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Determination of the in vivo distribution of nuclear matrix attachment regions using a polymerase chain reaction-based assay in Arabidopsis thaliana

Paper ID Volume ID Publish Year Pages File Format Full-Text
21744 43238 2009 9 PDF Available
Title
Determination of the in vivo distribution of nuclear matrix attachment regions using a polymerase chain reaction-based assay in Arabidopsis thaliana
Abstract

Matrix attachment regions (MARs) are the regions on genomic DNA that are attached to the nuclear matrix in eukaryotes. Previous in vitro and in silico MAR analyses have shown that MARs distribute at average intervals of about 5 kb on the Arabidopsis thaliana genome. However, the in vivo evidence for the distribution of MARs in A. thaliana is lacking. Therefore, we have used a polymerase chain reaction (PCR)-based method to investigate the in vivo locations of MARs across an 80 kb region of A. thaliana genome. This assay indicated that the average interval of MARs within this region is 4.7 kb (range 1 to 11 kb), well consistent with the previous in vitro and in silico MAR studies. This result suggests that average size of the chromatin loop in A. thaliana is smaller when compared with the other eukaryotes, in which the sizes are known to vary in the range from 9 to 100 kb. However, we found that the number of genes per chromatin loop (1–3 genes) in A. thaliana is similar to those found in other eukaryotes. Furthermore, as in animals' MARs, DNase I hypersensitive sites were also found in the MARs end-region in A. thaliana. Our results suggest that basic organization of chromatin loop in A. thaliana is similar to other eukaryotes in the view that it contains a few genes, and that the average size of chromatin loop in eukaryotes is possibly determined by genome structure, such as gene density and average gene size.

Keywords
Matrix attachment region; Chromatin loop; Nuclear matrix; In vivo MAR-PCR assay; In vitro MAR binding assay; DNase I hypersensitive site; Arabidopsis thaliana
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Determination of the in vivo distribution of nuclear matrix attachment regions using a polymerase chain reaction-based assay in Arabidopsis thaliana
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Publisher
Database: Elsevier - ScienceDirect
Journal: Journal of Bioscience and Bioengineering - Volume 108, Issue 1, July 2009, Pages 11–19
Authors
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Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us