Sequence-specific DNA binding by Ku autoantigen and its effects on transcription

Abstract

DNA-DEPENDENT protein kinase (DNA-PK) has been implicated in several nuclear processes including transcription^1–3, DNA replication^4,5, double-stranded DNA break repair, and V(D) J recombination^6–10. Linkage of kinase and substrate on DNA in cis is required for efficient phosphorylation¹¹. Recruitment of DNA-PK to DNA is by Ku autoantigen, a DNA-end-binding protein required for DNA-PK catalytic activity¹¹. Although Ku is known to translocate along naked DNA¹², how DNA-end binding by Ku might lead to DNA-PK-mediated phosphorylation of sequence-specific DNA-binding proteins in vivo has not been obvious. Here we report the identification of Ku as a transcription factor that recruits DNA-PK directly to specific DNA sequences. NRE1 (negative regulatory element 1) is a DNA sequence element (−394/ − 381) in the long terminal repeat of mouse mammary tumour virus (MMTV) that is important for repressing inappropriate viral expression^13–16. We show that direct binding of Ku/DNA-PK to NRE1 represses glucocorticoid-induced MMTV transcription.