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

Cell. 1992 Aug 21;70(4):631-45. doi: 10.1016/0092-8674(92)90432-c.


A human cDNA was cloned that encodes a DNA-binding protein (SATB1) that is expressed predominantly in thymus and binds selectively to the nuclear matrix/scaffold-associating DNAs (MARs/SARs). Missing nucleoside experiments showed that SATB1 selectively binds in a special AT-rich sequence context where one strand consists of mixed A's, T's, and C's, excluding G's (ATC sequences). When this feature is destroyed by mutation, SATB1 binding is greatly reduced even if the direct contact sequence remains intact. Conjunctional SATB1-binding sequences become stably unpaired in supercoiled DNA. Specific mutations that diminish the unwinding potential greatly reduce SATB1 binding. However, SATB1 does not bind single-stranded DNA. Chemical interference assays show that SATB1 binds along the minor groove with very little contact with the bases. This suggests that SATB1 recognizes the ATC sequence indirectly through the altered sugar-phosphate backbone structure present in the double-stranded DNA.

Publication types

  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Sequence
  • Antigens, Nuclear
  • Base Sequence
  • Binding Sites
  • DNA / metabolism*
  • DNA Mutational Analysis
  • DNA-Binding Proteins / biosynthesis*
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / genetics
  • DNA-Binding Proteins / metabolism
  • Humans
  • Matrix Attachment Region Binding Proteins*
  • Molecular Sequence Data
  • Nuclear Matrix / chemistry*
  • Nuclear Proteins / genetics
  • Nuclear Proteins / metabolism*
  • Thymus Gland / chemistry


  • Antigens, Nuclear
  • DNA-Binding Proteins
  • Matrix Attachment Region Binding Proteins
  • Nuclear Proteins
  • SATB1 protein, human
  • DNA

Associated data

  • GENBANK/L05499
  • GENBANK/M87278
  • GENBANK/M94264
  • GENBANK/M97287
  • GENBANK/M97694
  • GENBANK/S72766
  • GENBANK/S72767
  • GENBANK/S72768
  • GENBANK/S72769
  • GENBANK/S72771