In-silico prediction and observations of nuclear matrix attachment
Cellular & Molecular Biology Letters volume 11, pages 191–213 (2006)
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
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
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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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). https://doi.org/10.2478/s11658-006-0016-4
- Nuclear matrix
- Matrix attachment regions