title: Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium.
abstract: 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.
authors.affiliation: Center for Eukaryotic Gene Regulation and Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA.
authors.forename: Gue Su
authors.initials: GS
authors.lastname: Chang
authors.forename: Angelika A
authors.initials: AA
authors.lastname: Noegel
authors.forename: Travis N
authors.initials: TN
authors.lastname: Mavrich
authors.forename: Rolf
authors.initials: R
authors.lastname: Müller
authors.forename: Lynn
authors.initials: L
authors.lastname: Tomsho
authors.forename: Elissa
authors.initials: E
authors.lastname: Ward
authors.forename: Marius
authors.initials: M
authors.lastname: Felder
authors.forename: Cizhong
authors.initials: C
authors.lastname: Jiang
authors.forename: Ludwig
authors.initials: L
authors.lastname: Eichinger
authors.forename: Gernot
authors.initials: G
authors.lastname: Glöckner
authors.forename: Stephan C
authors.initials: SC
authors.lastname: Schuster
authors.forename: B Franklin
authors.initials: BF
authors.lastname: Pugh
mesh_terms: D000818:Animals; D002843:Chromatin / Q000235:genetics*; D004023:Dictyostelium / Q000235:genetics*; D005796:Genes; D009707:Nucleosomes / Q000235:genetics*; D010802:Phylogeny; D011061:Poly A / Q000235:genetics*; D011071:Poly T / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012319:RNA Polymerase II / Q000235:genetics; D016385:TATA Box / Q000235:genetics; D014157:Transcription Factors / Q000235:genetics
chemical_list: D002843:Chromatin; D009707:Nucleosomes; D014157:Transcription Factors; C118437:negative elongation factor; D011061:Poly A; D011071:Poly T; C008950:poly A-T; D012319:RNA Polymerase II