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The Determinants of Nucleosome Patterns and the Impact of Phosphate Starvation on Nucleosome Patterns and Gene Expression in Rice Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 3-14-2018 The etD erminants of Nucleosome Patterns and the Impact of Phosphate Starvation on Nucleosome Patterns and Gene Expression in Rice Qi Zhang Louisiana State University and Agricultural and Mechanical College, [email protected] Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Part of the Agronomy and Crop Sciences Commons, Bioinformatics Commons, Genetics Commons, Genomics Commons, and the Plant Breeding and Genetics Commons Recommended Citation Zhang, Qi, "The eD terminants of Nucleosome Patterns and the Impact of Phosphate Starvation on Nucleosome Patterns and Gene Expression in Rice" (2018). LSU Doctoral Dissertations. 4502. https://digitalcommons.lsu.edu/gradschool_dissertations/4502 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. THE DETERMINANTS OF NUCLEOSOME PATTERNS AND THE IMPACT OF PHOSPHATE STARVATION ON NUCLEOSOME PATTERNS AND GENE EXPRESSION IN RICE A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Biological Sciences by Qi Zhang B.S., Sichuan Agricultural University, 2012 May 2018 ACKNOWLEDGEMENTS The journey towards the completion of the degree hasn’t been easy, and I would like to express my heartfelt gratitude to everyone who has been around me, listening to me, and supporting me. I would like to thank my major professor, Dr. Aaron Smith for accepting me as his graduate student and providing financial support. I would like to thank him for his time and effort to train me to become an independent scientist, as well as his patience with me especially when facing difficulties. His guidance and encouragement has been invaluable throughout my graduate studies. I would like to thank my graduate committee members Dr. John Larkin, Dr. Maheshi Dassanayake, and Dr. David Donze for their continuous support, insightful comments, and encouragement. I thank Dr. Maud Walsh for her service as a Dean’s representative on my graduate committee. My special thanks to Dr. Larkin and Dr. Dassanayake for their useful discussions during joint lab meetings and their critical reading of my first manuscript. I would like to express my sincere gratitude to Dr. Dassanayake and Dr. Dong-Ha Oh for helping me start genomic data analysis and providing very useful suggestions and assistance on my research. I would like to acknowledge Sandra DiTusa for teaching me laboratory as well as lab management skills. I thank Dr. Scott Herke and Dr. Subbaiah Chalivendra for useful tips on experimental trouble-shooting. I would like to thank Dr. James Moroney, Dr. Marc Cohn, and Dr. Joomyeong Kim for their suggestions on my research and presentations. I thank current and former members of the Smith lab, Maryam Foorozani, Jifeng Li, Matthew Vandal, Dr. Elena Fontenot and Dr. Sarah Zahraeifard for their discussions, help, and encouragement. ii Lastly I would like to thank my parents Zhijian Zhang and Yaping Shen, and my uncle Prof. Pei-Yi Shen for their support and love. My family has been inspiring and encouraging since my first day of school. iii TABLE OF CONTENTS ACKNOWLEDGEMENTS ............................................................................................................ ii ABBREVIATIONS ........................................................................................................................ v ABSTRACT ................................................................................................................................... vi CHAPTER 1. BACKGROUND ..................................................................................................... 1 CHAPTER 2. NUCLEOSOME POSITIONING AND OCCUPANCY IN RICE ....................... 20 CHAPTER 3. THE IMPACT OF PHOSPHATE STARVATION ON NUCLEOSOME PATTERNS AND GENE EXPRESSION IN RICE .................................................................... 45 CHAPTER 4. CONCLUSIONS ................................................................................................... 60 REFERENCES ............................................................................................................................. 65 APPENDIX: COPYRIGHT INFORMATION ............................................................................. 75 VITA ............................................................................................................................................. 