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. 2006 Jun 1;11(2):191–213. doi: 10.2478/s11658-006-0016-4

In-silico prediction and observations of nuclear matrix attachment

Adrian E Platts 1, Amelia K Quayle 2, Stephen A Krawetz 1,2,3,✉
PMCID: PMC6276010  PMID: 16847565

Abstract

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, MARSCAN, MarFinder, MARWIZ, ChrClass, SMARTest, SIDD

Full Text

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Abbreviations used

ChrClass

a linear discriminant analysis approach to MAR prediction

CS

chromosomal scaffold

CT

chromosome territory

IUPAC

International Union of Pure and Applied Chemists

LDA

linear discriminant analysis

MAR

matrix attachment region

MARFinder

a cumulative probability MAR prediction tool

MARSCAN

a MAR prediction tool to detect the MRS

MRS

the bipartite MAR recognition signature

MARWIZ

a commercial implementation of marfinder

MHC

major histocompatibility complex

mRNP

messenger ribonucleic acid protein

NM

nuclear matrix

PWM

position weight matrices

SIDD

stress induced duplex destabilization

S/MAR

scaffold/matrix attachment regions (synonymous with MAR)

SMARTest

a MAR prediction tool developed commercially by Genomatix

Tw

number of helical turns in a constrained DNA loop

Wr

wumber of superhelical turns in a constrained loop

Footnotes

Invited paper

All referenced websites were verified. URLs and their content are subject to change. The content referenced in this paper can be accessed using internet archive tools such as www.archive.org with the query restricted to November 2005.

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