The Non-coding Landscape of the Genome of Arabidopsis thaliana

Sequencing and analysis of the genome of Arabidopsis thaliana has marked a milestone for plant genomics. Since analytical approaches to elucidate the gene function of the 27,000 genes and genome-wide functional studies, such as transcriptional characteristics, have revolutionized our functional and molecular understanding of a plants lifestyle. Classical target of such studies is the genic- and protein-coding space of the genome. However, the non-genic genomic space contains a multitude of important sequence elements that are essential for proper and regulated functioning of the genome. The analysis of cis elements as important information-containing sequence elements has been complicated by the experimental and algorithmic difficulties to detect them. For small RNAs and microRNAs hardly anything was known until turn of the century but since insights into their molecular nature and their important role in regulation of genome dynamics and biological processes has truly revolutionized not only plant biology. In this chapter we aim to give an overview about our current knowledge and analytical approaches to analyze these types of non-coding sequence elements as well as knowledge about their biological roles and molecular functioning.