Identification and characterization of scaffold-associated region (SAR) of rRNA gene of silkwormAttacus ricini

Abstract

identify the specific nuclear scaffold-bound DNA sequence in rRNA gene clusters of silkwormAttacus ricini, the detergent-like salt lithium 3', 5' diiodosalicylate (LIS) was used for the preparation of nuclear scaffold. Through Southern hybridization, using different DNA stretches of rRNA gene as the probe, a scaffold-associated region (SAR) in the 5-non transcribed spacer (NTS) of rRNA gene has been identified. Exonuclease III digestion was used to narrow down the sequence of matrix attachment fragment. It was defined as a specific attachment site within the SacII-EcoRI fragment. It is about 1 kb in length and AT-rich (> 70%). Computer analysis of the SAR sequencing data showed that there are topoisomerase II cleavage sites, ATATTT box, and yeast autonomously replication sequence (ARS). The d(AT)(18) specific DNA sequence of the SAR, which was determined previously, was an S1 nuclease hypersensitive site. It might be a cis-element of DNA-signal characteristic for SAR.