SATB1 specifically recognizes and binds to specialized genomic regions with an 
ATC sequence context with high base-unpairing propensity. Such base-unpairing 
regions (BURs) are typically identified within nuclear scaffold- or 
matrix-attachment regions (S/MARs). SATB1 is a homeodomain protein and is 
predominantly expressed in thymocytes. We obtained BHK cell lines expressing low 
levels of SATB1 by stable transfection and investigated its effect on stably 
integrated MAR-linked SV40 enhancer/promoter-driven luciferase reporter genes. 
For this study, both naturally occurring and synthetic MARs, as well as an 
AT-rich non-MAR control, were tested. Previous studies demonstrated that MAR 
sequences augment transcription of the linked reporter luciferase gene. Here, we 
show that SATB1 dramatically reduces the high levels of MAR-linked luciferase 
gene transcription. Transcription was virtually abolished for a reporter gene 
surrounded by two MARs at the 5' and 3' ends of the gene, which otherwise confer 
the highest level of transcriptional augmentation. On the other hand, SATB1 did 
not affect expression of an AT-rich non-MAR-linked luciferase gene or of 
endogenous housekeeping genes. This study shows that SATB1 acts as a strong 
transcriptional suppressor on a reporter gene linked to MARs when it is stably 
integrated into chromatin.