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Nucleic Acids Research 2005 33(1):e1; doi:10.1093/nar/gni001
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Published online 11 January 2005

© 2005, the authors Nucleic Acids Research, Vol. 33 No. 1 © Oxford University Press 2005; all rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.

Methods Online

Rapid, solid-phase based automated analysis of chromatin structure and transcription factor occupancy in living eukaryotic cells

Richard Ingram, Hiromi Tagoh, Arthur D. Riggs1 and Constanze Bonifer*

Molecular Medicine Unit, University of Leeds, St James's University Hospital Leeds LS9 7TF, UK 1 Division of Biology, Beckman Institute of City of Hope 1500 Duarte Road, Duarte, CA 91010, USA

*To whom correspondence should be addressed. Tel: +44 113 206 5676; Fax: +44 113 244 4475; Email: c.bonifer{at}leeds.ac.uk

Received October 13, 2004. Revised December 3, 2004. Accepted December 3, 2004.

Transcription factors, chromatin components and chromatin modification activities are involved in many diseases including cancer. However, the means by which alterations in these factors influence the epigenotype of specific cell types is poorly understood. One problem that limits progress is that regulatory regions of eukaryotic genes sometimes extend over large regions of DNA. To improve chromatin structure–function analysis over such large regions, we have developed an automated, relatively simple procedure that uses magnetic beads and a capillary sequencer for ligation-mediated-PCR (LM-PCR). We show that the procedure can be used for the rapid examination of chromatin fine-structure, nucleosome positioning as well as changes in transcription factor binding-site occupancy during cellular differentiation.


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