ABSTRACT
The main topic of the present chapter builds around functional genomics of legumes, more specifi cally cool season food legumes, though many insights into the biology of a specifi c legume derives from the so-called model plants such as Medicago truncatula and Lotus japonicus. Functional genomics describes the whole repertoire of large-scale and high-throughput techniques and subsequent computational analyses for deciphering the roles of DNA and RNA in the progression from information (DNA) to function (both RNA as well as protein). For example, specifi c gene disruption (gene knock-down, gene knock-in, gene knock-out) allows to reveal the function of a gene, the determination of gene expression patterns (i.e., expressed genes in a given cell, tissue, organ, or organism at a time by e.g., microarrays) relates gene function(s) to cellular processes, and the transfer and integration of foreign genes allow in studying their infl uence(s) on the activity of other resident genes. An ever-increasing area of functional genomics focuses on post-transcriptional events such as messenger RNA association with carrier and chaperon proteins, stability, export and compartmentalization, turnover rate and frequency of translation, but also the stability of the protein product and the many protein-protein interactions of a target protein with other proteins (as, e.g., detected by yeast two-hybrid analysis), to name a few. However, the real complexity cannot be caught by these parameters at all. On top of the genetic code (i.e., the sequence of bases in DNA), other codes emerged. The nucleosome positioning code decides what regions in a genome can easily be accessed by proteins to turn on transcription of a gene. Additionally, nucleosomal DNA is more highly methylated than fl anking DNA. So, nucleosome positioning infl uences DNA methylation patterning throughout, in this case, the A. thaliana genome, and DNA methyltransferases preferentially target nucleosome-bound DNA (see Chodavarapu et al. 2010).
