ATP-Dependent Chromatin Remodeling by Cockayne Syndrome Protein B and NAP1-Like Histone Chaperones Is Required for Efficient Transcription-Coupled DNA Repair

摘要

The Cockayne syndrome complementation group B (CSB) protein is essential for transcription-coupled DNA repair, and mutations in CSB are associated with Cockayne syndrome—a devastating disease with complex clinical features, including the appearance of premature aging, sun sensitivity, and numerous neurological and developmental defects. CSB belongs to the SWI2/SNF2 ATP–dependent chromatin remodeler family, but the extent to which CSB remodels chromatin and whether this activity is utilized in DNA repair is unknown. Here, we show that CSB repositions nucleosomes in an ATP–dependent manner in vitro and that this activity is greatly enhanced by the NAP1-like histone chaperones, which we identify as new CSB–binding partners. By mapping functional domains and analyzing CSB derivatives, we demonstrate that chromatin remodeling by the combined activities of CSB and the NAP1-like chaperones is required for efficient transcription-coupled DNA repair. Moreover, we show that chromatin remodeling and repair protein recruitment mediated by CSB are separable activities. The collaboration that we observed between CSB and the NAP1-like histone chaperones adds a new dimension to our understanding of the ways in which ATP–dependent chromatin remodelers and histone chaperones can regulate chromatin structure. Taken together, the results of this study offer new insights into the functions of chromatin remodeling by CSB in transcription-coupled DNA repair as well as the underlying mechanisms of Cockayne syndrome. Author Summary Cockayne syndrome is a devastating inherited disease; the average life span of those afflicted is 12 years. Cockayne syndrome patients have features of premature aging, are highly sensitive to sunlight, and suffer from numerous developmental and neurological disorders. The majority of Cockayne syndrome patients have mutations in the CSB protein; however, how these mutations can lead to Cockayne syndrome is largely unknown. CSB is essential for transcription-coupled DNA repair—a process that preferentially removes bulky DNA lesions that stall transcription, such as those created by ultraviolet light. In eukaryotes, DNA is packaged into nucleosomes, which consists of DNA wrapped around a set of core histone proteins, and nucleosomes can create barriers to the DNA repair process. In this study, we found that CSB can slide histones along DNA. We also found that histone chaperones, proteins that accept and donate histones, greatly facilitate this process. Importantly, we show that CSB derivatives that are unable to move nucleosomes or collaborate with histone chaperones cannot repair UV-induced DNA lesions. Our study reveals that nucleosome remodeling by CSB is important for transcription-coupled DNA repair and suggests that an inability to efficiently mobilize nucleosomes might contribute to the underlying mechanism of Cockayne syndrome.