ArticleGenome research2012
Unusual combinatorial involvement of poly-A/T tracts in organizing genes and chromatin in Dictyostelium.
Article in Genome research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
21 citing papers in PubMed, 33 citations in OpenAlex.
- Convergent pairs of highly transcribed genes restrict chromatin looping in Dictyostelium discoideum.Nucleic acids research · 2025Article
- The chromatin remodeler Ino80 mediates RNAPII pausing site determination.Genome biology · 2021Article
- Global characterization of the Dicer-like protein DrnB roles in miRNA biogenesis in the social amoeba Dictyostelium discoideum.RNA biology · 2018Article
- Generation of Single-Cell Transcript Variability by Repression.Current biology : CB · 2017Article
- Regulation of nucleosome positioning by a CHD Type III chromatin remodeler and its relationship to developmental gene expression inGenome research · 2017Article
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- Regulatory cis-elements are located in accessible promoter regions of the CAT2 promoter and affect activating histone modifications in Arabidopsis thaliana.Plant molecular biology · 2017Article
- Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin.Nucleic acids research · 2016Article
- A set of genes conserved in sequence and expression traces back the establishment of multicellularity in social amoebae.BMC genomics · 2016Article
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- S1-DRIP-seq identifies high expression and polyA tracts as major contributors to R-loop formation.Genes & development · 2016Article
- The nucleosome landscape of Plasmodium falciparum reveals chromatin architecture and dynamics of regulatory sequences.Nucleic acids research · 2016Article
- DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome.Genome research · 2015Article
- Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites.BMC genomics · 2014Article
- DNA-encoded nucleosome occupancy is associated with transcription levels in the human malaria parasite Plasmodium falciparum.BMC genomics · 2014Article
- Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes.Cell · 2014Article
- Determinants of nucleosome positioning.Nature structural & molecular biology · 2013Review
- Fungal genes in context: genome architecture reflects regulatory complexity and function.Genome biology and evolution · 2013Article
- Article
Corrections and comments
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Authors and funding
12 authors at 5 institutions in 3 countries.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.