IDENTIFICATION OF SCAFFOLD MATRIX ATTACHMENT REGION IN RECURRENT SITEOF WOODCHUCK HEPATITIS-VIRUS INTEGRATION/

Scaffold or matrix attachment regions (S/MARs) are noncoding genomic D NA sequences displaying in vitro selective binding affinity for nuclea r scaffold. They have been reported to be involved in the physical att achment of genomic DNA to the nuclear scaffold, and thus in the organi zation of the chromatin in functional loops or domains, and in the reg ulation of gene expression, In this work, we report the identification of an S/MAR in a woodchuck chromosomal locus, named b3n, previously d escribed as a recurrent site of woodchuck hepatitus virus (WHV) DNA in tegration in woodchuck hepatocellular carcinoma (HCC). The 4.3-kb sequ ence of this locus contains several Alu-like repeats and a gag-like co ding region with frameshift mutations, Computer analysis revealed the presence of a region with unusually high AT content, typical of most S /MARs, and of specific motifs (A boxes, T boxes, topoisomerase II site s, and unwinding elements) overlapping or in proximity to the region w ith high AT content, predicting that b3n might contain an S/MAR, Fragm ents of the b3n locus were isolated by conventional and inverse PCR te chniques. In in vitro binding experiments with both heterologous and a utologous scaffold preparations, a 592-bp fragment spanning the region rich in S/MAR features showed marked scaffold affinity, which was spe cific when autologous scaffolds were used. The presence of an S/MAR at the b3n locus and its nature as a recurrent WHV integration site in H CC suggest the involvement of S/MAR elements in some of the mechanisms leading to liver oncogenesis.