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Microarray Analysis of Differential Expression of Genes in Shoot Apex and Young Leaf of English Ivy (Hedera Helix L

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Microarray Analysis of Differential Expression of Genes in Shoot Apex and Young Leaf of English Ivy (Hedera Helix L MICROARRAY ANALYSIS OF DIFFERENTIAL EXPRESSION OF GENES IN SHOOT APEX AND YOUNG LEAF OF ENGLISH IVY (HEDERA HELIX L. CV. GOLDHEART) Seung-Geuk Shin A Dissertation Submitted to the Graduate College of Bowling Green State University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY August 2010 Committee: Dr. Scott O. Rogers, Advisor Dr. Kit C. Chan Graduate Faculty Representative Dr. Carmen F. Fioravanti Dr. Helen Michaels Dr. Paul F. Morris ii ABSTRACT Scott O. Rogers, Advisor Shoot apical meristems (SAMs) of higher plants maintain a population of pluripotent cells which continue to divide throughout the life of plant and provide cells for development of all the above-ground organs after embryogenesis. Since the plant is sessile, maintenance of stem cells in the SAM and appropriate differentiation are crucial for the plants to adapt to the changing environments. Shoot apex of the plant is the very tip of the shoot, in which the SAM resides. To analyze the differential gene expression patterns between the shoot apex and the very young leaf, transcriptomes from the two tissue types of a variegated variety of English ivy (Hedera helix L. cv. Goldheart) plants, were hybridized on Arabidopsis thaliana cDNA microarrays, using cross-species hybridization (CSH). Among 11,255 cDNA probes excluding ‘BLANK’ and ‘bad’ spots, 2,597 features produced signals that were greater than background levels, which constitutes 23% of the total number of usable probes on the microarray. One hundred seventy four genes were expressed statistically differentially (fold change >=2 and p=0.05). Of these, 60 were in the shoot apex and 114 were in the young leaf. Functional categorization based on the genome/protein databases and a pathway analysis revealed some of the tissue-specific biological processes and identified some of the genes involved. The annotated and/or predicted roles of those genes in the tissue-specific biological processes were described and discussed in relation to the plant development. iii I dedicate this dissertation to my parents, wife and daughter. Without their patience, encouragement, support, and most of all love, the completion of this work would not have been possible. iv ACKNOWLEDGEMENTS This dissertation would not be complete without expressing the deepest appreciation to my academic advisor, Professor Scott Orland Rogers, who continually and patiently supported me from the initiation to the end of this research project. Without his guidance and persistent help this dissertation would not have been possible. I would like to thank my dissertation committee members, Professor Carmen F. Fioravanti, Professor Helen Michaels and Professor Paul F. Morris whose productive suggestions and recommendations broadened my view on the subject. In addition, I thank Professor Kit C. Chan, the Graduate Faculty Representative, who warmly welcomed and chaired committee meetings. Special thanks are reserved for the late Muwydang Sir Chang Il Soon, who reopened my eyes to the world of the life. v TABLE OF CONTENTS PART 1. INTRODUCTION.................................................................................................. 1 1.1 Postembryogenic Development and Apical Meristems in Plants ................................... 1 1.2 Concepts of Shoot Apical Meristem ............................................................................... 1 1.3 Hedera helix as An Experimental Plant ........................................................................ 17 1.4 Cross-species Microarray Hybridization For Transcript Profiling.................................. 22 1.5 Microarray in Studies of SAM ....................................................................................... 26 PART 2. MATERIALS AND METHODS............................................................................ 27 2.1 Plant Material................................................................................................................ 27 2.2 Sample Tissue Preparation .......................................................................................... 28 2.3 Total RNA Extraction and Purification .......................................................................... 32 2.4 Labeling cDNA Targets with Fluorescent Dyes ............................................................ 35 2.5 Hybridization of Labeled cDNA Targets on Array Probes ............................................ 40 2.6 Washing and Drying Hybridized Microarray ................................................................. 46 2.7 Scanning Array Slides and Image Analysis.................................................................. 48 2.8 Data Analysis................................................................................................................ 50 2.9 Functional Analysis of Differentially Expressed Genes ................................................ 52 PART 3. RESULTS......................................................................................................... 55 3.1 Yield and Quality of Total RNA and Amino-Modified cDNA ......................................... 55 3.2 Labeling Efficiency of Amino-Modified cDNA ............................................................... 57 3.3 Scanned Arrays ............................................................................................................ 58 3.4 Statistical Microarray Data Analysis ............................................................................. 58 3.5 Verification of Expression Level ................................................................................... 69 3.6 Functional Analysis of Microarray Data ........................................................................ 74 3.7 Pathway Analysis ......................................................................................................... 78 vi PART 4. DISCUSSION.................................................................................................... 80 4.1 Cross-species Hybridization ......................................................................................... 80 4.2 Differential Hybridization between Shoot Apex and Young Leaves ............................. 81 4.3 Functional Categories of Differentially Expressed Genes ............................................ 82 4.4 Genes Involved in Regulatory Pathways In the Shoot Apex ........................................ 83 4.5 Genes Involved in Regulatory Pathways In the Young Leaf ........................................ 88 SUMMARY .................................................................................................................... 101 REFERENCES ............................................................................................................... 102 SUPPLEMENTARY DATA .............................................................................................. 120 vii LIST OF TABLES Table 1-1. Different features in vegetative and reproductive phases of English ivy (Hedera helix)......................................................................................................................... 18 Table 2-1. Amounts of tissue and reagents used for total RNA extraction and volume of retrieved aqueous phase.......................................................................................... 33 Table 2-2. Components of template/primer mixture added for each reaction for first-strand cDNA synthesis........................................................................................................ 36 Table 2-3. Components of reaction mixture added to each reaction for first-strand cDNA synthesis. ................................................................................................................. 37 Table 2-4. cDNA target sets labeled fluorescently with dye-swap.............................................. 38 Table 2-5. Ingredients of prehybridization solution..................................................................... 42 Table 2-6. Ingredients of hybridization chamber buffer. ............................................................. 43 Table 2-7. Ingredients of hybridization buffer solution................................................................ 44 Table 2-8. Ingredients of blocking solution................................................................................. 45 Table 2-9. Ingredients of hybridization mixture........................................................................... 45 Table 2-10. Array identification number and dye-swapped cDNA targets co-hybridized on each array. ........................................................................................................................ 46 Table 2-11. Concentrations of ingredients in wash buffer series................................................ 48 Table 2-12. Parameter values used for pathway analysis in GeneSpring GX............................ 54 Table 3-1. Concentrations of total RNA isolated from shoot apex and young leaf samples determined by spectrophotometry, and the ratios of absorbance readings (A260/ A280)......................................................................................................................... 55 Table 3-2. Biological processes in which genes that were expressed in either type of tissue were involved. .......................................................................................................... 75 Table 3-3. Gene products of the shoot apex participating in one or more relations in the metabolic
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