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 59 ends by poly-T tracts and precisely at their 39 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.

Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum

“…Sequencing of the TAP dependent PCR products from both wt and drnB - cells, revealed a few 5´-ends in close vicinity where the 5ʹ most nucleotide is an A-residue 42 bp upstream of the start codon (Figure 5(d) and S5E). The identified TSS for DDB_G0287713 is further corroborated by the poly-T tract immediately upstream, a feature of many protein coding genes in D. discoideum [51]. In conclusion, pri-mir-1177 is not merely part of a long 5ʹUTR belonging to the DSG.…”

“…This appears to be a general sequence feature associated with miRNA loci in D. discoideum since similar motifs are present in close vicinity to the 5ʹ most poly(A) RNA-seq reads of the 14 intergenic miRNA genes. Poly-T tracts immediately upstream of TSSs is a common feature for protein coding genes in D. discoideum [51], indicating that also D. discoideum pri-miRNAs are transcribed by RNA pol II. This idea is also supported by a previous study by Kruse et al ., who showed reduction of mir-1176 and mir-1177 upon treatment with α-amanitin [30] and is in agreement with the situation in animals and plants where most pri-miRNAs are transcribed by RNA Pol II [4–6].…”

DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome

“…Eukaryotic nucleosome organization is most distinct near the 5 ′ ends of genes, where regularly spaced nucleosomes lie downstream from a nucleosome-depleted region (Yuan et al 2005;Lee et al 2007;Mavrich et al 2008b;Lantermann et al 2010;Chang et al 2012;Chen et al 2013b). We find that this pattern is conserved in both Tetrahymena and yeast (Fig.…”

“…Genome-wide nucleosome maps in major model organisms have revealed strikingly similar nucleosome patterns near gene starts, where a nucleosome-depleted region upstream of the TSS is followed by a stereotypical array of nucleosomes inside the gene (Yuan et al 2005;Lee et al 2007;Mavrich et al 2008b;Lantermann et al 2010;Chang et al 2012;Chen et al 2013b;Zhang et al 2014). Recent studies have used Saccharomyces cerevisiae as a model to understand nucleosome positioning mechanisms underlying the stereotypical nucleosome pattern near eukaryotic TSSs.…”

Nucleosome Distribution near the 3′ Ends of Genes in the Human Genome

“…29,33,36) In order to determine further the effect of DNA sequences, GC content was calculated around polyA sites (Supplemental Fig. 7).…”