High-throughput technologies now afford the opportunity to directly determine the distribution of MARs (matrix attachment regions) throughout a genome. The utility of cosmid and oligonucleotide platforms to identify human chromosome 16 MARs from preparations that employed LIS (lithium di-iodosalicylic acid) and NaCl extraction protocols was examined. The effectiveness of the platforms was then evaluated by Q-PCR (quantitative real-time PCR). Analysis revealed that caution must be exercised, since the representation of non-coding regions varies among platforms. Nevertheless, several interesting trends were revealed. We expect that these technologies will prove useful in systems approaches directed towards defining the role of MARs in various cell types and cellular processes.
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June 2007
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Conference Article|
May 22 2007
Genomewide identification of nuclear matrix attachment regions: an analysis of methods
A.K. Linnemann;
A.K. Linnemann
*Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, U.S.A.
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A.E. Platts;
A.E. Platts
*Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, U.S.A.
†Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, U.S.A.
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N. Doggett;
N. Doggett
‡Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, U.S.A.
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A. Gluch;
A. Gluch
§HZI – Helmholtz Center for Infection Research (formerly GBF), Braunschweig, Germany
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J. Bode;
J. Bode
§HZI – Helmholtz Center for Infection Research (formerly GBF), Braunschweig, Germany
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S.A. Krawetz
S.A. Krawetz
1
*Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, U.S.A.
†Department of Obstetrics and Gynecology, Wayne State University, Detroit, MI, U.S.A.
1To whom correspondence should be addressed (email [email protected]).
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Publisher: Portland Press Ltd
Received:
October 26 2006
Online ISSN: 1470-8752
Print ISSN: 0300-5127
© 2007 Biochemical Society
2007
Biochem Soc Trans (2007) 35 (3): 612–617.
Article history
Received:
October 26 2006
Citation
A.K. Linnemann, A.E. Platts, N. Doggett, A. Gluch, J. Bode, S.A. Krawetz; Genomewide identification of nuclear matrix attachment regions: an analysis of methods. Biochem Soc Trans 1 June 2007; 35 (3): 612–617. doi: https://doi.org/10.1042/BST0350612
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