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In-silico prediction and observations of nuclear matrix attachment

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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.

Abbreviations

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

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Correspondence to Stephen A. Krawetz.

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Key words

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