Matrix association region (MAR) is the DNA sequences in eukaryotic genome which can specifically associate with the nuclear matrix. By means of specific interaction with some MAR-binding proteins, MAR plays important roles in eukaryotic gene's replication, expression and regulation, and chromosomal construction. MAR-binding proteins include some structural proteins in chromatin or nuclear matrix (such as histone H₁, topoisomerase Ⅰ & Ⅱ, HMG I/Y, lamin B₁, and matrins.) and some tissue-specifically expressed proteins, including SATB₁ (special AT-rich binding protein 1) and osteocalcin gene promoter-binding factors. By the relationship with the nuclear matrix, these MAR-binding proteins can be classified in three groups, nuclear matrix-abundant composition, rare composition and non-nuclear matrix composition. Their interactions with MARs were compared and analyzed as well.