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anities of TFs to dierent DNA sequences has been a signicant technical chal-
lenge in molecular biology for many years. The global relationships between TFs
and their targets on the genome can be described in the framework of network the-
ory: transcription regulatory networks (TRN) are formed by two types of nodes:
TFs and their target genes; edges are directed and always start from a TF. Many
dierent strategies have been employed to reconstruct TRNs, including computa-
tional and experimental methods.
2.2.1. Experimental approach
Protein-DNA interactions are required for accessing and protecting genetic infor-
mation within the cell and they have been studied in the past using genetic, bio-
chemical, and structural methods producing qualitative or semiquantitative data.
Today, and even more in the future, the focus will be on high throughput high
quality data, a goal that would allow the reliable modeling of a huge number of
interactions. The last ten years have witnessed the development and renement
of methods to crosslink proteins to DNA in vivo through which we can measure
the interaction of sequence-specic DNA-binding proteins with genomic DNA. The
methodology was then improved by combining DNA microarray technology with in
vivo crosslinking [12]. TRN identication today is mainly accomplished with the
combination of microarray techniques with chromatin immunoprecipitation (ChIP)
and, whereas initial uses of ChIP required prior knowledge of a potential binding
target DNA sequence to identify binding of TFs to DNA regions of interest, today
it allows the reconstruction of a TRN almost without prior knowledge. In the stan-
dard ChIP-on-chip protocol a DNA binding protein is covalently attached to its
target DNA using formaldehyde. After shearing of the chromatin, the protein-DNA
adduct is immunoprecipitated from cell extracts using an antibody specic for the
protein in question or for an epitope sequence appended to the end of the protein
(generally the hemagglutinin or myc tags). After immunoprecipitation, the enriched
DNA sample can be amplied using a variety of methods. DNA samples (enriched
and reference) are uorescently labeled and then they are hybridized to various mi-
croarrays. By using the ChIP-chip technique, Lee and collaborators [13] recovered
promoters bound to each TF encoded by the Saccharomyces cerevisiae genome. In
addition to providing an outline of global transcriptional regulation in yeast, these
results represent a quantitative estimate of the amount of combinatorial regulation
in yeast and they allowed to obtain a comprehensive set of DNA regulatory motifs
that are specic for each TF. Of course, there are still gaps in our understanding of
this TRN (presumably to be lled by more traditional, small scale genetic studies).
2.2.2. Computational approach
Identifying the repertoire of regulatory elements in a genome is one of the major
challenges in modern biology and it is today approached by using several high-
