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In-silico prediction and observations of nuclear matrix attachment


The nuclear matrix is a functionally adaptive structural framework interior to the nuclear envelope. The nature and function of this nuclear organizer remains the subject of widespread discussion in the epigenetic literature. To draw this discussion together with a view to suggest a way forward we summarize the biochemical evidence for the modalities of DNA-matrix binding alongside the in-silico predictions. Concordance is exhibited at various, but not all levels. On the one hand, both the reiteration and sequence similarity of some elements of Matrix Attachment Regions suggest conservation. On the other hand, in-silico predictions suggest additional unique components. In bringing together biological and sequence evidence we conclude that binding may be hierarchical in nature, reflective of a biological role in replicating, transcribing and potentiating chromatin. Nuclear matrix binding may well be more complex than the widely accepted simple loop model.



a linear discriminant analysis approach to MAR prediction


chromosomal scaffold


chromosome territory


International Union of Pure and Applied Chemists


linear discriminant analysis


matrix attachment region


a cumulative probability MAR prediction tool


a MAR prediction tool to detect the MRS


the bipartite MAR recognition signature


a commercial implementation of marfinder


major histocompatibility complex


messenger ribonucleic acid protein


nuclear matrix


position weight matrices


stress induced duplex destabilization


scaffold/matrix attachment regions (synonymous with MAR)


a MAR prediction tool developed commercially by Genomatix


number of helical turns in a constrained DNA loop


wumber of superhelical turns in a constrained loop


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Correspondence to Stephen A. Krawetz.

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Platts, A.E., Quayle, A.K. & Krawetz, S.A. In-silico prediction and observations of nuclear matrix attachment. Cell. Mol. Biol. Lett. 11, 191–213 (2006).

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Key words

  • Nuclear matrix
  • Matrix attachment regions
  • In-silico
  • Prediction
  • MarFinder
  • ChrClass
  • SMARTest
  • SIDD