CHAPTER 19
COMPUTATIONAL CHARACTERIZATION OF REGULATORY REGIONS
19.1 THE GENOME REGULATORY LANDSCAPE
Genomes are genetic information repositories on each cell of a living being. Yeast was the first eukaryote that was sequenced more than one decade ago [31]. Since then, the sequence of many other genomes has been published, becoming publicly available in most cases for the worldwide research community. We now can access from our computer the human genome [80, 39] and the sequence, among others, of the fruit fly [3], mouse [40], chicken [38], chimpanzee [70], cow [69], or rice [30, 41] using any of the popular genome browsers [46, 37].
Once the sequence of nucleotides on each chromosome is assembled, one of the initial tasks is to identify the catalogue of biological signals and regions that shape the genome landscape [11]. Genes are units of hereditary information in the organism. In response to variable internal and external conditions, cells increase or decrease the activation of multiple genes, expressing different gene regulatory programs during their lifetime. Protein-coding genes are translated into proteins, which perform diverse biological functions in the organisms (see more about protein-coding genes in [84]). Noncoding genes, such as those that give rise to microRNAs, are responsible for other essential processes in cells (see [29] for a comprehensive gene taxonomy).
Gene transcription initiation is considered to be one important control point in most ...
