Organization of mouse DNA polymerase beta gene silencer elements and identification of the silencer-binding factor(s)

Different portions of the 5'-upstream region of the mouse DNA polymerase beta gene were combined with bacterial chloramphenicol acetyltransferase (CAT) gene of the CAT vector. Transfection of these recombinant plasmids into mouse NIH/3T3 cells has revealed that each of the previously identified two negatively acting regions (silencers I and II) of this gene consists of multiple sub-domains. The distal silencer (silencer I) at around -1.5 kb consists of four sub-domains (-1852 to -1667, -1663 to -1616, -1564 to -1525 and -1355 to -1257). The promoter-proximal silencer (silencer II) at around -0.5 kb consists of two functional domains (-681 to -523 and -490 to -447) separated by a neutral region of 33 base pairs. Silencer II functioned efficiently when silencer I was deleted. Conversely, the distal silencer I functioned efficiently when silencer II was deleted. Thus, these silencers functioned redundantly to each other in NIH/3T3 cells. Nucleotide sequence analysis revealed no extensive sequence similarity between these two silencers. Significant sequence similarity is present between a distal portion of silencer II and the c-myc gene silencer, and also between a proximal portion of silencer II and the mouse F9 cell-specific silencer. A protein factor(s) that specifically bound to the silencer elements was detected in nuclear extracts of NIH/3T3 cells and mouse liver in which DNA polymerase beta was expressed at a rather low level. The same binding factor(s) can bind to both silencer I and II regions, although its affinity for silencer II is much higher than that for silencer I.