Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium

Genome Res. 2012 Jun;22(6):1098-106. doi: 10.1101/gr.131649.111. Epub 2012 Mar 20.

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.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Chromatin / genetics*
  • Dictyostelium / genetics*
  • Genes
  • Nucleosomes / genetics*
  • Phylogeny
  • Poly A / genetics*
  • Poly T / genetics*
  • Promoter Regions, Genetic
  • RNA Polymerase II / genetics
  • TATA Box / genetics
  • Transcription Factors / genetics

Substances

  • Chromatin
  • Nucleosomes
  • Transcription Factors
  • negative elongation factor
  • Poly A
  • Poly T
  • poly A-T
  • RNA Polymerase II