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  • Open Access

In-silico prediction and observations of nuclear matrix attachment

Cellular & Molecular Biology LettersAn International Journal200611:16

  • Received: 15 December 2005
  • Accepted: 26 February 2006
  • Published:


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.

Key words

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