Department of Immunology, Genetics and Pathology, Genomics and Neurobiology, Uppsala Universitet
The principles for how genes are activated and inactivated are known but from a genomic perspective our knowledge is very limited. Each cell type has a unique set of active genes that are regulated by the action of a collection of the 2000 transcription factors and other nuclear proteins that bind the DNA molecule.
Until recently this could only be studied in vitro and for parts of genes. We use chromatin immunoprecipitation (ChIP) to study this in vivo. For detection we have developed efficient massive parallel sequencing (ChIP-seq) techniques, which allows us to interrogate the whole genome.
The traditional view of a gene, with a single beginning and end, has been challenged and in addition to the previously known enhancers and other distant regulatory elements, multiple promoters and complex alternative splicing has been found. We therefore annotate all identified DNA-protein interactions relative to everything that is known about the genome.