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Matrix attachment region DNAs (MAR) are DNA sequences that bind to nuclear matrices after being digested by restriction enzymes.
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These S/MARs were tested for their ability to bind to nuclear matrix isolated from the organism.
The 15 putative S/MARs were then tested experimentally for their ability to bind to nuclear matrix.
It was seen that 8 of the 15 predicted S/MARs were able to bind to nuclear matrix proteins (GlSMAR7, GlSMAR10, GlSMAR16, GlSMAR20, GlSMAR22, GlSMAR26-1, GlSMand8 and GlSMAR66).
SATB1 is known to specifically bind to nuclear matrix attachment regions (MARs) and mediate formation of chromatin loops, a feature that has been attributed to the MeCP2 protein as well (Horike et al. 2005; Weitzel et al. 1997).
In this work, we have used all the available bioinformatics tools for predicting S/MARs from the genome of Giardia lamblia and used PCR based, as well as south-western assays to actually see how many of the predicted S/MARs were able to bind to nuclear matrix.
It is possible that in these early eukaryotes, the genome organization machinery is also in early stages of evolution and the S/MARs within the ORFs are actually the ones which in course of evolution would lose their ability to bind to the nuclear matrix completely.
The sequences flanking the core bind to the nuclear matrix and are therefore referred to as "matrix attachment regions" (MARs, denoted as M and M' in Figure 1).
The most common experimental method for identifying MAR uses re-association assays to define DNA fragments that bind to the nuclear matrix [ 12].
The most common experimental method for identifying S/MAR uses re-association assays to define DNA fragments that bind to the nuclear matrix [ 18].
MARs, DNA sequences which bind to the nuclear matrix, may function as anchoring sites for higher order chromatin structures including loops (41, 82).
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