A DNA Minor Groove-binding Ligan Both Potentiates and Arrests Transcription by RNA Polymerase II: Elongation Factor SII Enables Readthrough at Arrest Sites

Abstract

RNA polymerase II encounters various obstacles to transcript elongation both in vivo and in vitro. These include DNA sequence elements and protein bound to the major groove of DNA. Elongation factor SII binds to RNA polymerase II and enables the enzyme to bypass these impediments. SII also activates nascent RNA cleavage by the arrested transcription elongation complex, an activity intimately involved in the readthrough process. Here we identify another type of reversible blockage to RNA polymerase II transcription, the antitumor antibiotic distamycin, which binds in the minor groove of A+T rich DNA. SII facilitates readthrough of arrest sites resulting from DNA-binding of the drug. In response to SII, these complexes cleave their nascent RNA chains. These findings confirm that SII is a general elongation factor that potentiates transcription through a variety of impediments. They also strengthen the idea that SII stimulates transcription by activating nascent RNA cleavage. In some cases, distamycin can potentiate transcription through a naturally occurring pause site. We also show that the template undergoes a conformational change in the presence of distamycin. This suggests that distamycin can transform DNA from an elongation-non-permissive configuration into an elongation-permissive form and we take this as independent evidence confirming that DNA structure influences transcription elongation by RNA polymerase II.