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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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