DNA rotational positioning in a regulatory nucleosome is determined by base sequence. An algorithm to model the preferred superhelix

Piña, Benjamı́n; Truss, Mathias; Ohlenbusch, Heiko H.; Postma, J. P. M.; Beato, Miguel

doi:10.1093/nar/18.23.6981

Cited by 42 publications

(16 citation statements)

References 25 publications

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“…Comparison of the conserved periodicity pattern revealed by this analysis with other DNA sequences used for positioning studies revealed that an artificial positioning sequence consisting only of tandem 20-bp repeats (9) that fails to position nucleosomes translationally in vivo (47,48) lacked a significant periodicity minimum at the midpoint (Figure 2c). The average periodicity index for this sequence was of comparable magnitude to regions of high periodicity index in in vivo mapped nucleosomes.…”

Section: Resultsmentioning

confidence: 93%

A translational signature for nucleosome positioning in vivo

Caserta¹,

Agricola²,

Churcher³

et al. 2009

Nucleic Acids Research

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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 (∼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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Section: Resultsmentioning

confidence: 93%

A translational signature for nucleosome positioning in vivo

Caserta¹,

Agricola²,

Churcher³

et al. 2009

Nucleic Acids Research

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“…This depends on rotational preferences of different dinucleotides. 4,5 It has been considered that organization of nucleosomes and structure of histones are extremely conservative. However, this point of view appears to be oversimplified.…”

Section: Nucleosomes: Structural and Functional Differencesmentioning

confidence: 99%

Chromatin Domains and Regulation of Transcription

Razin

Iarovaia

Sjakste

et al. 2007

Journal of Molecular Biology

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“…Transcription of reconstituted chromatin with regularly spaced nucleosomes containing GAL4-VP16, prebound to DNA before reconstitution of either Hl-deficient or Hl-containing chromatin, yields similar efficiencies (216). A role for chromatin structure in MMTV regulation has been postulated based on functional studies with cell lines carrying stable minichromosomes (219, 220) and on in vitro nucleosome reconstitution studies (221)(222)(223). Preformed Hl-deficient chromatin, but not Hl-containing chromatin, can be activated by GAL-VP16 (216).…”

Section: Biochemical Evidence For a Role Of Chromatin In Transcriptiomentioning

confidence: 99%