Cockayne syndrome (CS) is an inherited neurodevelopmental disorder with progeroid features. Although the genes responsible for CS have been implicated in a variety of DNA repair-and transcription-related pathways, the nature of the molecular defect in CS remains mysterious. Using expression microarrays and a unique method for comparative expression analysis called L2L, we sought to define this defect in cells lacking a functional CS group B (CSB) protein, the SWI͞SNF-like ATPase responsible for most cases of CS. Remarkably, many of the genes regulated by CSB are also affected by inhibitors of histone deacetylase and DNA methylation, as well as by defects in poly(ADP-ribose)-polymerase function and RNA polymerase II elongation. Moreover, consistent with these microarray expression data, CSB-null cells are sensitive to inhibitors of histone deacetylase or poly(ADP-ribose)-polymerase. Our data indicate a general role for CSB protein in maintenance and remodeling of chromatin structure and suggest that CS is a disease of transcriptional deregulation caused by misexpression of growthsuppressive, inflammatory, and proapoptotic pathways.DNA repair ͉ L2L ͉ microarray ͉ transcription C ockayne syndrome (CS) is a devastating inherited disease characterized by severe postnatal growth failure and progressive neurological dysfunction, along with a variety of symptoms reminiscent of aging, including retinal degeneration, sensorineural hearing loss, cataracts, and loss of subcutaneous fat (1). The nature of the molecular defect that causes CS remains elusive, although CS has been intensively studied for many years, and much is known about the cellular functions of the five genes responsible for the disease. Most cases of CS are caused by defects in two genes: CS groups A (CSA) and B (CSB). The CSB protein is a SWI͞SNF-like DNA-dependent ATPase (2-4) that can wind DNA (5) and remodel chromatin in vitro (6). CSB is required for translocation of the CSA protein to the nuclear matrix after DNA damage (7). Rare alleles of three xeroderma pigmentosum (XP) genes (XPB, XPD, and XPG) are responsible for the remaining cases of CS; these patients usually lack the severe predisposition to skin cancer typical of XP (8). CS genes have been implicated, alone or in various combinations, in transcription-coupled repair (TCR) of UV-induced DNA lesions (9, 10), repair of oxidative DNA damage (11), transcription initiation by RNA polymerase I (pol I; refs. 12 and 13) and RNA polymerase II (pol II; ref. 14), elongation by pol II (15, 16), transcription of induced genes (17), protein ubiquitination (18), and metaphase chromosome condensation (19).To understand how CSB defects cause CS, we characterized the array of genes regulated by CSB. Previous expression array studies, although encouraging, had not been conclusive (20) or had focused on the role of CS genes in the transcriptional response to oxidative (17) or ultraviolet (21) DNA damage. Our hope was to work backwards from effect to cause, deducing the biochemical functions of CSB from genes it...