Understanding genome function: quantitative modeling of chromatin folding and chromatin-associated processes

The revolution in DNA sequencing technologies during the past decade and a
half has resulted in an outburst of genome sequence information for more
than 800 organisms. Genomes of many humans from different ethnic backgrounds
have been sequenced at varying degrees of coverage using multiple
technological platforms and strategies and the effort is ongoing; thousands
of human genomes will be available in the next few years for researchers
to analyze. A major challenge ahead is to determine the functional components
of the different genome sequences and how they vary across individuals and
species.
Traditionally most efforts have focused on the analysis of protein-coding genes.
These are typically annotated as exons separated by introns. Genes are transcribed
into messenger RNA (mRNA), the introns are spliced out, and the exons are
translated to protein. In addition we now know there is a plethora of information
in non-coding DNA sequence as to how to regulate the expression of the genecoding
regions. In this chapter we cover the major categories of genomic sequence
and the methods used to investigate them.