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DNA compaction by the higher-order assembly of PRH/Hex homeodomain protein oligomers.

TitleDNA compaction by the higher-order assembly of PRH/Hex homeodomain protein oligomers.
Publication TypeJournal Article
Year of Publication2010
AuthorsSoufi A, Sawasdichai A, Shukla A, Noy P, Dafforn T, Smith C, Jayaraman P-S, Gaston K
JournalNucleic Acids Res
Volume38
Issue21
Pagination7513-25
Date Published2010 Nov
ISSN1362-4962
KeywordsBinding Sites, DNA, Homeodomain Proteins, Humans, K562 Cells, Nucleic Acid Conformation, Protein Multimerization, Transcription Factors, Transcription, Genetic
Abstract

Protein self-organization is essential for the establishment and maintenance of nuclear architecture and for the regulation of gene expression. We have shown previously that the Proline-Rich Homeodomain protein (PRH/Hex) self-assembles to form oligomeric complexes that bind to arrays of PRH binding sites with high affinity and specificity. We have also shown that many PRH target genes contain suitably spaced arrays of PRH sites that allow this protein to bind and regulate transcription. Here, we use analytical ultracentrifugation and electron microscopy to further characterize PRH oligomers. We use the same techniques to show that PRH oligomers bound to long DNA fragments self-associate to form highly ordered assemblies. Electron microscopy and linear dichroism reveal that PRH oligomers can form protein-DNA fibres and that PRH is able to compact DNA in the absence of other proteins. Finally, we show that DNA compaction is not sufficient for the repression of PRH target genes in cells. We conclude that DNA compaction is a consequence of the binding of large PRH oligomers to arrays of binding sites and that PRH is functionally and structurally related to the Lrp/AsnC family of proteins from bacteria and archaea, a group of proteins formerly thought to be without eukaryotic equivalents.

DOI10.1093/nar/gkq659
Alternate JournalNucleic Acids Res.
PubMed ID20675722
PubMed Central IDPMC2995075
Grant List055663/Z/98/Z / / Wellcome Trust / United Kingdom
/ / Biotechnology and Biological Sciences Research Council / United Kingdom
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