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Molecular and Cellular Biology, March 2005, p. 1891-1899, Vol. 25, No. 5
0270-7306/05/$08.00+0     doi:10.1128/MCB.25.5.1891-1899.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.

A Motif within SET-Domain Proteins Binds Single-Stranded Nucleic Acids and Transcribed and Supercoiled DNAs and Can Interfere with Assembly of Nucleosomes

Wladyslaw A. Krajewski,1,2* Tatsuya Nakamura,2 Alexander Mazo,2 and Eli Canaani3*

Department of Biochemistry, Institute of Developmental Biology, Russian Academy of Sciences, Moscow, Russia,1 Kimmel Cancer Center and Department of Microbiology and Immunology, Thomas Jefferson University, Philadelphia, Pennsylvania,2 Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel3

Received 26 October 2004/ Accepted 29 November 2004

The evolutionary conserved SET domain is present in many eukaryotic chromatin-associated proteins, including some members of the trithorax (TrxG) group and the polycomb (PcG) group of epigenetic transcriptional regulators and modifiers of position effect variegation. All SET domains examined exhibited histone lysine methyltransferase activity, implicating these proteins in the generation of epigenetic marks. However, the mode of the initial recruitment of SET proteins to target genes and the way that their association with the genes is maintained after replication are not known. We found that SET-containing proteins of the SET1 and SET2 families contain motifs in the pre-SET region or at the pre-SET-SET and SET-post-SET boundaries which very tightly bind single-stranded DNA (ssDNA) and RNA. These motifs also bind stretches of ssDNA generated by superhelical tension or during the in vitro transcription of duplex DNA. Importantly, such binding withstands nucleosome assembly, interfering with the formation of regular nucleosomal arrays. Two representatives of the SUV39 SET family, SU(VAR)3-9 and G9a, did not bind ssDNA. The trxZ11 homeotic point mutation, which is located within TRX SET and disrupts embryonic development, impairs the ssDNA binding capacity of the protein. We suggest that the motifs described here may be directly involved in the biological function(s) of SET-containing proteins. The binding of single-stranded nucleic acids might play a role in the initial recruitment of the proteins to target genes, in the maintenance of their association after DNA replication, or in sustaining DNA stretches in a single-stranded configuration to allow for continuous transcription.

* Corresponding author. Mailing address for Wadyslaw A. Krajewski: Department of Biochemistry, Institute of Developmental Biology, Russian Academy of Sciences, Vavilova Str. 26, 117808 Moscow, Russia. Phone: 7-095-135887. Fax: 7-095-1358012. E-mail: wkrajewski{at}hotmail.com. Mailing address for Eli Canaani: Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel. Phone: 972-8934-2292. Fax: 972-8934-4125. E-mail: eli.canaani{at}weizmann.ac.il.

Molecular and Cellular Biology, March 2005, p. 1891-1899, Vol. 25, No. 5
0022-538X/05/$08.00+0     doi:10.1128/MCB.25.5.1891-1899.2005
Copyright © 2005, American Society for Microbiology. All Rights Reserved.



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