Computational Study of Nucleosome Positioning Sequence Patterns and the Effects of the Nucleosome Positioning on the Availability of the Transcription Factor Binding Sites in Study Systems

iii List of Abbreviations . x List of Figures . xii List of Tables . xv GENERAL INTRODUCTION . 1 Nucleosome positioning sequences of Drosophila . 1 Chromatin structure . 1 Regulatory role of Nucleosome positioning in genome . 2 Nucleosome positioning sequences . 4 Nucleosome with histone variant H2A.Z . 8 Objectives . 9 Ly49 gene clusters as a model system . 10 Ly49 gene family . 11 Ly49 receptors . 11 Ly49 expression on NK cells . 17 Ly49 gene cluster . 22 Objectives . 27 PART 1: NUCLEOSOME POSITIONING SEQUENCE PATTERNS . 30 Introduction . 30 Materials and Methods . 36 Identification of the nucleosome positions . 36 Nucleosome distribution . 37 Identifying the +1 nucleosomes of each gene . 38 Grouping genes based on the type of the +1 nucleosome . 38 Dinucleotide patterns of nucleosome sequences . 39 Detecting periodicities by Fourier transform . 40 Building a model for the periodic dinucleotide pattern . 41 viii Refining of the patterns by correlation . 41 Comparison of the histone structures . 42 Identifying core promoter elements . 42 Statistical testing of the co-occurrences . 43 Enriched biological functions of the H2A and H2A.Z +1 nucleosome . 43 Enriched biological functions of genes having NPS patterns . 44 Results . 45 Nucleosome distribution around transcription start site . 45 Selection of genes based on the +1 nucleosome . 48 Sequence analysis of NPS patterns of H2A nucleosome sequences. 54 Sequence analysis of NPS patterns of H2A.Z nucleosome sequences . 94 Comparison between H2A and H2A.Z NPS patterns . 105 Enriched biological functions of H2A-only, H2A.Z-only, and H2A/H2A.Z bound genes. 122 Co-occurrences of nucleosomes and core promoter elements . 132 Discussion . 136 PART 2: EFFECT OF NUCLEOSOME POSITIONING ON LY49 TRANSCRIPTION FACTOR BINDING AVAILABILITY. 143 Introduction . 143 Materials and Methods . 152 Prediction of the nucleosome positioning . 152 Accuracy of the prediction. 153 Nucleosome landscape around Ly49 gene promoters . 153 Search for hypersensitivity region . 154 Prediction of the transcription factor binding sites . 155 Distance distribution of the transcription factor binding sites to the nearest nucleosome . 155 Test the multimodality of the distribution . 156 Associations between various variables . 157 Association rule mining . 158 Enriched motif search . 159 ix Identifying the 10 bp periodicity of transcription factors . 160 Nucleosome map of RMA cells by ChIP-Seq . 161 Deviancy of nucleosome positioning in RMA from the prediction . 161 Statistical tests of the deviancy . 162 Ly49a expression on RMA cells . 162 Chromatin Immunoprecipitation of RMA cells for AML-1 binding sites . 162 Protein interaction . 163 Results . 164 Prediction of nucleosome positioning sites . 164 Identification of nucleosome coverage on transcription factor binding sites . 180 Quantitative assessment of the nucleosome positioning in the Ly49 gene promoters . 188 Nucleosome coverage of transcription factor binding sites . 189 Identification of the transcription factor binding sites displaying the 10 bp periodicity . 200 Ly49 expression state and in vitro nucleosome maps . 215 Association rule mining . 236 Enriched motifs on promoter regions. 237 Protein interaction of the factors . 256 Discussion . 257 GENERAL DISCUSSION . 265 References . 276 Contributions of Collaborators . 296 Curriculum Vitae . 297