Predictive chromatin signatures in the mammalian genome
1 Bioinformatics Program, 2 Ludwig Institute for Cancer Research and 3 Department of Cellular and Molecular Medicine, University of California, San Diego School of Medicine, 9500 Gilman Drive #0653, CMM East Room 3080, La Jolla, CA 92093-0653, USA
* To whom correspondence should be addressed. Tel: +1 8588225766; Fax: +1 8585347750; Email: biren{at}ucsd.edu
Received July 15, 2009; Accepted August 21, 2009
The DNA sequence of an organism is a blueprint of life: it harbors not only the information about proteins and other molecules produced in each cell, but also instructions on when and where such molecules are made. Chromatin, the structure of histone and DNA that has co-evolved with eukaryotic genome, also contains information that indicates the function and activity of the underlying DNA sequences. Such information exists in the form of covalent modifications to the histone proteins that comprise the nucleosome. Thanks to the development of high throughput technologies such as DNA microarrays and next generation DNA sequencing, we have begun to associate the various combinations of chromatin modification patterns with functional sequences in the human genome. Here, we review the rapid progress from descriptive observations of histone modification profiles to highly predictive models enabling use of chromatin signatures to enumerate novel functional sequences in mammalian genomes that have escaped previous detection.