victoriagugl.blogg.se - Protein scaffold in dna

Interestingly, even though many of these proteins have been thoroughly characterized, it has not been possible to gain an understanding of the mechanism of binding specificity in molecular terms, and it has also been difficult to decide which of the proteins are required for nuclear architecture in vivo. We have isolated and characterized the human nuclear proteins SAF-A (scaffold attachment factor A), also known as hnRNP-U because of its association with hnRNP particles ( 14, 15, 25, 44), and SAF-B ( 43). These proteins include ubiquitous, abundant proteins like topoisomerase II ( 1), histone H1 ( 20), lamin B1 ( 34), HMG I/Y ( 52), and nucleolin ( 12) but also proteins that are expressed primarily in certain cell types, like SATB1 ( 11) or p114 ( 51). Several SAR binding proteins have been identified and characterized in the last years. Natural SARs are usually between 600 and 3,000 bp long, suggesting a requirement for cooperative interactions between the SAR and cognate binding proteins in the nuclear scaffold.

In addition to the presence of A-tracts and other AT-rich sequence motifs, such as unwinding elements ( 3) or the recently described matrix attachment region recognition signature (MRS) ( 50), SARs need to have a certain length to exhibit a specific interaction.

dT) n sequences, thereby suppressing or dissociating interactions of SARs with the nuclear scaffold ( 24).

This minor-groove-binding peptide antibiotic selectively binds to (dA The importance of these A-tracts for the interaction of SARs with the nuclear scaffold has been demonstrated by experiments with distamycin. In fact, most characterized SARs contain homopolymeric runs of A or T (A-tracts) that result in a characteristically narrow minor groove of DNA (reviewed in reference 4). Instead, SARs may be recognized by structural features and/or short sequence motifs clustered in SAR but not non-SAR DNA. The recognition of SARs by their cognate binding proteins is not yet understood in molecular terms but apparently does not depend on a precise recognition sequence because a consensus sequence common to all SARs could not be identified. Termed SARs (scaffold attachment regions) or MARs (matrix attachment regions) ( 8, 17), these DNA elements are bound by nuclear scaffolds in an evolutionarily conserved manner ( 9), presumably because of one or more conserved binding proteins present in these scaffolds. Attachment of chromatin to the nuclear scaffold seems to occur via specialized AT-rich DNA elements that have been found in all eukaryotic organisms investigated and have been proposed to partition the genome into distinct, topologically independent loops of variable size ( 30). One much debated possibility is that structure and function of the nucleus are determined by a proteinaceous, skeletonlike entity called the nuclear scaffold or nuclear matrix and its interaction with architectural DNA elements in the genome ( 18). Despite many efforts to elucidate the molecular basis for nuclear architecture, a clear conception of higher-order structures in the nucleus has not yet emerged. In the eukaryotic nucleus, chromosomes occupy individual, nonoverlapping territories and reactions of DNA and RNA metabolism are confined to discrete structures in the nuclear interior (for review, see reference 40). 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.

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. 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. 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. This domain was first identified in human scaffold attachment factor A (SAF-A) and was thus designated SAF-Box. We describe a novel, evolutionarily conserved protein domain that specifically binds to SARs but is not related to SAR binding motifs of other proteins. 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. 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.