||Epigenetic Analysis for Genome-wide Profiles of Saccharomyces cerevisiae
||Institute of Computer Science and Information Engineering
In molecular biology, the study of gene expression plays an important role because the amount of gene expression reflects the amount of functional proteins, and there are many factors that can affect gene expression. In epigenetics, the research focuses on the factors rather than just changes in the underlying nucleotide sequence, and refers to relevant modifications to the genome that do not involve a change in DNA sequence. Gene expression can be controlled through epigenetic regulation such as chromatin remodeling or histone modification.
In this dissertation, multiple genome-wide profiles of epigenetic target in Saccharomyces cerevisiae were used for analysis on the chromatin regulation. For profiles of nucleosome positioning, we quantified the nucleosome stability by incorporating mass sequencing data, and provided a significant flanking pattern of sequence preference around nucleosomal DNA for a stable nucleosome. For profiles of histone-related proteins, the gene expression coupling with binding sites provide a framework to study the function of the histone variant in response to oleate, and to study the function of histone chaperone on the gene silencing at telomere-proximal regions.
Our analysis on epigenetics revealed the function of the histone-related proteins, and also provided a reliable measure for nucleosome stability. Both studies contribute to the field of epigenetic regulation, and relevant results can extend to further researches regarding the mechanism of chromatin remodeling.
摘 要 i
LIST OF TABLES vii
LIST OF FIGURES viii
Chapter 1. Introduction 1
1.1 Overview 1
1.2 Objective 3
1.3 Organization of dissertation 4
Chapter 2. Related Genome-wide Profiling Biotechnologies 6
2.1 Microarray 6
2.2 ChIP-on-chip 6
2.3 High-throughput next generation sequencing 8
2.4 MNase-seq 10
Chapter 3. Epigenetic Analysis on Nucleosome Stability 12
3.1 Background 12
3.2 Materials and Method 13
3.2.1 Datasets 13
3.2.2 Detection of nucleosome positions from sequencing data 15
3.2.3 Calculation of NCS of each base pair 19
3.2.4 Application of NCS for data of nucleosomes 20
3.2.5 Evaluation of the relationship of nucleosome score with dinucleotide frequency 22
3.2.6 Using fold change of dinucleotide certainty to partition nucleosomal region 24
3.3 Results and Discussion 26
3.3.1 NCS shows clear discrimination of A/T-based dinucleotide frequencies 26
3.3.2 NCS reveals the flanking pattern on the preference of A/T-based dinucleotides 31
3.3.3 The negative relationship between NCS and poly(dA:dT) 34
3.3.4 The opposite tendency between NCS and NCP/noise 35
3.3.5 Further analysis on Broggard’s score 39
3.4 Summery 44
Chapter 4. Epigenetic Analysis on Histone-related Proteins 47
4.1 Background 47
4.2 Materials and Method 50
4.2.1 Using transcript DNA microarray for the analysis of gene function 50
4.2.2 Using ChIP-on-chip data for the analysis of protein binding sites 51
4.2.3 Nucleosome detection using ChIP-on-chip data 54
4.3 Results and Discussion 56
4.3.1 Htz1p is required for a subset of oleic acid-responsive genes 56
4.3.2 Htz1p shows different preference on the oleate conditions 59
4.3.3 Chz1p, Gcn5p, and Swr1p are associated with Htz1p in oleate-response 62
4.3.4 Htz1p and Chz1p regulates transcription of telomere-proximal genes 64
4.3.5 Htz1p association with subtelomeric DNA is independent of Chz1p 68
4.3.6 Nucleosome detection on telomere regions 71
4.4 Summery 74
Chapter 5. Conclusion and Future Works 75
5.1 Conclusion Remarks 75
5.2 Future Works 76
5.2.1 Nucleosome dynamics caused from Sequence-based factors 77
5.2.2 Nucleosome dynamics caused from Protein-based factors 78
5.2.3 Nucleosome dynamics caused from DNA-chromosome factors 79
5.2.4 System approaches to determine the relationship between factors 79
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