ArticleGenome research2015
DNA-guided establishment of nucleosome patterns within coding regions of a eukaryotic genome.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 28 citations in OpenAlex.
- Unveiling a pervasive DNA adenine methylation regulatory network in the early-diverging fungus Rhizopus microsporus.Nature communications · 2025Article
- Evolutionary bioenergetics of ciliates.The Journal of eukaryotic microbiology · 2022Review
- Galaxy Dnpatterntools for Computational Analysis of Nucleosome Positioning Sequence Patterns.International journal of molecular sciences · 2022Article
- GC content, but not nucleosome positioning, directly contributes to intron splicing efficiency inGenome research · 2022Article
- Article
- The role of epigenetics and chromatin structure in transcriptional regulation in malaria parasites.Briefings in functional genomics · 2019Review
- Article
- Unraveling the 3D genome of human malaria parasites.Seminars in cell & developmental biology · 2019Review
- A unified computational framework for modeling genome-wide nucleosome landscape.Physical biology · 2018Article
- ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation.Briefings in functional genomics · 2018Review
- N6-adenine DNA methylation is associated with the linker DNA of H2A.Z-containing well-positioned nucleosomes in Pol II-transcribed genes in Tetrahymena.Nucleic acids research · 2017Article
- Hypomethylated domain-enriched DNA motifs prepattern the accessible nucleosome organization in teleosts.Epigenetics & chromatin · 2017Article
- The Role of Chromatin Structure in Gene Regulation of the Human Malaria Parasite.Trends in parasitology · 2017Review
- DNA methylation and chromatin accessibility profiling of mouse and human fetal germ cells.Cell research · 2017Article
- Dissecting relative contributions of cis- and trans-determinants to nucleosome distribution by comparing Tetrahymena macronuclear and micronuclear chromatin.Nucleic acids research · 2016Article
- Nucleosomal signatures impose nucleosome positioning in coding and noncoding sequences in the genome.Genome research · 2016Article
- Categorical spectral analysis of periodicity in nucleosomal DNA.Nucleic acids research · 2016Article
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
A conserved hallmark of eukaryotic chromatin architecture is the distinctive array of well-positioned nucleosomes downstream from transcription start sites (TSS). Recent studies indicate that trans-acting factors establish this stereotypical array. Here, we present the first genome-wide in vitro and in vivo nucleosome maps for the ciliate Tetrahymena thermophila. In contrast with previous studies in yeast, we find that the stereotypical nucleosome array is preserved in the in vitro reconstituted map, which is governed only by the DNA sequence preferences of nucleosomes. Remarkably, this average in vitro pattern arises from the presence of subsets of nucleosomes, rather than the whole array, in individual Tetrahymena genes. Variation in GC content contributes to the positioning of these sequence-directed nucleosomes and affects codon usage and amino acid composition in genes. Given that the AT-rich Tetrahymena genome is intrinsically unfavorable for nucleosome formation, we propose that these "seed" nucleosomes--together with trans-acting factors--may facilitate the establishment of nucleosome arrays within genes in vivo, while minimizing changes to the underlying coding sequences.
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