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Molecular and Cellular Biology, February 2007, p. 864-877, Vol. 27, No. 3
0270-7306/07/$08.00+0     doi:10.1128/MCB.01593-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Multiple Modes of Interaction between the Methylated DNA Binding Protein MeCP2 and Chromatin{triangledown}

Tatiana Nikitina,1 Xi Shi,2 Rajarshi P. Ghosh,2 Rachel A. Horowitz-Scherer,1 Jeffrey C. Hansen,3 and Christopher L. Woodcock1,2*

Department of Biology,1 Program in Molecular and Cellular Biology, University of Massachusetts, Amherst, Massachusetts 01003,2 Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado 805233

Received 25 August 2006/ Returned for modification 2 October 2006/ Accepted 5 November 2006

Mutations of the methylated DNA binding protein MeCP2, a multifunctional protein that is thought to transmit epigenetic information encoded as methylated CpG dinucleotides to the transcriptional machinery, give rise to the debilitating neurodevelopmental disease Rett syndrome (RTT). In this in vitro study, the methylation-dependent and -independent interactions of wild-type and mutant human MeCP2 with defined DNA and chromatin substrates were investigated. A combination of electrophoretic mobility shift assays and visualization by electron microscopy made it possible to understand the different conformational changes underlying the gel shifts. MeCP2 is shown to have, in addition to its well-established methylated DNA binding domain, a methylation-independent DNA binding site (or sites) in the first 294 residues, while the C-terminal portion of MeCP2 (residues 295 to 486) contains one or more essential chromatin interaction regions. All of the RTT-inducing mutants tested were quantitatively bound to chromatin under our conditions, but those that tend to be associated with the more severe RTT symptoms failed to induce the extensive compaction observed with wild-type MeCP2. Two modes of MeCP2-driven compaction were observed, one promoting nucleosome clustering and the other forming DNA-MeCP2-DNA complexes. MeCP2 binding to DNA and chromatin involves a number of different molecular interactions, some of which result in compaction and oligomerization. The multifunctional roles of MeCP2 may be reflected in these different interactions.

* Corresponding author. Mailing address: Biology Department, University of Massachusetts, Amherst, MA 01003. Phone: (413) 545-2825. Fax: (413) 545-3243. E-mail: chris{at}bio.umass.edu.

{triangledown} Published ahead of print on 13 November 2006.

Molecular and Cellular Biology, February 2007, p. 864-877, Vol. 27, No. 3
0270-7306/07/$08.00+0     doi:10.1128/MCB.01593-06
Copyright © 2007, American Society for Microbiology. All Rights Reserved.



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