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Table of contents
CHAPTER I INTRODUCTION TO CHROMATIN AND CHROMATIN-level GENOME ORGANISATION
Introduction
Histone post-translational modifications
DNA Methylation
Genomic Context of DNA Methylation
Establishment and maintenance of DNA methylation
Regulation of DNA methylation
Methods to identify DNA methylation
The bioinformatics of epigenome data analysis
R and Bioconductor support
Analysis of microarray ChIP-on-chip data
Peak Finding
Aims and organisation of the thesis
References
CHAPTER II GENOME-WIDE EVIDENCE FOR LOCAL DNA METHYLATION SPREADING FROM SMALL RNA TARGETED SEQUENCES IN ARABIDOPSIS
Introduction
Materials and Methods
DNA methylation analysis
Results
Discussion
References
Supplementary Information
Additional Methods
Data visualization and downstream analysis
CHAPTER III INTEGRATIVE EPIGENOMIC MAPPING DEFINES FOUR MAIN CHROMATIN STATES IN ARABIDOPSIS
Introduction
Results
Discussion
Materials and methods
References
Supplementary
Review process file
Additional Methods
Combinatorial Analysis
Co-association
Cluster Analysis
Cluster Validity and clustering tendency
CHAPTER IV SPATIAL & TEMPORAL DYNAMICS IN HISTONE H2BUB CHROMATIN MARK DURING LIGHT DRIVEN DEVELOPMENTAL ADAPTATION & THE ROLE THEREIN FOR FINE-TUNING OF GENE EXPRESSION
Introduction
Methods
ChIP-chip analysis
Transcriptome analysis
Results
The hub1-3 mutant shows defects in fine-tuning of gene expression
Cluster analysis of expression data for differentially expressed genes
Genome-wide dynamics of H2Bub distribution
Light-driven induction is associated with dynamic changes of H2Bub
Discussion
References
CHAPTER V DISCUSSION
References
