TY  - JOUR
A1  - Chang, Gue Su
A1  - Noegel, Angelika A.
A1  - Mavrich, Travis N.
A1  - Müller, Rolf
A1  - Tomsho, Lynn
A1  - Ward, Elissa
A1  - Felder, Marius
A1  - Jiang, Cizhong
A1  - Eichinger, Ludwig
A1  - Glöckner, Gernot
A1  - Schuster, Stephan C.
A1  - Pugh, B. Franklin
T1  - Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium
Y1  - 2012/06/01 
JF  - Genome Research 
JO  - Genome Research 
SP  - 1098 
EP  - 1106 
DO  - 10.1101/gr.131649.111 
VL  - 22 
IS  - 6 
UR  - http://genome.cshlp.org/content/22/6/1098.abstract 
N2  - Dictyostelium discoideum is an amoebozoa that exists in both a free-living unicellular and a multicellular 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 II. Indeed, we find a strong phylogenetic relationship between the presence of the NELF pausing factor and positioning of the +1 nucleosome. Pausing and +1 nucleosome positioning may have coevolved in animals. 
ER  -