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Molecular and Cellular Biology, October 2000, p. 7480-7489, Vol. 20, No. 20
0270-7306/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.

SAF-Box, a Conserved Protein Domain That Specifically Recognizes Scaffold Attachment Region DNA

Michael Kipp,1 Frank Göhring,1,2 Thorsten Ostendorp,1 Cornelis M. van Drunen,3,4 Roel van Driel,4 Michael Przybylski,5 and Frank O. Fackelmayer1,*

Departments of Biology1 and Chemistry,5 University of Konstanz, 78434 Konstanz, and GATC GmbH, 78467 Konstanz,2 Germany; Department of Anatomy of the Birmingham Medical School, Birmingham University, B15 2TT Birmingham, United Kingdom3; and E. C. Slater Institute, University of Amsterdam, TV1018 Amsterdam, The Netherlands4

Received 30 May 2000/Returned for modification 8 July 2000/Accepted 31 July 2000

SARs (scaffold attachment regions) are candidate DNA elements for partitioning eukaryotic genomes into independent chromatin loops by attaching DNA to proteins of a nuclear scaffold or matrix. The interaction of SARs with the nuclear scaffold is evolutionarily conserved and appears to be due to specific DNA binding proteins that recognize SARs by a mechanism not yet understood. We describe a novel, evolutionarily conserved protein domain that specifically binds to SARs but is not related to SAR binding motifs of other proteins. This domain was first identified in human scaffold attachment factor A (SAF-A) and was thus designated SAF-Box. The SAF-Box is present in many different proteins ranging from yeast to human in origin and appears to be structurally related to a homeodomain. We show here that SAF-Boxes from four different origins, as well as a synthetic SAF-Box peptide, bind to natural and artificial SARs with high specificity. Specific SAR binding of the novel domain is achieved by an unusual mass binding mode, is sensitive to distamycin but not to chromomycin, and displays a clear preference for long DNA fragments. This is the first characterization of a specific SAR binding domain that is conserved throughout evolution and has DNA binding properties that closely resemble that of the unfractionated nuclear scaffold.

* Corresponding author. Mailing address: Department of Biology, University of Konstanz, 78434 Konstanz, Germany. Phone: 49 7531-884238. Fax: 49 7531-884036. E-mail: Frank.Fackelmayer{at}uni-konstanz.de.

Molecular and Cellular Biology, October 2000, p. 7480-7489, Vol. 20, No. 20
0270-7306/00/$04.00+0
Copyright © 2000, American Society for Microbiology. All rights reserved.


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