New Chromatin Landscapes
FlyBase has incorporated genome-wide views of the chromatin landscape into GBrowse. Chromatin, composed of DNA and a variety of modified histone and non-histone proteins, is varied and complex, impacting many processes such as replication, gene expression and DNA repair. Two recent articles have sought to make sense of this complexity. Using integrative analyses of the genome-wide profiles of many histone marks or chromatin proteins, specific combinations of these factors have been identified to define distinct chromatin states: regions with regulatory capacity or regions of polycomb repression, for example.
Filion et al. (2010) have identified five principal chromatin states from the analysis of 53 chromatin protein genome-binding profiles in Kc167 cells. As part of the modENCODE project, Kharchenko et al. (2010) profiled the genome-wide localization of 18 histone marks in S2-DRSC and ML-DmBG3-c2 ('BG3') cells and identified nine prevalent combinatorial patterns. The significance of Kharchenko's nine chromatin states is further explored in the modENCODE consortium's integrative paper. Together, these models identify various regions of functional significance, such as promoters, regulatory regions, regions of polycomb repression and classic heterochromatin in the cell lines assayed.
FlyBase has incorporated these chromatin landscapes into GBrowse as color-coded tracks, each state represented by a different color. To view them, first go to GBrowse and select [D. melanogaster RNA-seq Data] in the Data Source pull down menu. Then scroll to the bottom of the page to the Tracks section, click on the desired 'Chromatin Domains' data sets, and hit the Update Image button (just under the GBrowse image display). Move the cursor over the color-coded track for a pop-up information window. The display of these and other GBrowse tracks can be customized using the Configure Tracks button.