Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium
- Gue Su Chang1,
- Angelika A. Noegel2,
- Travis N. Mavrich3,
- Rolf Muller2,
- Lynn P. Tomsho3,
- Elissa Ward3,
- Marius Felder4,
- Cizhong Jiang3,
- Ludwig Eichinger5,
- Gernot Glockner6,
- Stephan C. Schuster7 and
- B. Franklin Pugh1,8
- 1 Penn State Univ.;
- 2 Institute of Biochemistry I, Medical Faculty, Cologne Excellence Cluster on Cellular Stress Response;
- 3 Pennsylvania State University;
- 4 Fritz-Lipmann-Institute;
- 5 University of Cologne;
- 6 Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB;
- 7 PennState University
- ↵* Corresponding author; email: bfp2{at}psu.edu
Abstract
Dictyostelium discoideum is a member of the amoebozoa that exists in both a free-living unicellular and a multi-cellular form. It is situated in a deep branch in the evolutionary tree, and is particularly noteworthy in having a very A/T-rich genome. Dictyostelium provides an ideal system to examine the extreme to which nucleotide bias may be employed in organizing promoters, genes, and nucleosomes across a genome. We find that Dictyostelium genes are demarcated precisely at their 5' ends by poly-T tracts and precisely at their 3' ends by poly-A tracts. These tracts are also associated with nucleosome-free regions, and are embedded with precisely positioned TATA boxes. Homo- and heteropolymeric tracts of A and T demarcate nucleosome border regions. Together these findings reveal the presence of a variety of functionally distinct polymeric A/T elements. Strikingly, Dictyostelium chromatin may be organized in di-nucleosome units, but is otherwise organized as in animals. This includes a +1 nucleosome in a position, that predicts the presence of a paused RNA polymerase. Indeed, we find a strong phylogenetic relationship between the presence of the NELF pausing factor and positioning of the +1 nucleosome. Pausing and nucleosome positioning may have co-evolved with animal multi-cellularity.
- Received September 7, 2011.
- Accepted March 7, 2012.
- Copyright © 2012, Cold Spring Harbor Laboratory Press
