Characterization of matrix attachment sites in the upstream region of a tobacco chitinase gene

The nuclear matrix is thought to partition the genome into functional and structural loop domains, and it has been implicated in several cellular processes, such as the replication and transcription of DNA and the processing of RNA. Therefore, the analysis of scaffold/matrix-associated DNA regions (S/MARs) might enhance our understanding of the functional roles of the higher-order organization of chromatin. In this study, the upstream region between positions -3320 and -1095 of the basic class I chitinase gene, CHN50, was shown to have specific affinity for the tobacco nuclear scaffold. Detailed analysis of nuclear scaffold-DNA binding in vitro revealed that two regions (positions -3320 to -2621 and -2221 to -1371) bound specifically to the nuclear scaffold. These S/MAR elements, designated S/M I and S/M II II, are A+T-rich sequences with 75% and 74% A+T residues, respectively, and may include a number of sequence motifs that have frequently been found in other S/MARs. Moreover, S/M II contains a curved DNA sequence with anomalous mobility on polyacrylamide gels. A circular permutation assay revealed that the center of this curved region was located between positions -1767 and -1759. The possible functions and structural features of the S/MAR elements in the upstream region of CHN50 are discussed.