abscission zone of Arabidopsis thaliana | - |
| dc.type | Thesis | - |
| dc.identifier.doi | 10.22677/THESIS.200000798093 | - |
| dc.description.degree | Doctor | - |
| dc.contributor.department | Department of New Biology | - |
| dc.identifier.bibliographicCitation | Seonghwan Kim. (2024). Molecular mechanism of transdifferentiation of residuum cells in the abscission zone of Arabidopsis thaliana. doi: 10.22677/THESIS.200000798093 | - |
| dc.contributor.coadvisor | Soon-Ki Han | - |
| dc.date.awarded | 2024-08-01 | - |
| dc.publisher.location | Daegu | - |
| dc.description.database | dCollection | - |
| dc.citation | XT.ND 김54 202408 | - |
| dc.date.accepted | 2024-07-24 | - |
| dc.contributor.alternativeDepartment | 뉴바이올로지학과 | - |
| dc.subject.keyword | Abscission, Transdifferentiation, Single cell transcriptome, MYB74, KNAT1/BP, Residuum cell (REC), iREC and oREC, Fate transition | - |
| dc.contributor.affiliatedAuthor | Seonghwan Kim | - |
| dc.contributor.affiliatedAuthor | June M. Kwak | - |
| dc.contributor.affiliatedAuthor | Soon-Ki Han | - |
| dc.contributor.alternativeName | 김성환 | - |
| dc.contributor.alternativeName | June M. Kwak | - |
| dc.contributor.alternativeName | 한순기 | - |
| dc.rights.embargoReleaseDate | 2029-08-31 | - |