76 iv ABBREVIATIONS ChIP chromatin immunoprecipitation COR coronatine DEG differentially expressed gene DHS DNase I hypersensitivity site FDR false discovery rate FPKM fragments per kilobase of transcript per million mapped reads GB gene body GO gene ontology MNase-seq sequencing of micrococcal nuclease digested chromatin NDR nucleosome depleted region NFR nucleosome free region PCC Pearson's correlation coefficient PCG protein-coding gene PSG pseudogenes PSR phosphate starvation response RNAP II RNA polymerase II RNA-seq RNA sequencing SCC Spearman's correlation coefficient TE transposable element TEG transposable element related gene TF transcription factor TSS transcription start site TTS transcription termination site v ABSTRACT In eukaryotic cells, DNA is a large molecule that must be greatly condensed to fit within the nucleus. DNA is wrapped around histone proteins to form nucleosomes, which facilitate DNA condensation, but on the other hand, may limit DNA processes. Organisms must respond to environmental stress in order to survive, and one strategy is by remodeling nucleosomes to promote changes in DNA accessibility to alter gene expression. Studies have demonstrated a clear correlation between nucleosome dynamics and transcriptional change in some eukaryotes, however factors that affect nucleosome positioning in plants are largely unknown, and the correlation between nucleosome dynamics and transcriptional changes in response to environmental perturbation remain unclear. We report a high-resolution map of nucleosome patterns in the rice (Oryza sativa) genome by deep sequencing of micrococcal nuclease digested chromatin. The results reveal that nucleosome patterns at rice genes were affected by both cis- and trans- determinants, including GC content and transcription. A negative correlation between nucleosome occupancy across the transcription start site (TSS) and transcription was observed, and the nucleosome patterns across the TSS were correlated with distinct functional categories of genes. A parallel experiment was done monitoring nucleosome dynamics and transcription changes in response to phosphate starvation for 24 hours. Phosphate starvation resulted in numerous instances of nucleosome dynamics across the genome which were enhanced at differentially expressed genes. This work demonstrates that rice nucleosome patterns are suggestive of gene functions, and reveal a link between chromatin remodeling and transcriptional changes in response to deficiency of a major macronutrient. The findings help to enhance the understanding towards eukaryotic gene regulation at the chromatin level. vi CHAPTER 1. BACKGROUND Primary structure of eukaryotic chromatin Eukaryotic DNA must be condensed to fit into a small space within the nucleus. Studies on primary chromatin structure reveal that 146 bp of DNA wrap around a histone octamer consisting of each of two copies of H2A, H2B, H3 and H4 to comprise a nucleosome (Luger et al., 1997). Linker DNA refers to the region in between nucleosomes, and can be bound by histone H1. The length of linker DNA between nucleosomes varies among species, cell types and developmental stages, ranging from ~20 bp to ~50 bp (Teif et al., 2012; Beh et al., 2015; Zhang et al., 2015). Longer linkers facilitate the packaging of DNA and are related to silent genes and heterochromatin (Valouev et al., 2011), whereas shorter linkers are related to higher expression levels (Zhang et al., 2015). The formation of nucleosomes along DNA facilitates DNA compaction, however it makes the DNA inaccessible for important cellular processes including DNA replication, recombination, repair and transcription (Annunziato, 2005; Radman- Livaja and Rando, 2010; Price and D'Andrea, 2013; Pulivarthy et al., 2016). Hence, nucleosome distribution is not static but rather is modified in accordance with these processes. The development of genome sequencing technology enables the rapid growth in determining genome-wide nucleosome positions at a high resolution. Genome-wide nucleosome maps have been widely reported in a variety of species including in yeast (Lee et al., 2007), C. elegans (Valouev et al., 2008), Drosophila (Mavrich et al., 2008b), human (Valouev et al., 2011), Arabidopsis (Li et al., 2014) and rice (Wu et al., 2014). In observing the common patterns from the reported nucleosome maps, a stereotypical nucleosome pattern can be summarized across the transcription start site (TSS) of actively transcribed genes: a nucleosome depleted region (NDR, sometimes termed ‘nucleosome free region (NFR)’ depending on the context. I use NDR 1 throughout this dissertation) localized just upstream of the TSS. Regions upstream of the TSS (promoters) are
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