A tissue-specific MAR SAR DNA-binding protein with unusual binding site recognition

  title={A tissue-specific 
                DNA-binding protein with unusual binding site recognition },
  author={Liliane A. Dickinson and Tadashi Joh and Yoshinori Kohwi and Terumi Kohwi-Shigematsu},
A Novel Matrix Attachment Region DNA Binding Motif Identified Using a Random Phage Peptide Library (*)
Phage display may provide a general tool for rapid identification of DNA binding peptide motifs and show that a nine amino acid sequence in SATB1 represents a key MAR binding motif.
Nucleolin is a matrix attachment region DNA-binding protein that specifically recognizes a region with high base-unpairing potential
Nucleolin effectively distinguishes between a double-stranded wild-type synthetic MAR sequence with a high base-unpairing potential and its mutated version that has lost the unpairing capability but is still A+T rich.
The regulatory element 3' to the A gamma-globin gene binds to the nuclear matrix and interacts with special A-T-rich binding protein 1 (SATB1), an SAR/MAR-associating region DNA binding protein.
Binding of SATB1 to two sites within the 3' A gamma regulatory element and its MAR/SAR activity suggests that this element may influence gene expression through interaction with the nuclear matrix.
Nuclear matrix protein ARBP recognizes a novel DNA sequence motif with high affinity.
The results indicate that ARBP recognizes a novel DNA sequence motif containing the central sequence 5'-GGTGT-3' and flanking AT-rich sequences andStructural elements of the sequence motif are probably also recognized.
The combination of sequence-specific and nonspecific DNA-binding modes of transcription factor SATB1.
It is believed that the lack of highly conserved basic residues in the helix relevant to the base recognition loosens its fitting into the DNA groove and impairs the specific binding, and the combination of the sequence-specific and nonspecific DNA-binding modes of SATB1 should be advantageous in a search for target loci during transcriptional regulation.
PDZ domain-mediated dimerization and homeodomain-directed specificity are required for high-affinity DNA binding by SATB1
A model for SATB1–DNA complex in which the HDs bind in an antiparallel fashion to the palindromic consensus element via minor groove, bridged by the PDZ-like dimerization domain is proposed.
Structural basis for recognition of the matrix attachment region of DNA by transcription factor SATB 1
A significant number of equivalent contacts are observed for typically four-helix POU-specific domains of POUhomologous proteins, indicating that these domains share a common framework of the DNA-binding mode, recognizing partially similar DNA sequences.
An Atypical Homeodomain in SATB1 Promotes Specific Recognition of the Key Structural Element in a Matrix Attachment Region*
Site-directed mutagenesis of the core unwinding element in the 3′ MAR of the immunoglobulin heavy chain gene enhancer revealed the sequence 5′-(C/A)TAATA-3′ to be essential for the increase in affinity mediated by the homeodomain.
A Large DNA-binding Nuclear Protein with RNA Recognition Motif and Serine/Arginine-rich Domain (*)
Human NP220 is a novel type of nucleoplasmic protein with multiple domains that binds to double-stranded DNA fragments by recognizing clusters of cytidines and has an arginine/serine-rich domain commonly found in pre-mRNA splicing factors.


Avian nuclear matrix proteins bind very tightly to cellular DNA of the beta-globin gene enhancer in a tissue-specific fashion.
Avian nuclear matrices are examined for the presence of very tight cellular DNA-protein complexes in the region of the beta-globin gene enhancer and of several other avian genes to suggest certain regions of cellular DNA are very tightly, perhaps covalently, attached to nuclear matrix-associated proteins.
A mammalian high mobility group protein recognizes any stretch of six A.T base pairs in duplex DNA.
Findings indicate that, rather than binding to a few specific DNA sequences, alpha-protein recognizes a configuration of the minor groove characteristic of short runs of A X T base pairs.
Detection of an altered DNA conformation at specific sites in chromatin and supercoiled DNA.
The results suggest that well-defined regions of DNA with effectively unpaired bases occur in intact nuclei and that these structures may be important for specific recognition because they are tissue specific and are found at putative regulatory regions.
Hierarchical binding of DNA fragments derived from scaffold-attached regions: correlation of properties in vitro and function in vivo.
A rational approach is proposed for predicting the SAR mediated transcriptional enhancements in vivo from their binding properties in a standardized in vitro assay and a model involving a multiple-site attachment to protein scaffolds is suggested.
The missing nucleoside experiment: a new technique to study recognition of DNA by protein.
A new technique for quickly determining which nucleosides in a DNA molecule are contacted by a sequence-specific DNA-binding protein is reported, and the missing nucleoside data show that the amino-terminal arms of lambda repressor make energetically important contacts with positions 7 and 8 and the central dyad base pair of the operator.
In situ detection of sequence-specific DNA binding activity specified by a recombinant bacteriophage.
We have used a recombinant bacteriophage that expresses the DNA-binding domain of C/EBP to optimize conditions for a screening technique that may facilitate the cloning of genes that encode