ArticleNucleic acids research2009
A translational signature for nucleosome positioning in vivo.
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 17 papers.
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Who cites it
17 citing papers in PubMed.
- The Active Mechanism of Nucleosome Depletion by Poly(dA:dT) Tracts In Vivo.International journal of molecular sciences · 2021Review
- Absolute nucleosome occupancy map for theGenome research · 2019Article
- High-resolution biophysical analysis of the dynamics of nucleosome formation.Scientific reports · 2016Article
- Nucleosome positioning in yeasts: methods, maps, and mechanisms.Chromosoma · 2015Review
- BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE.Biomaterials science · 2014Article
- Nucleosome Positioning with Set of Key Positions and Nucleosome Affinity.The open biomedical engineering journal · 2014Article
- Global remodeling of nucleosome positions in C. elegans.BMC genomics · 2013Article
- Snf1/AMPK regulates Gcn5 occupancy, H3 acetylation and chromatin remodelling at S. cerevisiae ADY2 promoter.Biochimica et biophysica acta · 2012Article
- Remodelers organize cellular chromatin by counteracting intrinsic histone-DNA sequence preferences in a class-specific manner.Molecular and cellular biology · 2012Article
- Activator-independent transcription of Snf1-dependent genes in mutants lacking histone tails.Molecular microbiology · 2011Article
- Gene repression by minimal lac loops in vivo.Nucleic acids research · 2010Article
- Structural constraints revealed in consistent nucleosome positions in the genome of S. cerevisiae.Epigenetics & chromatin · 2010Article
- Direct measurements of the nucleosome-forming preferences of periodic DNA motifs challenge established models.Nucleic acids research · 2010Article
- Article
- Structure-based analysis of DNA sequence patterns guiding nucleosome positioning in vitro.Journal of biomolecular structure & dynamics · 2010Article
- The DNA sequence-dependence of nucleosome positioning in vivo and in vitro.Journal of biomolecular structure & dynamics · 2010Article
- DNA curvature and flexibility in vitro and in vivo.Quarterly reviews of biophysics · 2010Review
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Authors and funding
7 authors.
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Abstract
In vivo nucleosomes often occupy well-defined preferred positions on genomic DNA. An important question is to what extent these preferred positions are directly encoded by the DNA sequence itself. We derive here from in vivo positions, accurately mapped by partial micrococcal nuclease digestion, a translational positioning signal that identifies the approximate midpoint of DNA bound by a histone octamer. This midpoint is, on average, highly A/T rich ( approximately 73%) and, in particular, the dinucleotide TpA occurs preferentially at this and other outward-facing minor grooves. We conclude that in this set of sequences the sequence code for DNA bending and nucleosome positioning differs from the other described sets and we suggest that the enrichment of AT-containing dinucleotides at the centre is required for local untwisting. We show that this signature is preferentially associated with nucleosomes flanking promoter regions and suggest that it contributes to the establishment of gene-specific nucleosome arrays.
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