ArticleNucleic acids research2009
The coexistence of the nucleosome positioning code with the genetic code on eukaryotic genomes.
Article in Nucleic acids research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Association of DNA methylation with steroidogenic enzymes in Cushing's adenoma.Endocrine-related cancer · 2022Article
- Proximal-end bias from in-vitro reconstituted nucleosomes and the result on downstream data analysis.PloS one · 2021Article
- Human exonization through differential nucleosome occupancy.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Adenine Enrichment at the Fourth CDS Residue in Bacterial Genes Is Consistent with Error Proofing for +1 Frameshifts.Molecular biology and evolution · 2017Article
- Regulation of chromatin folding by conformational variations of nucleosome linker DNA.Nucleic acids research · 2017Article
- Sister chromatid telomere fusions, but not NHEJ-mediated inter-chromosomal telomere fusions, occur independently of DNA ligases 3 and 4.Genome research · 2016Article
- Homopolymer tract organization in the human malarial parasite Plasmodium falciparum and related Apicomplexan parasites.BMC genomics · 2014Article
- Probing sequence-specific DNA flexibility in a-tracts and pyrimidine-purine steps by nuclear magnetic resonance (13)C relaxation and molecular dynamics simulations.Biochemistry · 2012Article
- Chromatin and epigenetic regulation of pre-mRNA processing.Human molecular genetics · 2012Review
- Predicting nucleosome binding motif set and analyzing their distributions around functional sites of human genes.Chromosome research : an international journal on the molecular, supramolecular and evolutionary aspects of chromosome biology · 2012Article
- Codons support the maintenance of intrinsic DNA polymer flexibility over evolutionary timescales.Genome biology and evolution · 2012Article
- Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes.Genome research · 2011Article
- DNA shape, genetic codes, and evolution.Current opinion in structural biology · 2011Review
- Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae.Epigenetics & chromatin · 2010Article
- Abundant oligonucleotides common to most bacteria.PloS one · 2010Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
It is known that there are several codes residing simultaneously on the DNA double helix. The two best-characterized codes are the genetic code--the code for protein production, and the code for DNA packaging into nucleosomes. Since these codes have to coexist simultaneously on the same DNA region, both must be degenerate to allow this coexistence. A-tracts are homopolymeric stretches of several adjacent deoxyadenosines on one strand of the double helix, having unusual structural properties, which were shown to exclude nucleosomes and as such are instrumental in setting the translational positioning of DNA within nucleosomes. We observe, cross-kingdoms, a strong codon bias toward the avoidance of long A-tracts in exon regions, which enables the formation of high density of nucleosomes in these regions. Moreover, long A-tract avoidance is restricted exclusively to nucleosome-occupied exon regions. We show that this bias in codon usage is sufficient for enabling DNA organization within nucleosomes without constraints on the actual code for proteins. Thus, there is inter-dependency of the two major codes within DNA to allow their coexistence. Furthermore, we show that modulation of A-tract occurrences in exon versus non-exon regions may result in a unique alternation of the diameter of the '30-nm' fiber model.
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